I have participated in genomic and metagenomic analysis projects. My main interest is bioinformatics and open-source software development. I am interested in participating in activities where knowledge from different areas of knowledge is shared.
+He participado en proyectos de análisis genómicos y metagenómicos. Mi principal interés es la bioinformática y el desarrollo de software de código abierto. Me interesa participar en actividades donde se comparten conocimientos de distintas áreas del conocimiento.
+Desarrollo en R, Bioinformática, Metagenómica
R Development, Bioinformatics, Metagenomics
diff --git a/index.json b/index.json index b2e7a03..a3fda25 100644 --- a/index.json +++ b/index.json @@ -1 +1 @@ -[{"authors":["admin"],"categories":null,"content":"Welcome to the Community of Bioinformatics Software Developers (CDSB in Spanish)!\nWe are a group interested in helping members of Latin American countries acquire the necessary skills to contribute to open source software development. R is now used by many industries and has been a long time favorite in academia. As R users grow more familiar with the language, they typically end up writing their own functions and sharing them with others via packages. These packages can be distributed via GitHub or via formal repositories like CRAN and Bioconductor. Bioconductor is a project centered around open source software for bioinformatics made with R that has been helpful to many of us. We want to improve the representation of Latin American countries in open source developer communities to make them more diverse. Thus, our main goal is to help teach Latin Americans how to make R packages and share them via GitHub, CRAN and Bioconductor.\nYou can find some of our recorded videos available on our YouTube channel.\nCDSB2022 CDSB2021 scRNAseq CDSB2021 workflows Mini courses RMB 2020-2021 CDSB2020 ","date":1685318400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1685318400,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"http://comunidadbioinfo.github.io/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Welcome to the Community of Bioinformatics Software Developers (CDSB in Spanish)!\nWe are a group interested in helping members of Latin American countries acquire the necessary skills to contribute to open source software development. R is now used by many industries and has been a long time favorite in academia. As R users grow more familiar with the language, they typically end up writing their own functions and sharing them with others via packages.","tags":null,"title":"CDSB","type":"authors"},{"authors":["lcollado"],"categories":null,"content":" Leonardo uses R daily and contributes R packages to the Bioconductor project as part of his work at LIBD. He is interested in high-throughput genomics assays such as RNA-seq, developments in R and helping others get started in their R journey. Leonardo has been learning and teaching R since 2008 and is a co-founder of the LIBD rstats club.\n","date":1611705600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1611705600,"objectID":"59aecbe3d862df17fbda914be3a22015","permalink":"http://comunidadbioinfo.github.io/authors/lcollado/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lcollado/","section":"authors","summary":"Leonardo uses R daily and contributes R packages to the Bioconductor project as part of his work at LIBD. He is interested in high-throughput genomics assays such as RNA-seq, developments in R and helping others get started in their R journey. Leonardo has been learning and teaching R since 2008 and is a co-founder of the LIBD rstats club.","tags":null,"title":"Leonardo Collado-Torres, PhD","type":"authors"},{"authors":["erickcufe"],"categories":null,"content":"I am a Biological Data Scientist. I am also a Scientist and Entrepreneur in training. I have a Masters degree in Biochemical Sciences at UNAM and I am currently a Ph.D. student at UNAM.\n","date":1597968000,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1597968000,"objectID":"899f8150894e1d8b384f08811787b1b5","permalink":"http://comunidadbioinfo.github.io/authors/erickcufe/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/erickcufe/","section":"authors","summary":"I am a Biological Data Scientist. I am also a Scientist and Entrepreneur in training. I have a Masters degree in Biochemical Sciences at UNAM and I am currently a Ph.D. student at UNAM.","tags":null,"title":"Erick Cuevas-Fernández, MsC","type":"authors"},{"authors":["areyes"],"categories":null,"content":"I am a Data Scientist for Early Drug Development at Novartis Institute for BioMedical Research. I develop computational strategies to translate large amounts of data into biological knowledge. I implement my analyses in documented workflows, software packages and graphic interphases. I am a contributor of software to the Bioconductor project.\n","date":1536891202,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1536891202,"objectID":"e39f632bdf1febdce36f1533983ddebd","permalink":"http://comunidadbioinfo.github.io/authors/areyes/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/areyes/","section":"authors","summary":"I am a Data Scientist for Early Drug Development at Novartis Institute for BioMedical Research. I develop computational strategies to translate large amounts of data into biological knowledge. I implement my analyses in documented workflows, software packages and graphic interphases. I am a contributor of software to the Bioconductor project.","tags":null,"title":"Alejandro Reyes, PhD","type":"authors"},{"authors":["delfinog"],"categories":null,"content":"","date":1520369358,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1520369358,"objectID":"ea39f799b3ec580a1fb8bda0917c928d","permalink":"http://comunidadbioinfo.github.io/authors/delfinog/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/delfinog/","section":"authors","summary":"","tags":null,"title":"Delfino García-Alonso","type":"authors"},{"authors":["aescalante"],"categories":null,"content":"Con formación como Actuario por la Benemérita Universidad Autónoma de Puebla (BUAP), inicié mi camino profesional como Data Scientist hace 4 años. Actualmente, trabajo como Analytics Developer en el equipo global de Kantar, en donde hago desarrollo de software con R.\nDisfruto aplicar conocimientos en desarrollo y ciencia de datos para crear y mantener paquetes para facilitar los procesos de análisis.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"0e740809f90d8045be45c23b25a4276d","permalink":"http://comunidadbioinfo.github.io/authors/aescalante/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/aescalante/","section":"authors","summary":"Con formación como Actuario por la Benemérita Universidad Autónoma de Puebla (BUAP), inicié mi camino profesional como Data Scientist hace 4 años. Actualmente, trabajo como Analytics Developer en el equipo global de Kantar, en donde hago desarrollo de software con R.\nDisfruto aplicar conocimientos en desarrollo y ciencia de datos para crear y mantener paquetes para facilitar los procesos de análisis.","tags":null,"title":"Ángel Escalante, Actuario","type":"authors"},{"authors":["alabasti"],"categories":null,"content":"Aurora Labastida Martínez estudió la Licenciatura en Investigación Biomédica Básica y la Maestría en Ciencias Bioquímicas en la UNAM. Se dedica al análisis de datos de secuenciación masiva de ADN y ha formado parte de distintos equipos de de biólogos y programadores en instituciones públicas y privadas.\nActualmente dirige el servicio de análisis de datos OMICs Analysis, que brinda sus servicios a científicos y empresas en proyectos de metagenómica y transcriptómica.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"7f84e7c295f8352289c9fb68c64b45f4","permalink":"http://comunidadbioinfo.github.io/authors/alabasti/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/alabasti/","section":"authors","summary":"Aurora Labastida Martínez estudió la Licenciatura en Investigación Biomédica Básica y la Maestría en Ciencias Bioquímicas en la UNAM. Se dedica al análisis de datos de secuenciación masiva de ADN y ha formado parte de distintos equipos de de biólogos y programadores en instituciones públicas y privadas.\nActualmente dirige el servicio de análisis de datos OMICs Analysis, que brinda sus servicios a científicos y empresas en proyectos de metagenómica y transcriptómica.","tags":null,"title":"Aurora Labastida Martínez, M.C.","type":"authors"},{"authors":["amedina"],"categories":null,"content":"Alejandra obtained her Ph.D. in 2012 from the Biomedical Sciences Program at the National University of Mexico (UNAM). Since her Ph.D., she has been focused on developing bioinformatic tools, and strategies to study gene regulatory mechanisms, most of the developed tools are now part of the Regulatory Sequence and Analysis Tools suite (RSAT, http://rsat.eu/). Currently, using computational approaches, her research will incorporate functional genomics data into Genome Wide Association Studies (GWAS), aiming to identify variants that lead to misregulation of gene expression.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"11e5c4662ac478bfb20ecc7657b80649","permalink":"http://comunidadbioinfo.github.io/authors/amedina/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/amedina/","section":"authors","summary":"Alejandra obtained her Ph.D. in 2012 from the Biomedical Sciences Program at the National University of Mexico (UNAM). Since her Ph.D., she has been focused on developing bioinformatic tools, and strategies to study gene regulatory mechanisms, most of the developed tools are now part of the Regulatory Sequence and Analysis Tools suite (RSAT, http://rsat.eu/). Currently, using computational approaches, her research will incorporate functional genomics data into Genome Wide Association Studies (GWAS), aiming to identify variants that lead to misregulation of gene expression.","tags":null,"title":"Alejandra Medina Rivera, PhD","type":"authors"},{"authors":["anabva"],"categories":null,"content":"Ana B learned to program in R, currently, she uses it daily, and has given workshops, classes, and consultancies at all levels. She is co-founder of Rladies-Querétaro, uses R in her transcriptomic analysis, and has created a package in R and several web applications. She also programs in Python for her analyses, uses Django for web applications, and has experience in relational databases such as MySQL.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a61eac9bb0a7d9ac89410e86d5bff317","permalink":"http://comunidadbioinfo.github.io/authors/anabva/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/anabva/","section":"authors","summary":"Ana B learned to program in R, currently, she uses it daily, and has given workshops, classes, and consultancies at all levels. She is co-founder of Rladies-Querétaro, uses R in her transcriptomic analysis, and has created a package in R and several web applications. She also programs in Python for her analyses, uses Django for web applications, and has experience in relational databases such as MySQL.","tags":null,"title":"Ana Beatriz Villaseñor Altamirano, PhD","type":"authors"},{"authors":["andresarredondo"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"32d79e9ff810dc74e425ea614ff831f0","permalink":"http://comunidadbioinfo.github.io/authors/andresarredondo/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/andresarredondo/","section":"authors","summary":"","tags":null,"title":"Andrés Arredondo Cruz, M.C.","type":"authors"},{"authors":["aponce"],"categories":null,"content":"Hi !!! I Studied Food Technology at UIA and my masters and PhD in Biotechnology and Bioengineering at CINVESTAV. I\u0026rsquo;ve have had several years in postdocs and jobs at many Institutions (ECOSUR, UNSIJ, INIFAP, CONABIO, UAM-X). I\u0026rsquo;m interested in numerical ecology, data visualization and agrobiodiversity. Finally, I practice touring bike and admire Thomas Bernhard, WG Sebald and Glenn Gould.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a432943019f570a576c17a87326e4eaf","permalink":"http://comunidadbioinfo.github.io/authors/aponce/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/aponce/","section":"authors","summary":"Hi !!! I Studied Food Technology at UIA and my masters and PhD in Biotechnology and Bioengineering at CINVESTAV. I\u0026rsquo;ve have had several years in postdocs and jobs at many Institutions (ECOSUR, UNSIJ, INIFAP, CONABIO, UAM-X). I\u0026rsquo;m interested in numerical ecology, data visualization and agrobiodiversity. Finally, I practice touring bike and admire Thomas Bernhard, WG Sebald and Glenn Gould.","tags":null,"title":"Alejandro Ponce-Mendoza, PhD","type":"authors"},{"authors":["bcarvalho"],"categories":null,"content":"Statistician (BS, M.Sc.), biostatistician (Ph.D.) Instructor: Statistics - Regression Models; Database designer and developer: MySQL, PHP; Teacher Assistant: Biocomputing, Statistical Computing and Statistical Methods in Public Health; Developer: BioConductor - oligo, makePlatformDesign, crlmm, pdInfoBuilder. Specialties: High-throughput genotyping, microarray preprocessing, statistical modeling, gene-expression analyzes, genetic epidemiology, statistical computing, programming (R, C / C ++, MATLAB)\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"6b72e93d4828c9e878b7d78fbae5bde5","permalink":"http://comunidadbioinfo.github.io/authors/bcarvalho/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/bcarvalho/","section":"authors","summary":"Statistician (BS, M.Sc.), biostatistician (Ph.D.) Instructor: Statistics - Regression Models; Database designer and developer: MySQL, PHP; Teacher Assistant: Biocomputing, Statistical Computing and Statistical Methods in Public Health; Developer: BioConductor - oligo, makePlatformDesign, crlmm, pdInfoBuilder. Specialties: High-throughput genotyping, microarray preprocessing, statistical modeling, gene-expression analyzes, genetic epidemiology, statistical computing, programming (R, C / C ++, MATLAB)","tags":null,"title":"Benilton S Carvalho, PhD","type":"authors"},{"authors":["brettbaker"],"categories":null,"content":"Brett Baker is an assistant professor in marine science at the Marine Science Institute, University of Texas at Austin. His research seeks to understand the ecology and evolution of uncultured bacteria and archaea.\nHis laboratory leverages computational approaches to characterize the genomic diversity of marine sediments primarily. The reconstruction of uncultured genomes from his team in recent years has provided the first glimpses of the physiological capabilities of new branches on the tree of life.\nDr. Baker’s research group also uses a variety of activity-based methods to track the metabolic activity of these novel microbes in nature. His laboratory has also been instrumental in the characterization of archaea that are related to eukaryotes that have advanced our understanding of the origin of complex cellular life.\nIn 2014, he received his Ph.D. in geological sciences from the University of Michigan, where he studied the geomicrobiology of deep-sea hydrothermal plumes and estuary sediments. Prior to doing so he was a research assistant at the University of California, Berkeley for 10 years, studying the microbes associated with acid mine drainage\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"edd0bac58be7ddfc1246cd337f835205","permalink":"http://comunidadbioinfo.github.io/authors/brettbaker/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/brettbaker/","section":"authors","summary":"Brett Baker is an assistant professor in marine science at the Marine Science Institute, University of Texas at Austin. His research seeks to understand the ecology and evolution of uncultured bacteria and archaea.\nHis laboratory leverages computational approaches to characterize the genomic diversity of marine sediments primarily. The reconstruction of uncultured genomes from his team in recent years has provided the first glimpses of the physiological capabilities of new branches on the tree of life.","tags":null,"title":"Brett Baker, PhD","type":"authors"},{"authors":["carbarjon"],"categories":null,"content":"Author of regutools that was submitted to Bioconductor.\n Description from here:\n I\u0026rsquo;m (also) a graduate of the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM). My current project in MorenoLab involves the analysis of identity-by-descent genomic segments to determine the population structure of Mexico and their implications in biomedical traits using the data from the Mexican BioBank. I am also involved in other projects as the Oceanian Genome Variation Project. I like photography, surrealist paintings, and good-looking cocktails, I also love rats; one of my dreams is to have a pet rat named Bojack.\n ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"f2296ef237d3a57e44d1f4b5241a16d3","permalink":"http://comunidadbioinfo.github.io/authors/carbarjon/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/carbarjon/","section":"authors","summary":"Author of regutools that was submitted to Bioconductor.\n Description from here:\n I\u0026rsquo;m (also) a graduate of the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM). My current project in MorenoLab involves the analysis of identity-by-descent genomic segments to determine the population structure of Mexico and their implications in biomedical traits using the data from the Mexican BioBank. I am also involved in other projects as the Oceanian Genome Variation Project.","tags":null,"title":"Carmina Barberena-Jonas","type":"authors"},{"authors":["CitlaliGA"],"categories":null,"content":"I studied genomic sciences at UNAM. I\u0026rsquo;d worked on various projects focused on population genetics and evolution. Some of my current interests are: philosophy, programming (R, python and trying arduino), science communication ( Más ciencia por México ), I really love teaching and learning from others.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"d7f5cdb0479a508e26be441dde701091","permalink":"http://comunidadbioinfo.github.io/authors/citlaliga/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/citlaliga/","section":"authors","summary":"I studied genomic sciences at UNAM. I\u0026rsquo;d worked on various projects focused on population genetics and evolution. Some of my current interests are: philosophy, programming (R, python and trying arduino), science communication ( Más ciencia por México ), I really love teaching and learning from others.","tags":null,"title":"Citlali Gil Aguillon","type":"authors"},{"authors":["emarquezz"],"categories":null,"content":" Elisa integrates multiple omics and phenotypic data with genome-scale metabolic modeling for rational strain design and bioprocess optimization project as part of his work at CCG with Utrilla Lab. She is interested in the integration of different types of data such as RNA-seq, proteomics, Ribo-seq and fitness information, with metabolism and expression models built with thepython module COBRAme. Her objective is to make a quantitative comparison between genome and proteome reduction strategies for redirecting cellular resources to synthetic functions.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"70cf7c97cec87510b0ca1f458d7daccc","permalink":"http://comunidadbioinfo.github.io/authors/emarquezz/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/emarquezz/","section":"authors","summary":"Elisa integrates multiple omics and phenotypic data with genome-scale metabolic modeling for rational strain design and bioprocess optimization project as part of his work at CCG with Utrilla Lab. She is interested in the integration of different types of data such as RNA-seq, proteomics, Ribo-seq and fitness information, with metabolism and expression models built with thepython module COBRAme. Her objective is to make a quantitative comparison between genome and proteome reduction strategies for redirecting cellular resources to synthetic functions.","tags":null,"title":"Elisa Márquez Zavala, MsC Candidate","type":"authors"},{"authors":["eveliacoss"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"18efa430de6ac5b9f6cde704726f6236","permalink":"http://comunidadbioinfo.github.io/authors/eveliacoss/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/eveliacoss/","section":"authors","summary":"","tags":null,"title":"Evelia Lorena Coss Navarrete, PhD","type":"authors"},{"authors":["hsalgado"],"categories":null,"content":"Bioinformatician. I am interested in disseminating and supporting the teaching of bioinformatics in Mexico and LA ( @swcarpentry, @ComunidadBioInfo and NNB)\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2fe4b6df35220a9de4414e4c7c7e01d0","permalink":"http://comunidadbioinfo.github.io/authors/hsalgado/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/hsalgado/","section":"authors","summary":"Bioinformatician. I am interested in disseminating and supporting the teaching of bioinformatics in Mexico and LA ( @swcarpentry, @ComunidadBioInfo and NNB)","tags":null,"title":"Heladia Salgado Osorio","type":"authors"},{"authors":["jemilianosf"],"categories":null,"content":"Author of regutools that was submitted to Bioconductor.\n regrnalab member.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"3fa59542a2f5d63ef66e1d561c6ce2ea","permalink":"http://comunidadbioinfo.github.io/authors/jemilianosf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jemilianosf/","section":"authors","summary":"Author of regutools that was submitted to Bioconductor.\n regrnalab member.","tags":null,"title":"Jesus Emiliano Sotelo-Fonseca","type":"authors"},{"authors":["joseovando"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"220e663aba981e28ff4b8ac28dc8163b","permalink":"http://comunidadbioinfo.github.io/authors/joseovando/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/joseovando/","section":"authors","summary":"","tags":null,"title":"José Antonio Ovando Ricárdez, M.C.","type":"authors"},{"authors":["josschavezf"],"categories":null,"content":"During my PhD project, in the Computational Genomics Laboratory at IBT-UNAM, I focused on the study of bacterial transcriptional regulators through evolution. Additionally, I gained experience in writing R/Bioconductor packages and teaching R.\nCurrently, I\u0026rsquo;m a Postdoctoral Fellow in the Department of Personalized Medicine of the Icahn School of Medicine at Mount Sinai, in New York City. My main interest is bioinformatics and the development of open source software for the analysis of single cell and spatial transcriptomics.\nBesides my research project, I enjoy teaching R and participating in activities that help expand the community of software developers in Latin America.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"72e346927b1c9c105a022174b2388839","permalink":"http://comunidadbioinfo.github.io/authors/josschavezf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/josschavezf/","section":"authors","summary":"During my PhD project, in the Computational Genomics Laboratory at IBT-UNAM, I focused on the study of bacterial transcriptional regulators through evolution. Additionally, I gained experience in writing R/Bioconductor packages and teaching R.\nCurrently, I\u0026rsquo;m a Postdoctoral Fellow in the Department of Personalized Medicine of the Icahn School of Medicine at Mount Sinai, in New York City. My main interest is bioinformatics and the development of open source software for the analysis of single cell and spatial transcriptomics.","tags":null,"title":"Joselyn C. Chávez-Fuentes, Ph.D","type":"authors"},{"authors":["lgomez"],"categories":null,"content":" Laura enjoys teaching bioinformatic courses. Her research interest are focused on genomic variation and its link with human diseases. She has wide experience with R, python and other programming languages oriented to solve biological questions.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"d813a570ce60c36151b5f8193458aba5","permalink":"http://comunidadbioinfo.github.io/authors/lgomez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lgomez/","section":"authors","summary":"Laura enjoys teaching bioinformatic courses. Her research interest are focused on genomic variation and its link with human diseases. She has wide experience with R, python and other programming languages oriented to solve biological questions.","tags":null,"title":"Laura Gómez-Romero, PhD","type":"authors"},{"authors":["mirnavrl"],"categories":null,"content":"I am an evolutionary ecologist who seeks to understand microbial life, what are the ecological and evolutionary factors that shape microbial populations, as well as understanding the dynamics of their genomes in the light of evolution.\nI’m currently an associate professor at the UNAM Institute of Marine and Limnology Sciences, where I study the microbial life of the ocean. My work explores questions about biogeography, evolution, ecology, and physiology of microorganisms. I use computational and experimental approaches to answer these questions and my main interest is to understand the factors that determine the distribution of microbial species in the ocean, what are the genomic bases of adaptation leading to speciation, what is their role in the Earth’s biogeochemistry and how they interact with other organisms within the ecosystem.\nI did my PhD at the Institute of Ecology UNAM, where I studied the evolution of bacteria using comparative and population genomics. For this research, I isolated bacteria from the pools of Cuatro Ciénegas and looked for genes associated with local adaptation. During my first postdoc, I studied the interaction between plants, insects and microbes, using transcriptomic tools and 16s RNA amplicone libraries.\nDuring my postdoc at the microbial ecology lab at the University of Texas at Austin, my research focused on the discovery of new lineages and metabolic pathways of ocean microorganisms through the reconstruction of genomes obtained with metagenomics.\nI like the R community, I am co-organizer of R-Ladies Xalapa and San Cristobal, and also part of the board team of the Community of Software Developers in Bioinformatics (CDSB). Currently, I am working on my first R package called Rbims that it\u0026rsquo;s focused on the analysis of metabolism.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"482d2e9e74e0afb6c3d37a6acd27d032","permalink":"http://comunidadbioinfo.github.io/authors/mirnavrl/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mirnavrl/","section":"authors","summary":"I am an evolutionary ecologist who seeks to understand microbial life, what are the ecological and evolutionary factors that shape microbial populations, as well as understanding the dynamics of their genomes in the light of evolution.\nI’m currently an associate professor at the UNAM Institute of Marine and Limnology Sciences, where I study the microbial life of the ocean. My work explores questions about biogeography, evolution, ecology, and physiology of microorganisms.","tags":null,"title":"Mirna Vázquez Rosas Landa, PhD","type":"authors"},{"authors":["mramos"],"categories":null,"content":" Marcel has written or contributed to over 9 packages in Bioconductor and CRAN. He is interested in Bioconductor data classes and representations for the analysis of multi-omic and multi-modal data. He is the developer of the MultiAssayExperiment package, currently in the top 10% most downloaded in Bioconductor. Marcel also has teaching appointments at the CUNY School of Public Health on introductory topics in Biostatistics, R, and SAS.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b6f8733c519ba6fcbff7526bca2a4081","permalink":"http://comunidadbioinfo.github.io/authors/mramos/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mramos/","section":"authors","summary":"Marcel has written or contributed to over 9 packages in Bioconductor and CRAN. He is interested in Bioconductor data classes and representations for the analysis of multi-omic and multi-modal data. He is the developer of the MultiAssayExperiment package, currently in the top 10% most downloaded in Bioconductor. Marcel also has teaching appointments at the CUNY School of Public Health on introductory topics in Biostatistics, R, and SAS.","tags":null,"title":"Marcel Ramos Perez, MPH","type":"authors"},{"authors":["mteresa"],"categories":null,"content":"I am a data analyst with experience in ecology and marketing, I currently work in Kantar where I do software development with R.\nI also enjoy teaching, I teach statistic courses to master students in Data Science and to bachelors in Mathematics and Actuarial Sciences at ITAM. Lastly, I love R, I am co-organizer of R-Ladies CDMX and I regularly give short courses in R.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b92f6a30b831499900664c8e88fb5510","permalink":"http://comunidadbioinfo.github.io/authors/mteresa/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mteresa/","section":"authors","summary":"I am a data analyst with experience in ecology and marketing, I currently work in Kantar where I do software development with R.\nI also enjoy teaching, I teach statistic courses to master students in Data Science and to bachelors in Mathematics and Actuarial Sciences at ITAM. Lastly, I love R, I am co-organizer of R-Ladies CDMX and I regularly give short courses in R.","tags":null,"title":"Maria Teresa Ortiz, MA","type":"authors"},{"authors":["mtmorgan"],"categories":null,"content":"Dr. Morgan spent 10 years as an Assistant Professor and Associate then at Washington State University, before joining the Fred Hutchinson Cancer Research Center in 2005. At the Hutch, Dr. Morgan worked on the Bioconductor project for the analysis and comprehension of high-throughput genomic data; which he has led since 2008. Dr. Morgan recently moved to Roswell Park in Buffalo Comprehensive Cancer Center, NY, where the Bioconductor project is now based.\nSpecial Interests:\n Statistical methods in computational biology Analysis and comprehension of ‘next generation’ high-throughput sequence data Integrative analysis of large-scale multiple ‘omics data sets Inference of single-cell evolutionary processes in cancer development ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"c41a22cf279d8d85cf21b8fb94509259","permalink":"http://comunidadbioinfo.github.io/authors/mtmorgan/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mtmorgan/","section":"authors","summary":"Dr. Morgan spent 10 years as an Assistant Professor and Associate then at Washington State University, before joining the Fred Hutchinson Cancer Research Center in 2005. At the Hutch, Dr. Morgan worked on the Bioconductor project for the analysis and comprehension of high-throughput genomic data; which he has led since 2008. Dr. Morgan recently moved to Roswell Park in Buffalo Comprehensive Cancer Center, NY, where the Bioconductor project is now based.","tags":null,"title":"Martin Morgan, PhD","type":"authors"},{"authors":["robamezquita"],"categories":null,"content":"Robert Amezquita is a Postdoctoral Fellow in the Immunotherapy Integrated Research Center (IIRC) at Fred Hutch under the mentorship of Raphael Gottardo. His current research focuses on utilizing computational approaches leveraging transcriptional and epigenomic profiling at single-cell resolution to understand how novel anti-cancer therapeutics - ranging from small molecule therapies to biologics such as CAR-T cells - affect immune response dynamics. Extending from his graduate work at Yale’s Dept. of Immunobiology, Robert’s research aims to better understand the process of immune cell differentiation under the duress of cancer as a means to inform future immunotherapies. To accomplish this, Robert works collaboratively across the Fred Hutch IIRC with experimental collaborators, extensively utilizing R and Bioconductor for data analysis.\nRobert is one of the authors of the Orchestrating Single-Cell Analysis with Bioconductor book.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"5a79396d0960df7b636f4b0d80bd4cc6","permalink":"http://comunidadbioinfo.github.io/authors/robamezquita/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/robamezquita/","section":"authors","summary":"Robert Amezquita is a Postdoctoral Fellow in the Immunotherapy Integrated Research Center (IIRC) at Fred Hutch under the mentorship of Raphael Gottardo. His current research focuses on utilizing computational approaches leveraging transcriptional and epigenomic profiling at single-cell resolution to understand how novel anti-cancer therapeutics - ranging from small molecule therapies to biologics such as CAR-T cells - affect immune response dynamics. Extending from his graduate work at Yale’s Dept. of Immunobiology, Robert’s research aims to better understand the process of immune cell differentiation under the duress of cancer as a means to inform future immunotherapies.","tags":null,"title":"Robert Amezquita, PhD","type":"authors"},{"authors":["roramirezf"],"categories":null,"content":" Ricardo uses statistics to analyze multiomics data at different scales. His research interests are focused in the study of tissue architecture and its disruption during disease. He uses single cell data and spatial technologies to achieve this.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b7f51e5d62a2fbb56a24357f1535471e","permalink":"http://comunidadbioinfo.github.io/authors/roramirezf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/roramirezf/","section":"authors","summary":"Ricardo uses statistics to analyze multiomics data at different scales. His research interests are focused in the study of tissue architecture and its disruption during disease. He uses single cell data and spatial technologies to achieve this.","tags":null,"title":"Ricardo O. Ramírez Flores, BSc","type":"authors"},{"authors":["sfernandez"],"categories":null,"content":"Selene Fernandez is a bioinformatician / genomic data scientist studying the evolution of gene regulatory mechanisms underlying the phenotypic diversity and differentiation in multicellular eukaryotes cell. She is particularly interested in the evolution of regulatory roles of non-coding RNAs.\nIn addition to her academic roles, she participates in initiatives that link scientists and the general public (such as Más Ciencia por Mexico, Clubes de Ciencia Mexico), programs to introduce researchers to computing (Software/Data Carpentry) as well as mentoring programs (Ekpapalek).\nExpertise: Analysis of high-throughput (next generation) sequencing data, transcriptomics, genome annotation, non-coding RNAs.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"809889e334034eaafacb3b24ecf1fde1","permalink":"http://comunidadbioinfo.github.io/authors/sfernandez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/sfernandez/","section":"authors","summary":"Selene Fernandez is a bioinformatician / genomic data scientist studying the evolution of gene regulatory mechanisms underlying the phenotypic diversity and differentiation in multicellular eukaryotes cell. She is particularly interested in the evolution of regulatory roles of non-coding RNAs.\nIn addition to her academic roles, she participates in initiatives that link scientists and the general public (such as Más Ciencia por Mexico, Clubes de Ciencia Mexico), programs to introduce researchers to computing (Software/Data Carpentry) as well as mentoring programs (Ekpapalek).","tags":null,"title":"Selene L. Fernandez-Valverde, PhD","type":"authors"},{"authors":["Yalbibalderas"],"categories":null,"content":"Yalbi Balderas is interested in studying respiratory diseases through high-throughput assays such as microarrays, bulk or single cell RNA-seq. She teaches several courses of statistics and bioinformatics at UNAM.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"17c7e91d920e689ef6f6a52d96486901","permalink":"http://comunidadbioinfo.github.io/authors/yalbibalderas/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/yalbibalderas/","section":"authors","summary":"Yalbi Balderas is interested in studying respiratory diseases through high-throughput assays such as microarrays, bulk or single cell RNA-seq. She teaches several courses of statistics and bioinformatics at UNAM.","tags":null,"title":"Yalbi I. Balderas-Martínez, PhD","type":"authors"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":" TIB2023 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Writting R/Bioconductor packages for scRNAseq analysis as part of the National Bioinformatics Meeting Mexico 2023.\n Level: Intermediate-Advanced. Language: Spanish. Where: This workshop will be held online on Zoom. When: 07-11 August 2023, 9:00am - 5:00pm (Mexico City timezone). Registration Twitter: @CDSBMexico Facebook: @CDSBMexico GitHub: https://github.com/ComunidadBioInfo/cdsb2023 Workshop webpage: https://comunidadbioinfo.github.io/cdsb2023 Calendar What are you going to learn? In recent years, the generation of scRNAseq data has become very important in biomedical research; however, the tools needed for its analysis are still under development.\nIn this workshop, we will review the existing statistical tools to analyze scRNAseq data using Bioconductor, how to document your analysis and check some tools for interpreting results.\nAt the same time, you will learn the crucial steps to develop an R package and some good practices for code generation. With the integration of these tools, you will have the opportunity to create your first package and contribute to the developers community.\nWho is it for? This course is aimed at people who want to learn how to develop packets to analyze scRNAseq data using R/Bioconductor tools.\nPre-requirements This workshop is Advanced, so you’ll need some background knowledge:\n Basic knowledge of RNAseq. Basic knowledge of RStudio: Rscripts creation, RStudio console management, display space management. Intermediate knowledge of R: Managing variables, reading files, creating and managing data frames and lists. Generation of graphs. How to install packages from CRAN and Bioconductor. Technical requirements\n Computer with at least 8Gb of memory. Access to a Linux terminal. Have R and RStudio installed in their latest version. Instructors Instructors\n Dra. Joselyn Cristina Chávez Fuentes: Postdoctoral Fellow at Icahn School of Medicine at Mount Sinai. Dra. Yalbi Balderas Martínez: Investigator at Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Dr. Leonardo Collado Torres: Investigator at Lieber Institute for Brain Development. M.C. Erick Cuevas Fernández: PhD Student at Universidad Nacional Autónoma de México. Dra. Mirna Vázquez Rosas Landa: Associate Professor at Instituto de Ciencias de Mar y Limnología de la UNAM. Dra. Alejandra Medina Rivera: Associate Professor at Laboratorio Internacional de Investigación de Medicina Genómica, UNAM. Invited speakers\n Dra. Evelia Lorena Coss Navarrete M.C. José Antonio Ovando Ricárdez M.C. Andrés Arredondo Cruz TAs\n M. C. Diego Ramírez M. C. Luis Alberto Meza Program Day 1: scRNAseq analysis workflow Part I\n Presentation of the CDSB. Structure and importing of data. Quality control. Normalization. Day 2: scRNAseq analysis workflow Part II\n Selection of highly variable genes. Dimension reduction. Clustering. Marker genes. Annotation of cellular types. Day 3: Writting R/Bioconductor packages Part I\n New features of RStudio, Quarto. Version control with GitHub and RStudio. Troubleshooting with Rstudio package versions. Infrastructure of an R/Bioconductor package. Talk: Converting your analysis workflow into an R/Bioconductor package. Documentation of functions. Social session: Getting to know the community. Day 4: Writting R/Bioconductor packages Part II\n Design of tests. Vignettes. Compilation and installation of packages. Collaborative projects Part I. Day 5: Collaborative projects\n Collaborative projects Part II. Projects presentation. Closure. Looking forward to see you!\nOrganizers \n \n \nWith the support of: \n","date":1685318400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1685318400,"objectID":"348b5ffa3ea6e0f92da60aa48f0a0841","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2023-workshop/","publishdate":"2023-05-29T00:00:00Z","relpermalink":"/post/cdsb-2023-workshop/","section":"post","summary":"TIB2023 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Writting R/Bioconductor packages for scRNAseq analysis as part of the National Bioinformatics Meeting Mexico 2023.","tags":null,"title":"CDSB Workshop 2023: Writting R/Bioconductor packages for scRNAseq analysis.","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":" TIB2022 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Advanced analysis of metagenomes. Creating workflows with R/Bioconductor as part of the National Bioinformatics Meeting Mexico 2022.\n Level: Advanced. Language: Spanish. Where: This workshop will be held online on Zoom. When: 01-05 August 2022, 9:00am - 5:00pm (Mexico City timezone). Registration Twitter: @CDSBMexico Facebook: @CDSBMexico GitHub: https://github.com/ComunidadBioInfo/cdsb2022 Workshop webpage: https://comunidadbioinfo.github.io/cdsb2022 Calendar What are you going to learn? In recent years metagenomics has gained importance for discovering new groups of microorganisms and metabolic pathways. In this workshop, we will review the latest methods for analyzing metagenomic data, using free software tools and specialized R packages freely available via Bioconductor.\nDuring this workshop, you will learn to reconstruct genomes from metagenomes using different free software tools. We will review different binning and metabolic prediction strategies, and we will identify areas of opportunity for software development in metagenomics; you will also learn how to document your code using RMarkdown.\nWho is it for? This course is designed for people who want to learn how to reconstruct genomes from metagenomes, make metabolic predictions, and contribute to the development of bioinformatics tools in this area. Participants who wish to register for the workshop must know Linux, R, NGS sequence quality analysis, and metagenomic assembly.\nPre-requirements Basic knowledge of metagenome sequencing and assembly Know what reads are. Quality control of NGS sequences. Assembly of metagenomes. Basic knowledge of RStudio. Technical requirements\n Computer with at least 8Gb of memory. Access to a Linux terminal. Have R and RStudio installed in their latest version. Instructors Instructors\n Dra. Mirna Vázquez Rosas Landa: Estancia Postdoctoral en la Universidad de Texas en Austin. Dra. Joselyn Chávez Fuentes: Estancia Postdoctoral en Icahn School of Medicine at Mount Sinai. M.C. Erick Cuevas Fernández: Estudiante de Doctorado en la Universidad Nacional Autónoma de México. Dra. Alejandra Medina Rivera: Investigadora Asociada en el Laboratorio Internacional de Investigación de Medicina Genómica, UNAM. Dra. Yalbi Balderas Martínez: Investigadora en el Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Invited speakers\n Dr. Brett Baker Dra. Valerie De Anda Dr. Leonardo Collado-Torres Program Day 1: Generating reports and workflows with R markdown\n Presentation to CDSB. Talk: The latest version of the tree of life. Version control with GitHub and RStudio. Report generation with R markdown. Day 2: Reconstruction of genomes\n Talk: Turning your analysis flow into a R/Bioconductor package. Talk: Bioconductor packages related to metagenomics. Reconstruction of genomes. Day 3: Metabolic reconstruction and phylogenetic inference\n Taxonomic assignment. Analysis of metabolic pathways. MEBs Social session: Building the community. Day 4:\n Collaborative metagenome projects. Day 5:\n Collaborative metagenome projects. Project presentation. Closure. Looking forward to see you!\nOrganizers \n \n \n \nWith the support of: \n \n","date":1652227200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1652227200,"objectID":"6464941fee83bdd045edd7b665505eba","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2022-workshops/","publishdate":"2022-05-11T00:00:00Z","relpermalink":"/post/cdsb-2022-workshops/","section":"post","summary":"TIB2022 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Advanced analysis of metagenomes. Creating workflows with R/Bioconductor as part of the National Bioinformatics Meeting Mexico 2022.","tags":null,"title":"CDSB Workshop 2022: Advanced analysis of metagenomes. Creating workflows with R/Bioconductor.","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing two week-long workshops this summer as part of the National Bioinformatics Meeting Mexico 2021. These are:\n Workflows with RStudio and creating shiny apps Analysis of scRNA-seq data with Bioconductor These workshops will be held online on August 9 to 13, 2021 and you can register here.\nWe are looking forward to seeing you soon!\nThis summer CDSB organizes 2 workshops as part of the National Bioinformatics Meeting Mexico 2021\nJoin us! #rstats @Bioconductor\n🗓️ August 2-13\n🙏🏽 @codeforsociety @RConsortium\nOrg @RBioinformatica@nnb_unam\nRegisterhttps://t.co/UJ1FAnxp52https://t.co/tTwX0RAm0K pic.twitter.com/mUZ7DeSudB\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) July 2, 2021 ","date":1623974400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1623974400,"objectID":"709dff01ba882fe0e12abc52adb04759","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2021-workshops/","publishdate":"2021-06-18T00:00:00Z","relpermalink":"/post/cdsb-2021-workshops/","section":"post","summary":"We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing two week-long workshops this summer as part of the National Bioinformatics Meeting Mexico 2021. These are:\n Workflows with RStudio and creating shiny apps Analysis of scRNA-seq data with Bioconductor These workshops will be held online on August 9 to 13, 2021 and you can register here.","tags":null,"title":"Workshops CDSB 2021: RStudio workflows and scRNA-seq with Bioconductor","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"We are delighted to announce that Code for Science and Society has selected our application for their first cohort of Event Fund grant recipients as announced on January 25, 2021. The CS\u0026amp;S Event Fund program is made possible through award number GBMF8449 from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF8449).\nThanks to this support, CDSB along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG) will be able to carry out a series of short courses throughout 2021 (including one event from December 2020) that will end with the National Bioinformatics Meeting 2021 that will be composed of 6 week-long courses.\nIf you are interested in taking part in the short courses, please check the RMB website for how to register.\nFelicidades @ErickCuevasF y @josschavezf1 por completar el primer mini curso de R de este ciclo ^^\nSon organizados por la CDSB y @RBioinformatica @nnb_unam con apoyo de @codeforsociety y @MooreFound\nEl resto del calendario propuesto está disponible acá #rstatsES https://t.co/Gx1WHdnKgp\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) December 19, 2020 As stated in our application, our goals are:\n Over the years, the workshops organized by NNB-CCG and, more recently, with the support of RMB have helped introduce an average of 40 participants per workshop every year into the world of open-source data analysis applied to bioinformatics. Many students, researchers, and industry members have found these workshops highly valuable to acquire skills at relatively low costs that empower them to succeed in the world of biological data. There are now participants who attend the introductory workshops one year and come back the next year for either other introductory workshops or those focusing on advanced material, which is where the CDSB steps in.\nCDSB has fostered the inclusion and collaboration of Latin American participants in the R and Bioconductor communities in the past three years. During the summer, one week CDSB courses (2018, 2019, and 2020) focused on developing advanced R programming skills. Supplemented by a Slack workspace, CDSB has set up the foundation for an inclusive community that supports and fosters collaboration, respect, and community building, as noted at https://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico and BioC2020, JSM2020 and CDSB2020 presentations at https://speakerdeck.com/lcolladotor (CDSB2020 video about CDSB in Spanish: https://www.youtube.com/watch?v=rtP4zmbR3p4).\nWith the proposed short courses, RMB and CDSB, together with NNB-CCG, will provide a structured path to advance on software developing skills in R, and in bioinformatics, throughout the year. This will have a strong impact on integrating more members into the community. In our experience, many people in Latin America underestimate their programming abilities and avoid advanced courses that would provide them with additional skills to become tool developers. The proposed program will allow us to integrate people in different programming knowledge stages to the CDSB, reassess their programming skills, or improve them to get to the next stage. Our series of events will culminate with week-long workshops in the summer at the National Bioinformatics Meeting 2021.\n We greatly appreciate all the support and trust that has been placed on our CDSB + RMB + NNB-CCG team.\nThank you!\n⭐️ co-founder; 💫 board member\n Leonardo Collado Torres, CDSB ⭐️💫 Joselyn Chavez, CDSB 💫 Alejandro Reyes, CDSB ⭐️💫 Erick Cuevas Fernández, CDSB 💫 Irma Martínez, Education coordinator at Mexican Bioinformatics Network (RMB in Spanish), National Bioinformatics Node representative (NNB in Spanish) Alejandra Medina Rivera, CDSB ⭐️💫, President RMB Shirley Alquicira, Project Manager at RMB, NNB Yalbi Balderas, Members Committee Coordinator at RMB ","date":1611705600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1611705600,"objectID":"011746eb29b06aa44a587bebb2978d7b","permalink":"http://comunidadbioinfo.github.io/post/cs_and_s_event_fund_award/","publishdate":"2021-01-27T00:00:00Z","relpermalink":"/post/cs_and_s_event_fund_award/","section":"post","summary":"We are delighted to announce that Code for Science and Society has selected our application for their first cohort of Event Fund grant recipients as announced on January 25, 2021. The CS\u0026amp;S Event Fund program is made possible through award number GBMF8449 from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF8449).\nThanks to this support, CDSB along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG) will be able to carry out a series of short courses throughout 2021 (including one event from December 2020) that will end with the National Bioinformatics Meeting 2021 that will be composed of 6 week-long courses.","tags":["Latin American","Bioconductor","RMB","NNB"],"title":"CS\u0026S Event Fund award announcement","type":"post"},{"authors":["Erick Cuevas-Fernández, MsC"],"categories":["rstats"],"content":"By Erick Cuevas Fernández, M. Sc., Bioinformatician. Universidad Nacional Autonoma de Mexico. Universidad Autonoma del Estado de Morelos. Systems Biology and Translational Medicine Laboratory. @ErickCuevasF\nIn 2018 I heard of a workshop where Martin Morgan was performing in Mexico, at that time I had only a few months learning to use R, and I did not know who Martin Morgan was and had vague notions of Bioconductor. That year I started taking the international bioinformatics workshops.\nIt was thanks to taking the 2019 CDSB workshop that I was able to have a new international panorama of R development, know that there were events such as useR, BioC, rstudio :: global(), etc., It was highly motivated that a Mexican community was doing a effort to spread knowledge, inspire and expand the perspective of collaboration and development of free software to Mexicans. As a graduate student and with the science cuts that are becoming more frequent in Mexico, it is difficult to travel to another country to attend a workshop or a congress, due to the issue of VISA, passport, paying for a flight, accommodation, meals and registration. That is why the CDSB workshop of international quality accessible by its location and cost are valued to many Mexican students. And not only that, the same CDSB helps and promotes the application for scholarships for Mexican students in workshops and congresses for R developers in other countries.\nThis 2020 with the pandemic and the promotion of the CDSB, was that I had the opportunity to attend the BioC2020. The dedication and effort of each speaker to explain a relevant and specialized topic was amazing. The knowledge that was displayed in just one hour was shocking. Despite having been virtually, it was to admire Bioconductor\u0026rsquo;s commitment so that each exhibitor will generate interaction with all attendees. The inclusion and support of the Bioconductor community is impressive, willing to cooperate and help. Regardless of their age, nationality, gender, or grade, they all intended to help, cooperate, and share. There was a huge emotion to see Mexicans displaying their own packages, people you know physically, students like me. At the end of the workshop I finished with a feeling of happiness, enthusiasm, inspiration, wanting to learn and share.\n#BioC2020 @CDSBMexico My first BioC, I really enjoyed it a lot, opened up a universe for me. I feel responsible and enthusiastic to share what I have learned in my academic community and continue learning. I look forward to exhibiting my first first pack in BioC2021 next year pic.twitter.com/1K9dscoB1e\n\u0026mdash; Erick Cuevas (@ErickCuevasF) July 31, 2020 The CDSB 2020 workshop was no exception, the entire community transmitted that spark of enthusiasm, to expand and improve. Of course, the academic content and knowledge that was shown was a lot, such as maintaining the R sessions, working with github, choosing appropriate names for each project, quality testing the functions, debugging, workflows for handling scRNAseq data and an application of it with space expression.\nAs I think about the CDSB and the international communities that support inclusion and diversity, I think of this excerpt from the poem “sembrando” by the poet Marcos Rafael Blanco Belmonte (originally in Spanish):\n When the world sad, I contemplate, I toil and set myself a hard task\nand I know that my poor example is worth a lot\nAlthough poor and humble it seems and be\nWe must fight for all those who do not fight!\nWe must ask for all those who do not implore!\nWe must make those who do not listen hear us!\nWe must cry for all those who do not cry!\nHave to be like bees in the hive\nmake sweet honeycombs for everyone.\nHave to be like the water that goes serene\ngiving the whole world fresh streams.\nMust imitate the wind, which sows flowers\nthe same in the mountains as in the plains,\nand have to live life sowing loves,\nwith the sight and the soul always in the height.\nThe madman said and with noble melancholy\nthrough the scrublands of the mountain he continued to climb,\nand when lost in the shadows, he still repeated:\nHave to live sowing! Always sowing!\u0026hellip;\n ","date":1597968000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1597968000,"objectID":"af5db10436acf76d8d2eea5dd6c99ca4","permalink":"http://comunidadbioinfo.github.io/post/the_impact_of_cdsb_on_me/","publishdate":"2020-08-21T00:00:00Z","relpermalink":"/post/the_impact_of_cdsb_on_me/","section":"post","summary":"By Erick Cuevas Fernández, M. Sc., Bioinformatician. Universidad Nacional Autonoma de Mexico. Universidad Autonoma del Estado de Morelos. Systems Biology and Translational Medicine Laboratory. @ErickCuevasF\nIn 2018 I heard of a workshop where Martin Morgan was performing in Mexico, at that time I had only a few months learning to use R, and I did not know who Martin Morgan was and had vague notions of Bioconductor. That year I started taking the international bioinformatics workshops.","tags":["Latin American","Bioconductor"],"title":"The impact of CDSB on me","type":"post"},{"authors":["CDSB"],"categories":["rstats"],"content":"This useR!2020 session and video was organized by Laura Acion, Yanina Bellini Saibene, Paola Corrales, and Paloma Rojas Saunero. Leonardo Collado Torres coordinated the blog post submission. This blog post was originally submitted to the R Consortium blog and published there on July 7th 2020.\nOn June 19th 2020 we filmed a video for useR!2020 showcasing the communities and organizations we are involved in that are for Latin Americans or have Latin American participants. In this blog post, we wanted to highlight these initiatives and remind everyone that we are more than happy to help you launch similar initiatives in your local communities.\n LatinR: LatinR is a trilingual international conference on the use of R in research and development across Latin America. Since launching in 2018, our annual meetings have been a starting point for new packages, local user groups, reading clubs, R-Ladies chapters, translations, and other initiatives in the region. ConectaR: ConectaR 2019 took place during January 24-26, 2019 at the University of Costa Rica, in San José, Costa Rica. It was the first event in Central America endorsed by The R Foundation, and it was held completely in Spanish. You can find more information here. satRday: satRday is a conference about R and its applications, that happens all over the world, and it is organized by the local community. Two satRdays events happened in Latin America: in Santiago - Chile and São Paulo - Brazil. If you want to organize a satRday anywhere in Latin America, please get it touch so we can help each other! R-Ladies: R-Ladies is a global organisation that promotes gender diversity in the R community. It has 123 active chapters in 51 countries around the world, of which 49 are found across 10 Latin American countries. Some Latin Americans are part of the R-Ladies Global Team, including its leadership. COVID-19 has not stopped us, instead, we have migrated online and fostered alliances among different chapters. All in an effort to give gender minorities in the R community the opportunity to learn R in a safe and supportive environment. Join us! rOpenSci: R for open science, rOpenSci, provides free technical review of R packages to improve the quality of open source software in order to maximize readability, usability, usefulness, and minimize redundancy. Their peer-review process will soon be translated to Spanish and you can get involved! CDSB: the Community of Bioinformatics Software Developers (CDSB in Spanish) was born in 2018 with the goal of helping Latin American R users become R \u0026amp; Bioconductor developers and increase the representation of Latinx in these communities. For more information about CDSB check bit.ly/cdsbpost2020. RUGs: there are several R User Groups in Latin America, some of which are officially sponsored by the R Consortium. We believe that creating a welcoming space is crucial for keeping the ideas flowing, which allows for meaningful networking and, consequently, the development of new projects. We can help you start your own group! R4DS in Spanish + datos package: the resources to learn R in English are many, awesome, online, and free. But in Latin America few people can afford to learn English, and the resources in Spanish are few. To help solve this problem, we community-translated to Spanish the “R for Data Science” book and developed a package with the translation of all the datasets used in it: datos. The workflow to contribute to the package was designed to engage first-time contributors, and is now guiding the development of a new version in Portuguese that will be released in the next few months. #DatosDeMiércoles + #30díasdegráficos: The @R4DS_es Twitter account was created as a way to share projects like the R4DS translation and to develop initiatives to foster the Spanish-speaking R community, like #datosdemieRcoles, the Latin American cousin of #TidyTuesday. The idea is not only to use datasets that are in Spanish, but also datasets that are relevant for our Region. This initiative has been complemented with the 30 days plot challenge #30díasdegráficos. If you want to participate proposing a dataset for #datodemiéRcoles, please visit our github repo. The Carpentries: The Carpentries builds global capacity in essential data and computational skills for conducting efficient, open, and reproducible research. Building a sustainable and active community in Latin America includes several initiatives: lesson translations, instructor training, workshop coordination, and fundraising. Get in touch with us through the mailing list and the carpentries-es channel at the Carpentries Slack workspace. ReproHack: ReproHack is a growing community for researchers that are fighting the reproducibility crisis by sharing their experiences across disciplines. It is focused on organizing hackathons where participants attempt to reproduce published research from a list of proposed papers with public code and data. We are planning the first ReproHack in Spanish for October 2020 and you can get in touch with us through Twitter. AI Inclusive: AI Inclusive is an organization that promotes diversity in the AI Community. We want to bring awareness around Artificial Intelligence issues and empower the community so they can enter in the AI field, a field that is not diverse at all. In December 2019, we had our launch events in Rio de Janeiro, Brazil and San Francisco, California. Follow us and join us! Data Latam: in May 2016 we started with the first Data Latam podcast, aimed at offering an easy entry point, in Spanish, to those interested in data science. We always ask our interviewees: “How did you get where you are?”, and the diversity of stories has been enormous. Today Data Latam is a Latin American community of professionals and academics, who apply data science in their day to day work and we invite you to participate! What happens in the R Community doesn’t stay in the R Community. All the good practices of inclusive and diverse communities learned in several of the initiatives presented before, generate strong work teams within and beyond the R community. There is still a lot to be done, but what we’ve already achieved is very encouraging and provides a solid foundation for the future.\nThese initiatives are sustained by many people making a great, mostly volunteer, effort behind the scenes. Some of the challenges that the communities face are translated into multiple positives, sustained, and a lot of invisible hard work. Some of them are: finding international funding due to limited local options, translating content, joining forces across organizations, organizing regional conferences, and becoming active developers of the technology.\nThe Latin American R community is growing fast and so does the responsibility to make this growth solid and safe. Some of the future work that we, as community builders, look forward to fulfilling are: consolidating regional conferences with support of international sponsors; acquiring funding to sustain translations; amplifying the voices of regional minorities; importing educational material and work opportunities; connecting expats with their local communities; helping other groups such as RUGs and RLadies; connecting with other initiatives such as R-Forwards, Africa-R, MiR, among others; Increase our and other minorities representation in the R Core Team, the R Foundation, and the R Consortium.\nThank you! Please watch our useR! 2020 video on YouTube.\n","date":1594166400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1594166400,"objectID":"71909b2620f5f7395bc1280acda4986a","permalink":"http://comunidadbioinfo.github.io/post/user_latin_american_community/","publishdate":"2020-07-08T00:00:00Z","relpermalink":"/post/user_latin_american_community/","section":"post","summary":"This useR!2020 session and video was organized by Laura Acion, Yanina Bellini Saibene, Paola Corrales, and Paloma Rojas Saunero. Leonardo Collado Torres coordinated the blog post submission. This blog post was originally submitted to the R Consortium blog and published there on July 7th 2020.\nOn June 19th 2020 we filmed a video for useR!2020 showcasing the communities and organizations we are involved in that are for Latin Americans or have Latin American participants.","tags":["Latin American","R Consortium"],"title":"Latin American communities and organizations: useR!2020 video","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"This blog post was submitted to the R Consortium blog where it was published on 03/18/2020.\nI have been attending R conferences since 2008, and while I’ve seen the R community grow rapidly, I generally don’t encounter as many Latin Americans (LatAm) among communities of R developers. Traditionally, a lab lead investigator invested in R or Bioconductor would teach their trainees and students these skills, becoming a local R hotspot. However, that scenario is uncommon in Mexico for several reasons. Recognizing some of these challenges and driven to promote R in our home country and LatAm, in 2017 Alejandro Reyes and I teamed up with Alejandra Medina Rivera and Heladia Salgado to eventually launch the Community of Bioinformatics Software Developers ( CDSB in Spanish) in 2018. One of our goals is to facilitate and encourage the transition from R user to R/Bioconductor developer. We have organized yearly one-week long workshops together with NNB-UNAM and RMB and just announced our 2020 workshop (August 3-7 2020 Cuernavaca, Mexico).\nIf you are fighting for change, know that even when things feel hard and progress is slow (or seems nonexistent), you are still creating and holding space for those who will come after you. Even if you can’t see it now, the impact of your work will be visible in the future.\n\u0026mdash; Jen Heemstra (@jenheemstra) March 5, 2020 Now unto our third workshop, I feel like we’ve had several success stories.\nCDSB2018 alumni wrote a blog post about their R GitHub package: rGriffin. CDSB2018 alumni secured BioC2019 travel scholarships and presented their work. Three CDSB2018 and 2019 alumni submitted the first package to Bioconductor (regutools), representing a significant percent-wise increase in the representation of LatAms in the Bioconductor developers community.\nWe have greatly benefited from the logistics and organization support by NNB-UNAM and RMB local teams, allowing us to focus on designing the workshop curriculum and inviting a diverse set of instructors, including Maria Teresa Ortiz who is an RLadiesCDMX co-founder and has been supporting us from the beginning. However, we face economic challenges as the budget for the national science foundation (CONACyT) has decreased in recent years. The support by the small R conference fund by R Consortium and other sponsors has been instrumental, as well as diversity and travel scholarships some of our instructors have secured at R conferences. We just recently revamped our sponsor page and answered the question: why should you support us?.\nHowever, while we are just getting started, one of our highlights was born by rOpenSci’s icebreaker exercise at CDSB2019. We were able to really build a sense of community and desire to perform outreach activities at our local communities. Particularly, a CDSB2018 and 19 alumni, Joselyn Chávez, volunteered to join the CDSB board. At CDSB2019 we also created an #rladies channel in our Slack where at the time we had members of 3/4 Mexico’s RLadies chapters ( Qro, Xalapa, CDMX) and now have 5/6 ( Cuerna, Monterrey), as CDSB2018 and CDSB2019 alumni have been co-founders of two chapters: Ana Beatriz Villaseñor-Altamirano for Qro and Joselyn Chávez for Cuerna.\nI am proud and excited of what we have achieved with our one-week long CDSB workshops, but also with how we used the tools we’ve learnt from other communities in order to keep interacting and communicating throughout the rest of the year. Time will tell if our efforts created a ripple that grew into a wave or if we’ll end burning out. Sustainability is a challenge, but we are greatly motivated by the impact we’ve had and can only imagine a brighter future.\nvia GIPHY\nCommunity of Bioinformatics Software Developers (CDSB): The story of a diversity and outreach hotspot in Mexico that hopes to empower local R developers - https://t.co/QMcNRUy1gl @fellgernon @andrewejaffe @LieberInstitute @lcgunam @jhubiostat @jtleek @LIBDrstats @CDSBMexico pic.twitter.com/TmZmxTRwOv\n\u0026mdash; R Consortium (@RConsortium) March 18, 2020 ","date":1584403200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1584403200,"objectID":"81f421d9bc994ebe19c303f803f85d42","permalink":"http://comunidadbioinfo.github.io/post/csdb-story-of-a-diversity-and-outreach-hotspot-in-mexico/","publishdate":"2020-03-17T00:00:00Z","relpermalink":"/post/csdb-story-of-a-diversity-and-outreach-hotspot-in-mexico/","section":"post","summary":"This blog post was submitted to the R Consortium blog where it was published on 03/18/2020.\nI have been attending R conferences since 2008, and while I’ve seen the R community grow rapidly, I generally don’t encounter as many Latin Americans (LatAm) among communities of R developers. Traditionally, a lab lead investigator invested in R or Bioconductor would teach their trainees and students these skills, becoming a local R hotspot. However, that scenario is uncommon in Mexico for several reasons.","tags":["Bioconductor","R Consortium"],"title":"CDSB: the story of a diversity and outreach hotspot in Mexico that hopes to empower local R developers","type":"post"},{"authors":["CDSB"],"categories":["Bioconductor","Conduct"],"content":"For the English version of this statement, please go to the BioC2019 Code of Conduct website. At CDSB\u0026rsquo;s website you can find the translated Spanish version of this statement.\n","date":1583778600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1583778600,"objectID":"24b044c1d14d7d76cb54e82cf7362518","permalink":"http://comunidadbioinfo.github.io/post/bioc2019-code-of-conduct-violation-response/","publishdate":"2020-03-09T18:30:00Z","relpermalink":"/post/bioc2019-code-of-conduct-violation-response/","section":"post","summary":"For the English version of this statement, please go to the BioC2019 Code of Conduct website. At CDSB\u0026rsquo;s website you can find the translated Spanish version of this statement.","tags":null,"title":"BioC2019 Code of Conduct violation response","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"This workshop is part of the Mexican Bioinformatics Encounter (EBM in Spanish) 2020 organized by CDSB with:\n TIB2020 RMB NNB CCG-UNAM Community of Bioinformatics Software Developers (CDSB) Workshop webpage\n Level: intermediate - advanced\n Language: Spanish\n When: August 3 - August 7, 2020 (9 am to 5:30 pm, Friday until 2:30 pm)\n Where: Online through the Zoom platform. Hours are based on Mexico\u0026rsquo;s central time zone.\n Twitter: @CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/cdsb2020\n Registration\n Summary Join us for our 2020 workshop! This year we’ll teach you how to improve your skills for interacting with the R programming language with diverse strategies for organizing your code and projects. This will help you document your analyses such that they are easily to reproduce and for sharing them with your collaborators (from academia to industry). As a use case, we will learn the statistical tools needed for analyzing single cell transcriptomics (scRNA-seq) data using Bioconductor. Completing this workshop will help you in all your R projects and your analyses of biological data: all your analyses will benefit from the organization skills and the ideas behind scRNA-seq are used in many bioinformatics projects.\nvia GIPHY\nRequirements Requirements prior knowledge\n Participants should have basic to intermediate knowledge of the R programming language: variable assignment, reading files: read.csv; data structures: matrix, data.frame, list; data types: character, numeric, factor, logical, etc; installation and use of packages. Know how to use RStudio. Be interested in learning good practices for organizing your work and sharing your work with others. Be interested in learning how to analyze biological data using R/Bioconductor packages. Technical requirements\n Personal computer. Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Overview In recent years, R has become one of the most used programming languages for data science. The explosion in data available in many fields has increased the demand for data analysts, which is the case in Bioinformatics. R users start by learning how to use the tools others have openly shared with the international community. These R users acquire skills as they continue to analyze data and might even start to interact with R software developers through community websites such as RStudio Community, Bioconductor Support or via Twitter using the #rstats hashtag. Eventually some R users will want to write their own functions and organize their code across several projects. It is at this point that it’s useful to learn how to organize your code in order to make your life as an R programmer easier, such that you spend more time on your projects instead of remembering where your code is or what you did a few weeks ago. In order to practice these concepts, we will review the most recent methods for analyzing single cell RNA sequencing (scRNA-seq) data using R packages specialized for this goal that are freely available through Bioconductor.\nThe instructors of this workshop have participated at CDSB since its foundation and have gone to conferences such as BioC2019 and rstudio::conf(2020), among others. In recent years we taught how to make R and Bioconductor packages, which are of great use for sharing code with others. Recently, CDSB alumni sent their first R package to Bioconductor, which represented a huge percent increase of Latin American representation in the Bioconductor developers community, thus demonstrating that participating at a CDSB workshop has an impact beyond the one week workshop. For 2020 we will have an applied focus while maintaining our goals at CDSB which are:\n Turn (bioinformatics) software users into (bioinformatics) software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for (biological) data analysis.\n Help train users that can become local instructors and continue to grow their local communities.\n The scRNA-seq portion of the workshop will be based on the book Orchestrating Single Cell Analysis with Bioconductor that was published by Nature Methods ( DOI) and is among the most publicized papers in 2020.\nThis workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram 9 am to 5:30 pm on Mexico\u0026rsquo;s central time zone (Friday we end at 2:30 pm) with breaks and time to eat. The detailed schedule and the Zoom links will be provided to those participants that register for the event through the private CDSB Google Calendar. For more schedule details check the CDSB2020 workshop GitHub repository.\nEvery day we will have a help session from 8 to 9 am for those that need help installing the required software for the workshop.\nDay 1\n EBM2020 inauguration Welcome to CDSB Participants self introductions Workflow around RStudio projects: Introduction to the project-oriented workflow. Working with projects against scripts. Creating a project. Using safe paths. How should I name my file? Day 2\n Using Git and GitHub. Modifying the R startup files. Writing and documenting functions. Debugging R code. Day 3\n Good practice for configuring and maintain workspaces. Remote picture / video. Installing R packages from source. General overview of single cell RNA-seq (scRNA-seq) data processing Community-building activities Overview of the scRNA-seq material Day 4\n Introduction to scRNA-seq Introduction to scRNA-seq with Bioconductor Data infrastructure and data import Quality control Data normalization Day 5\n Feature selection Dimension reduction Clustering and differential gene expression analysis spatialLIBD: analyzing data from the Visium assay by 10x Genomics Workshop evaluation Closing ceremony and CDSB reminders Instructors Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Querétaro, Mexico) Alejandra recently presented a keynote at the Women in Data Science event in Mexico City.\n Alejandro Reyes (Data Scientist, Novartis, Basel, Switzerland). Alejandro recently worked on the regutools project with CDSB alumni that was published at Oxford Bioinformatics.\n Joselyn Chávez (IBT-UNAM, Cuernavaca, Morelos, Mexico). Joselyn presented her work at BioC2019 thanks to a travel award, attended rstudio::conf(2020) thanks to a diversity scholarship where she took the What They Forgot to Teach You about R workshop, and recently was part of the first R package submission to Bioconductor by CDSB alumni. She initially was a CDSB2018 student.\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, MD, USA). Leonardo recently published a pre-print on spatial transcriptomics using 10xGenomics Visium data.\n Marcel Ramos Perez (Roswell Park Comprehensive Cancer Center and CUNY School of Public Health, USA). Marcel is part of the Bioconductor Core Team and is the author of many Bioconductor packages including MultiAssayExperiment.\n Maria Teresa Ortiz (CONABIO and ITAM, Mexico). Teresa presented at rstudio::conf(2020) her work on fast counting algorithms for Mexican presidential elections.\n Organizing committee Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Querétaro, Mexico)\n Alejandro Reyes (Data Scientist, Novartis, Basel, Switzerland)\n Joselyn Chávez (IBT-UNAM, Cuernavaca, Morelos, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, MD, USA)\n Code of Conduct Sponsors Become our sponsor\nPlatinum level Gold level Silver level \n \nOrganizers CDSB is a node of the Mexican Bioinformatics Network (RMB in Spanish) and jointly organizes the yearly workshop with the National Node of Bioinformatics (NNB).\n \n \n \n \nWith support from:\n \n \n","date":1583415000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1583415000,"objectID":"eebba06807993bba897a7d43257f8aeb","permalink":"http://comunidadbioinfo.github.io/post/cdsb2020-building-workflows-with-rstudio-and-scrnaseq-with-bioconductor/","publishdate":"2020-03-05T13:30:00Z","relpermalink":"/post/cdsb2020-building-workflows-with-rstudio-and-scrnaseq-with-bioconductor/","section":"post","summary":"This workshop is part of the Mexican Bioinformatics Encounter (EBM in Spanish) 2020 organized by CDSB with:\n TIB2020 RMB NNB CCG-UNAM Community of Bioinformatics Software Developers (CDSB) Workshop webpage\n Level: intermediate - advanced\n Language: Spanish\n When: August 3 - August 7, 2020 (9 am to 5:30 pm, Friday until 2:30 pm)","tags":null,"title":"CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":" A couple years ago we started the Community of Bioinformatics Software Developers (CDSB in Spanish) as because we were concerned with the very low representation of Latin Americans in the Bioconductor community, and the R community in general. For the full story check this this blog post.\n Since we started CDSB, part of our goal been to help Bioconductor users transition into developers. To achieve this, we organized one week long courses in Mexico at low cost during the summers of 2018 and 2019 in partnership with the TIBs leadership (NNB-UNAM) and RMB. We plan to continue organizing these courses: except a 2020 announcement next week!\nWhile these workshops allow us to reach up to 40 students in person for a week, we have been borrowing methods from others to try to interact more frequently and help throughout this process 1. But we now went a bit further.\nIn 2018, CDSB students worked on R/Bioconductor packages for two days during our workshop. One of them, Joselyn Chávez, picked up the regutools project and continued working on it with advice from Heladia Salgado. We eventually set up meetings where Alejandro Reyes and myself would advice Joselyn, Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca on how to best proceed.\nI just sent @Bioconductor\u0026#39;s 2020 conf deadline reminders to @CDSBMexico @LieberInstitute @GenomicsAtJHU @LatinR_Conf @rOpenSci @jhubiostat 🗓️\nIt\u0026#39;s the conf that started my #rstats career \u0026amp; I highly recommend it!\nBioC usage intro https://t.co/8NaV68vUsAhttps://t.co/ATzkKs7c04 pic.twitter.com/km8vRfyHcY\n\u0026mdash; 🇲🇽 Leonardo Collado-Torres (@lcolladotor) February 21, 2020 We’ve known for months that the deadline for BioC2020 talk/poster proposals was March 3rd. So we designed a plan that would allow them to submit regutools prior to that deadline, then submit a proposal to present it (as well as submit proposals to present their own research projects) in order to increase their likelihood of getting a BioC2020 travel scholarship.\nAnd we were able to accomplish this plan! Well, at least the part under their and our control. That is, check out the regutools Bioconductor submission. Thus we are incredibly excited to announce that the CDSB website now has a “Bioconductor Developers Alumni” section!\nWe are also thrilled to announce that the RegulonDB team has given us the go ahead signal to write a manuscript about regutools. So you’ll soon see a pre-print about it.\n via GIPHY Though I personally really hope that Joselyn, Carmina, Emiliano and many other CDSB alumni will be able to go to BioC2020 and other R conferences.\nWe couldn’t have gotten this far without all the support we’ve received over the years. So I would like to thank all our previous sponsors 2, colleagues who’ve encouraged us to keep going, and CDSB alumni like Joselyn, Carmina, and Emiliano who believed in our ideas and spent their own time making them a reality.\n via GIPHY I leave you here with a short introduction to regutools.\nregutools The goal of regutools is to provide an R interface for extracting and processing data from RegulonDB. This package was created as a collaboration by members of the Community of Bioinformatics Software Developers (CDSB in Spanish).\nFor more details, please check the documentation website or the Bioconductor package landing page here.\nInstallation You can install the released version of regutools from Bioconductor with:\nif (!requireNamespace(\u0026quot;BiocManager\u0026quot;, quietly = TRUE)) install.packages(\u0026quot;BiocManager\u0026quot;) BiocManager::install(\u0026quot;regutools\u0026quot;) ## Check that you have a valid Bioconductor installation BiocManager::valid() And the development version from GitHub with:\n## Since the package is currently going through the Bioconductor ## revision process, you need to use this code instead: BiocManager::install(\u0026quot;ComunidadBioinfo/regutools\u0026quot;) Example This is a basic example which shows you how to use regutools. For more details, please check the vignette.\nlibrary(\u0026#39;regutools\u0026#39;) ## basic example code ## Connect to the RegulonDB database if necessary if(!exists(\u0026#39;regulondb_conn\u0026#39;)) regulondb_conn \u0026lt;- connect_database() ## snapshotDate(): 2019-10-29 ## Build a regulondb object e_coli_regulondb \u0026lt;- regulondb( database_conn = regulondb_conn, organism = \u0026quot;E.coli\u0026quot;, database_version = \u0026quot;1\u0026quot;, genome_version = \u0026quot;1\u0026quot; ) ## Get the araC regulators araC_regulation \u0026lt;- get_gene_regulators( e_coli_regulondb, genes = c(\u0026quot;araC\u0026quot;), format = \u0026quot;multirow\u0026quot;, output.type = \u0026quot;TF\u0026quot; ) ## Summarize the araC regulation get_regulatory_summary(e_coli_regulondb, araC_regulation) ## regulondb_result with 3 rows and 7 columns ## TF Regulated_genes_per_TF Percent Activator Repressor Dual ## \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; ## 1 AraC 1 33.3333333333333 0 0 1 ## 2 CRP 1 33.3333333333333 1 0 0 ## 3 XylR 1 33.3333333333333 0 1 0 ## Regulated_genes ## \u0026lt;factor\u0026gt; ## 1 araC ## 2 araC ## 3 araC Citation Below is the citation output from using citation('regutools') in R. Please run this yourself to check for any updates on how to cite regutools.\ncitation(\u0026#39;regutools\u0026#39;) ## ## Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J, ## Salgado H, Collado-Torres L, Reyes A (2020). _regutools: an R package ## for data extraction from RegulonDB_. doi: 10.18129/B9.bioc.regutools ## (URL: https://doi.org/10.18129/B9.bioc.regutools), ## https://github.com/comunidadbioinfo/regutools - R package version ## 0.99.0, \u0026lt;URL: http://www.bioconductor.org/packages/regutools\u0026gt;. ## ## Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J, ## Salgado H, Collado-Torres L, Reyes A (2020). \u0026quot;Programmatic access to ## bacterial regulatory networks with regutools.\u0026quot; _bioRxiv_. doi: ## 10.1101/xxxyyy (URL: https://doi.org/10.1101/xxxyyy), \u0026lt;URL: ## https://doi.org/10.1101/xxxyyy\u0026gt;. ## ## To see these entries in BibTeX format, use \u0026#39;print(\u0026lt;citation\u0026gt;, ## bibtex=TRUE)\u0026#39;, \u0026#39;toBibtex(.)\u0026#39;, or set ## \u0026#39;options(citation.bibtex.max=999)\u0026#39;. Reproducibility information options(width = 120) sessioninfo::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── ## setting value ## version R version 3.6.2 (2019-12-12) ## os macOS Catalina 10.15.2 ## system x86_64, darwin15.6.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz America/New_York ## date 2020-02-29 ## ## ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── ## package * version date lib source ## acepack 1.4.1 2016-10-29 [1] CRAN (R 3.6.0) ## AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor ## AnnotationFilter 1.10.0 2019-10-29 [1] Bioconductor ## AnnotationHub 2.18.0 2019-10-29 [1] Bioconductor ## askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0) ## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) ## backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0) ## base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0) ## Biobase 2.46.0 2019-10-29 [1] Bioconductor ## 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Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.2) ## matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.0) ## memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.0) ## mime 0.9 2020-02-04 [1] CRAN (R 3.6.0) ## munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) ## nnet 7.3-12 2016-02-02 [1] CRAN (R 3.6.2) ## openssl 1.4.1 2019-07-18 [1] CRAN (R 3.6.0) ## pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.0) ## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1) ## png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0) ## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2) ## progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.0) ## promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.0) ## ProtGenerics 1.18.0 2019-10-29 [1] Bioconductor ## purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.0) ## R.methodsS3 1.7.1 2016-02-16 [1] CRAN (R 3.6.0) ## R.oo 1.23.0 2019-11-03 [1] CRAN (R 3.6.0) ## R.utils 2.9.2 2019-12-08 [1] CRAN (R 3.6.1) ## R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1) ## rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.0) ## RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) ## Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.0) ## RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 3.6.0) ## RCy3 2.6.3 2020-01-12 [1] Bioconductor ## regutools * 0.99.0 2020-02-29 [1] Github (comunidadbioinfo/regutools@0cb5b18) ## RJSONIO 1.3-1.4 2020-01-15 [1] CRAN (R 3.6.0) ## rlang 0.4.4 2020-01-28 [1] CRAN (R 3.6.0) ## rmarkdown 2.1 2020-01-20 [1] CRAN (R 3.6.0) ## rpart 4.1-15 2019-04-12 [1] CRAN (R 3.6.2) ## Rsamtools 2.2.1 2019-11-06 [1] Bioconductor ## RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.0) ## rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.0) ## rtracklayer 1.46.0 2019-10-29 [1] Bioconductor ## S4Vectors 0.24.3 2020-01-18 [1] Bioconductor ## scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.1) ## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) ## shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.0) ## stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.0) ## stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) ## SummarizedExperiment 1.16.1 2019-12-19 [1] Bioconductor ## survival 3.1-8 2019-12-03 [1] CRAN (R 3.6.2) ## tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) ## tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.0) ## VariantAnnotation 1.32.0 2019-10-29 [1] Bioconductor ## vctrs 0.2.3 2020-02-20 [1] CRAN (R 3.6.0) ## withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) ## xfun 0.12 2020-01-13 [1] CRAN (R 3.6.0) ## XML 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.0) ## xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0) ## XVector 0.26.0 2019-10-29 [1] Bioconductor ## yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.0) ## zlibbioc 1.32.0 2019-10-29 [1] Bioconductor ## ## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library As always, thank you rOpenSci unconf 2018!↩︎\n Sponsors are listed on each year’s workshop announcement. If you would like to sponsor our 2020 workshop, please get in touch with us. Thanks!!↩︎\n ","date":1582995600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1582995600,"objectID":"7b80692a9a96c383e026445e7bf8f537","permalink":"http://comunidadbioinfo.github.io/post/from-bioconductor-users-to-developers-our-first-community-submission/","publishdate":"2020-02-29T17:00:00Z","relpermalink":"/post/from-bioconductor-users-to-developers-our-first-community-submission/","section":"post","summary":"A couple years ago we started the Community of Bioinformatics Software Developers (CDSB in Spanish) as because we were concerned with the very low representation of Latin Americans in the Bioconductor community, and the R community in general. For the full story check this this blog post.\n Since we started CDSB, part of our goal been to help Bioconductor users transition into developers. To achieve this, we organized one week long courses in Mexico at low cost during the summers of 2018 and 2019 in partnership with the TIBs leadership (NNB-UNAM) and RMB.","tags":["Bioconductor","Developer Alumni"],"title":"From Bioconductor users to developers: our first community submission","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/building-tidy-tools-CDSB-runconf-2019/\n Level: intermediate - advanced\n Language: Spanish^[If you speak English but not Spanish please let us know so we can plan accordingly.]\n When: July 29 - August 2, 2019\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/tidy-tools-CDSB-runconf-2019\n Registration\n Requirements Requirements prior knowledge\n Participants should have basic to intermediate knowledge of the R programming language: variable assignment, reading files: read.csv, read.delim, read.table; data structures: matrix, dataframe, list; data types: character, numeric, factor, logical, etc; installation and use of packages. R: know how to install packages RStudio: know how to use. Technical requirements\n Personal computer. Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Overview In recent years, R has become one of the most used programming languages for data science. The explosion in data available in many fields has increased the demand for data analysts, which is the case in Bioinformatics. R users start by learning how to use the tools others have openly shared with the international community. These R users acquire skills as they continue to analyze data and might even start to interact with R software developers through community websites such as RStudio Community, Bioconductor Support or via Twitter using the #rstats hashtag. Eventually some R users will want to write their own functions and share them online with others. They can do so via creating their own R packages and sharing them via repositories likes CRAN and Bioconductor or simply via GitHub. In this workshop participants will work through the Building Tidy Tools rstudio::conf 2019 workshop and then build their own R packages by collaborating with each other, similar to what was done at rOpenSci unconf18.\nThis workshop is aimed at students and researchers interested in data analysis that have experience using R. We encourage applications from experts in diverse disciplines, including but not limited to biologists, bioinformaticians, data scientists, software engineers and programmers and R users at large. The main goals of the workshop are:\n Teach participants the principles of reproducible data science through the development of R/Bioconductor packages.\n Turn (bioinformatics) software users into (bioinformatics) software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for (biological) data analysis.\n Help train users that can become local instructors and continue to grow their local communities.\n This workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram Overall TIB2019 program (registration, sessions and breaks) is available here.\n Day 1: July 29, 2019 08:00-09:00 Registration 09:00-09:30 TIB2019 Inauguration 09:30-10:00 Welcome to CDSB: the history of our community and where we are going. Code of conduct review Leonardo Collado-Torres 10:00-10:30 Why make an R package? Alejandro Reyes 10:30-11:00 Preliminaries Leonardo Collado-Torres 11:00-11:30 Coffee break 11:30-12:30 Packages Leonardo Collado-Torres 12:30-14:00 Testing Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 API Design Leonardo Collado-Torres 17:30-18:30 Welcome cocktail Day 2: July 30, 2019 09:00-11:00 Functional Programing Leonardo Collado-Torres 11:00-11:30 Coffee break 11:30-14:00 Errors Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 Object Oriented Programming Alejandro Reyes Day 3: July 31, 2019 09:00-11:00 Tidy Evaluation Leonardo Collado-Torres 11:00-11:30 Group picture 11:30-12:00 Coffee break 12:00-14:00 Document and Share Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 Introduction to GitHub Alejandra Medina-Rivera Day 4: August 1, 2019 09:00-09:30 Introduction to runconf Leonardo Collado-Torres 09:30-11:00 Community building activities 11:00-11:30 Coffee break 11:30-12:00 Voting and selection of projects to work on 12:00-14:00 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz 14:00-15:30 Break 15:30-17:30 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz Day 5: August 2, 2019 09:00-09:15 (optional) change project 09:15-11:00 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz 11:00-11:30 Coffee break 11:30-12:00 Workshop evaluation 12:00-12:30 Prepare presentations of the collaborative project 12:30-13:00 Presentations of collaborative projects 13:00-13:30 Closing remarks and community participation opportunities 13:30-14:00 TIB2019 Closing Ceremony Building Tidy Tools Charlotte Wickham and Hadley Wickham were the instructors of the original version of this workshop at rstudio::conf 2019. They have kindly shared their materials with us, which we will translate to Spanish.\n This is a two-day hands on workshop for those who have embraced the tidyverse and now want to expand it to meet their own needs. We\u0026rsquo;ll discuss API design, functional programming tools, the basics of object design in S3, and the tidy eval system for NSE.\nLearn efficient workflows for developing high-quality R functions, using the set of conventions codified by a package. You\u0026rsquo;ll also learn workflows for unit testing, which helps ensure that your functions do exactly what you think they do. Master the art of writing functions that do one thing well and can be fluently combined together to solve more complex problems.We\u0026rsquo;ll cover common function writing pitfalls and how to avoid them.\nLearn how to write collections of functions that work well together, and adhere to existing conventions so they\u0026rsquo;re easy to pick up for newcomers.\nYou should take this workshop if you have experience programming in R and want to learn how to tackle larger scale problems. You\u0026rsquo;ll get the most from it if you\u0026rsquo;re already familiar with functions and are comfortable with R’s basic data structures (vectors, matrices, arrays, lists, and data frames).\n Instead of two days, we will teach this workshop in two and a half days such that we can give you more time to digest the material and work through an introduction to Git and GitHub.\nCDSB runconf R unconference events (runconf) typically involve two stages and an optional third one. First, participants create issues weeks ahead of the runconf where they share ideas that they can work through in collaboration with others during the two days of the runconf. In the second stage, participants meet each other and get to know each other through some icebreakers. They then work together for two days on the projects that received the most votes. This is where participants get to learn skills from each other and get a taste of developing open source software in a collaborative environment. At the end, everyone shares their work with the whole group. In the third and final stage, runconf attendees might continue to interact with each other to further polish the packages they worked on during the runconf event, start new collaborations and/or write blog posts about their experience.\nThere are many blog posts about rOpenSci unconf events. A recent runconf was the chirunconf which you can read more about on this blog post by Sharla Gelfand.\nIf you are attending our workshop, we will ask you to propose at least one R package idea by creating a GitHub Issue in our GitHub repository for the workshop. If you want some inspiration, take a look at rOpenSci unconf18\u0026rsquo;s GitHub repository. You will need to get familiarized with all the proposal before the workshop starts.\nInstructors: Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA). Leonardo attended rstudio::conf 2019 thanks to a diversity scholarship where he took the original Building Tidy Tools workshop. He also attended rOpenSci unconf 2018.\n Maria Teresa Ortiz (CONABIO and ITAM, Mexico)\n Organizing committee: Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Delfino García (Center for Genomic Sciences, Cuernavaca, Mexico)\n Heladia Salgado (Center for Genomic Sciences, Cuernavaca, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA)\n Code of Conduct Sponsors Become our sponsor\n ","date":1554471000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554471000,"objectID":"02b4e7b64a3fd0ff1397bdcb98b6a6ef","permalink":"http://comunidadbioinfo.github.io/post/building-tidy-tools-cdsb-runconf-2019/","publishdate":"2019-04-05T13:30:00Z","relpermalink":"/post/building-tidy-tools-cdsb-runconf-2019/","section":"post","summary":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/building-tidy-tools-CDSB-runconf-2019/\n Level: intermediate - advanced\n Language: Spanish^[If you speak English but not Spanish please let us know so we can plan accordingly.]\n When: July 29 - August 2, 2019\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/tidy-tools-CDSB-runconf-2019\n Registration","tags":null,"title":"CDSB Workshop 2019: How to Build and Create Tidy Tools","type":"post"},{"authors":["CDSB"],"categories":["Events"],"content":"The National Node of Bioinformatics (NNB-UNAM), the Mexican Bioinformatics Network (RMB) and the Community of Bioinformatics Software Developers (CDSB) invite you to Bioinformatics Mexican Meeting 2019 composed by\nInternational Bioinformatics Workshops (TIB2019) \u0026amp;\nCDSB Workshop: How To Build and Create Tidy Tools UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 29 to August 9, 2019\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network) Community of Bioinformatics Software Developers (CDSB) Mexican Bioinformatics Network (RMB) thanks to the:\n Center for Genomic Sciences (CCG-UNAM) Undergrad on Genomic Sciences (LCG-UNAM) For information on how to register, check the TIB2019 website.\nWorkshops Each workshop is a week long.\nFrom July 29 to August 2, 2019\n T1: Introduction workshop R and RStudio\n T2. Introduction to Genome Assembly and Annotation\n T3. Comparative genomics with microbes: pangenomics and phyloinformatics\n CDSB Workshop 2019: How to Build and Create Tidy Tools\nFrom August 5 to August 9, 2019\n T4. Tutoring for the assembly and annotation of your genome of choice\n T5: Introduction to programming with Python\nInterested in becoming our sponsor?\n","date":1554465600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554465600,"objectID":"d0685a87782c0a6f951997e458175085","permalink":"http://comunidadbioinfo.github.io/post/talleres-internacionales-de-bioinformatica-2019/","publishdate":"2019-04-05T12:00:00Z","relpermalink":"/post/talleres-internacionales-de-bioinformatica-2019/","section":"post","summary":"The National Node of Bioinformatics (NNB-UNAM), the Mexican Bioinformatics Network (RMB) and the Community of Bioinformatics Software Developers (CDSB) invite you to Bioinformatics Mexican Meeting 2019 composed by\nInternational Bioinformatics Workshops (TIB2019) \u0026amp;\nCDSB Workshop: How To Build and Create Tidy Tools UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 29 to August 9, 2019\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network) Community of Bioinformatics Software Developers (CDSB) Mexican Bioinformatics Network (RMB) thanks to the:","tags":null,"title":"Bioinformatics Mexican Meeting 2019","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"Last year the Community of Bioinformatics Software Developers (CDSB in Spanish) organized a one week workshop designed to train R users how to write R packages and ideally contribute them to Bioconductor. The workshop itself was a success as described in our summary post about the event. However, we didn’t want to stop there. We formed CDSB and teamed up with TIB (“Talleres Internacionales de Bioinformática”) from NNB-UNAM with the goal of simulating the BioC yearly meeting where attendees can learn R, mature as R users and become R developers. We also organized this workshop because we want to see more Latin Americans at BioC.\nBioC2019 application process Time passed since our 2018 workshop as everyone continued on their regular jobs and training programs. BioC2019 was then announced and with it were announced the application guidelines for:\n Presenting a talk or poster Applying for a travel award Proposing a workshop Basically, those applying for a travel award had to:\n Create a website or upload their CV to a publicly available website Answer in about 150 words or less How have you participated in the Bioconductor project in the past? Answer in about 150 words or less What do you hope to get out of the conference? Write a scientific abstract of 300 words or less for the talk/poster proposal^[Or propose a workshop, but that’s too much to ask from those just starting their BioC journeys. It’s more appropriate for BioC veterans.]. The whole process, while designed to be welcoming, can be a bit daunting if this is your first time applying and if English is not your native language. Thus, when we reminded our community members about BioC2019 we offered our help for this application process.\nHelping CDSB members Given their experience with Bioconductor, Alejandro Reyes and Leonardo Collado Torres volunteer to help CDSB members. The reminder blog post and individually contacting some CDSBMexico 2018 attendees helped find and motivate members to apply. Simply encouraging them and telling them that they had a realistic chance made a big difference, that is, believing in them and the work that we’ve done already as a community. There were many emails, Slack message channels and documents shared, but ultimately the clean version of the process was the following.\n A CSDB member expressed interest in BioC2019 to a CDSB volunteer (Alejandro or Leonardo). A CSDB volunteer reminded them of the BioC2019 application process and clarified any rule questions they had. If appropriate, the CDSB volunteer also explained some options for creating websites hosted on GitHub. The CDSB member wrote their draft answers to the two questions, plus their draft abstract, in a Google Doc that they shared with the CDSB volunteers with edit permissions. Similarly, the CDSB member created a draft website. All CDSB volunteers provided suggestions on how to present their information more clearly to the application reviewers keeping in mind what the CDSB member wanted to express about themselves or their work. The CDSB member made modifications and if appropriate asked for another round of feedback. Basically, the CDSB volunteers passed on the best practices they know for filling out these applications and writing abstracts, including here some timely advice from Wolfgang Huber ( a longtime Bioconductor Project contributor).\nThe generic paper abstract\n1. Why is it important? (1)\n2. What is \u0026quot;it\u0026quot;? (1)\n3. But what is the problem with it? (1)\n4. What did you do about the problem? (1)\n5. What was your result? (n)\n6. What are some wider implications? (1)\n(in parentheses: number of sentences)\n\u0026mdash; Wolfgang Huber 🇺🇦 (@wolfgangkhuber) February 22, 2019 The end result In the end, three CDSB members went through the whole process and created their websites:\n Ana Beatriz Villaseñor-Altamirano César Miguel Valdez Córdova Joselyn Chavez They all submitted their applications for the BioC2019 travel award before the deadline expired on March 15th 2019, something that we emphasized they should do!\nA couple of weeks passed, and on April 2nd we were delighted to report that all three of them got 10 minute talks 🎙and travel awards ✈️approved. This is an enormous win for CDSB and a huge morale boost 🎉🥳.\nThank you @Bioconductor!! Today 4 of our members got travel scholarships, talks and workshops approved. 6 total will attend #bioc2019 Please welcome them!@AnaBetty2304 @josschavezf1 @cmvaldezcordova @doctor_calvo @areyesq @fellgernon#rstats #diversityhttps://t.co/apxYxSpE5Z pic.twitter.com/tmSYbZvi7B\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) April 3, 2019 We cannot hide our excitement about these news and are looking forward to seeing them at BioC2019! We hope that all of them will have a great experience 🙌🏽😃\nA word from our CDSB members going to BioC2019 Like we’ve said, this is just the beginning and we want to keep helping others in years to come. We thus asked Ana, César and Joselyn to share a few words to future CDSB members on the BioC2019 travel award application process and the feedback they got from CDSB volunteers.\nAna The application process for BioC2019 and the travel award is not so difficult at the end but when I read the requirements for the first time I was overwhelmed, I had never published a web page before and I needed it to cover one of the requirements that asked for a personal website or public CV! It crossed my mind that I would not apply but Leo and Alejandro cheered me up, supported and guided me to create my own website (now I do webpages in R for anything that I can, hehe). They also helped me with the remaining requirements and at the end, I was able to enjoy the application process, I truly appreciate all the assistance they provided me and I can’t wait to meet them in NY. Without a doubt, Leo and Alejandro are accessible and inspiring bioinformaticians and people, as a consequence CDSB is a friendly and engaged community with the aim to impulse Mexican bioinformatic development to the world.\n César When I attended CDSB Mexico 2018, the last thing I imagined was that the process would culminate in me receiving a travel scholarship for BioC2019; Impostor syndrome is absolutely real. When talking about my master’s thesis with both Alejandro and Leo, they encouraged me to go all the way with its code and try and make a contribution to the Bioconductor project in the process. Said task seemed insurmountable in the beginning. However, after attending CDSB Mexico 2018, my perspective changed significantly. A deciding factor in me taking the plunge to actually go through with the contribution and consequent conference application was the overwhelmingly constructive support I received from the community at every stage in the process, from my original idea, all the way up to the conference’s application. Along the process, I noticed that even when we often expect to have an absolutely perfect product (a personal webpage, an online CV or an r package and all that it entails) from the get-go, this is rarely the way in which things happen. Cliché as it may sound, Rome wasn’t built in a day. Being able to shift my mindset and recognize the incremental nature of contributing has definitely set a precedent for how i’ll be handling most career oriented endeavors from now on; hopefully with continued contributions to the Bioconductor project and the open-source domain! If there’s anything I have to say to future applicants and CDSB members is just that: Do it! Reach out! Apply while embracing the community that’s there for you! With a little luck and elbow grease, things might just go your way, as they did for me.\n Joselyn When Alejandro Reyes and Leonardo Collado told me about applying to BioC2019 I felt nervous. I did not consider to submit my work and even less to apply for a scholarship before receiving their e-mail. They gave me all their trust and support through the process. Now I have been elected and feel very excited with this huge opportunity. I realize how warm the CDSBMexico community can be and that is possible to be part of meetings like BioC2019, all you have to do is let go of the fear to do it.\n ","date":1554418247,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554418247,"objectID":"784b67641b4e5219388330c21faded47","permalink":"http://comunidadbioinfo.github.io/post/path-from-cdsbmexico-2018-to-bioc2019/","publishdate":"2019-04-04T22:50:47Z","relpermalink":"/post/path-from-cdsbmexico-2018-to-bioc2019/","section":"post","summary":"Last year the Community of Bioinformatics Software Developers (CDSB in Spanish) organized a one week workshop designed to train R users how to write R packages and ideally contribute them to Bioconductor. The workshop itself was a success as described in our summary post about the event. However, we didn’t want to stop there. We formed CDSB and teamed up with TIB (“Talleres Internacionales de Bioinformática”) from NNB-UNAM with the goal of simulating the BioC yearly meeting where attendees can learn R, mature as R users and become R developers.","tags":["Bioconductor","Applications"],"title":"The path from CDSBMexico 2018 to BioC2019","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America. The National Bioinformatics Node ( NNB-UNAM in Spanish) has organized workshops in bioinformatics and R since 2006 and more frequently since 2010. Last year, 2018, there were five simultaneous one week workshops:\n Introduction to R and RStudio\n Exploratory data analysis (EDA) of biological data with R\n EDA of RNA-seq data and differential expression studies\n Genome assembly and annotation from high-throughput sequencing data\n And our Latin American R/Bioconductor Developers Workshop\n Overall it was a success as described in A recap of CDSB 2018: the start of a community. However, we are not done yet! 💪🏽As we have stated several times, our goal is to turn R users into developers and to increase the representation of Mexicans and Latin Americans at other R events.\nBioC2019 The one R event that we followed as a guide last year is the Bioconductor yearly meeting, or BioC. This year, BioC2019 will be held during June 24 to 27 at New York City in the United States. If you are an academic the registration fee is 300 USD prior to May 24th. As of today (Feb 28th), a round trip from Mexico City on June 23 to 28th is about 320-410 USD1. The accommodation options listed start at 118 USD plus tax a night. As you can see, these numbers add up fairly fast which is a limiting factor for scientists from Mexico (and Latin American in general) to attend BioC2019.\nTravel scholarships However, we want to remind you that there are travel scholarships available! And we, CDSB, want to help you! 🙌🏽\nAll the details about the travel scholarship and different types of submission proposals are available on the BioC2019 website. But let us summarize the process for you.\n You have to apply for either a talk, poster or workshop.\n You need a professional website, GitHub profile or your CV to be available online.\n You need to answer two questions:\n How have you participated in the Bioconductor project in the past?\n What do you hope to get out of the conference?\n For a talk or poster proposal you have a maximum of 300 words while workshop proposals involve filling out a template.\nThis is quite a bit of work, but the payoff is immense! You will compete for the opportunity to travel basically for free: free registration and hotel, plus $500 for travel expenses. This can be a career changing opportunity as it was the case for L. Collado-Torres (see his keynote slides) and others.\nGet started on your scholarship application! We know that many of us have a tendency to do things at the last minute. However, we hope 🙏🏽 that you start your application materials as soon as you can. Remember that the deadline is March 15th and no exceptions are made.\nWebsite If you don’t have a professional website, we recommend that you make one following Emily Zabor’s tutorial. This is the tutorial that one of your fellow CDSBMexico 2018 attendees used to create his website: joseaia.github.io. Alternatively, check out the Chromebook Data Science: intro to R course (available for free if you can’t afford it) which includes a lesson that walks you through this process.\nBioconductor project participation Next, we know that each of you worked at least in one R package during CDSBMexico 2018 such as rGriffin (check the blog post). Maybe you even submitted your package to Bioconductor. At least, you met and interacted with longtime Bioconductor members such as Martin Morgan and Benilton Carvalho. Since then, you might have worked on other R packages, shiny applications, etc. You might have also answered questions on the Bioconductor support website, reported bugs or opened issues in existing packages, joined the developers mailing list, joined the Bioconductor Slack workspace, etc. Ultimately, you could potentially present a poster or give a talk about the package you worked on last summer, but you’ll need to coordinate with your team members and/or lab principal investigator.\nBenefitting from BioC2019 As for what you hope to get out of the conference, well, we will remind you that BioC has different workshops that can help you advance your R skills and knowledge. Furthermore, there’ll be scientific talks from excellent bioinformatics researchers. Then, once you return from the conference, you can spread the knowledge you acquired in a variety of ways: implementing it on your work, teaching at your local university or research institute, participating in the Bioconductor community (Slack, the support website, contributing an R package, etc), presenting at a local R meetup, and participating in other forums. You can also benefit personally from attending the conference by networking with other users and developers that will attend it. From it, you might start new collaborations, find about graduate school programs, find potential postdoc advisors, among other opportunities. Hey, you might help us out with future CDSBMexico events!\nCDSBMexico hands on help If you need help directly, please get in touch with us via the CDSBMexico Slack workspace. If you either don’t remember the Slack workspace or you couldn’t attend CDSBMexico 2018, please get in touch with us via Twitter at twitter.com/CDSBMexico.\nWe understand that not many will be able to attend BioC2019, so keep an eye open for CDSBMexico 2019! We are hoping to announce our plans soon.\n","date":1551414287,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1551414287,"objectID":"b19c492880b141146c5a943d45932d51","permalink":"http://comunidadbioinfo.github.io/post/cdsbmexico-remember-to-apply-for-bioc2019-travel-scholarships/","publishdate":"2019-03-01T04:24:47Z","relpermalink":"/post/cdsbmexico-remember-to-apply-for-bioc2019-travel-scholarships/","section":"post","summary":"About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America. The National Bioinformatics Node ( NNB-UNAM in Spanish) has organized workshops in bioinformatics and R since 2006 and more frequently since 2010. Last year, 2018, there were five simultaneous one week workshops:\n Introduction to R and RStudio\n Exploratory data analysis (EDA) of biological data with R","tags":null,"title":"CDSBMexico: remember to apply for BioC2019 travel scholarships","type":"post"},{"authors":["Alejandro Reyes, PhD"],"categories":["rstats"],"content":"Organizing an event is a lot of work, much more than you plan for it. But harvesting the fruits of a successful event makes the workload worth it.\nIn July, we kicked off the first Bioconductor Latin American Developers Workshop 2018 (LatAmBioc2018). The main goals of this meeting were to encourage the development of the Bioconductor project in Mexico and to start a community of Mexican bioinformatic software developers – the Community of Bioinformatic Software Developers (CDSB, from its acronym in Spanish).\n \nThe program of the workshop included talks, posters and lessons sessions as well as a two-day hands-on development hackathon. We had over 30 participants with strong quantitative background and experience in R programming from several LatAm countries.\nExcited about #CDSBMexico? It starts tomorrow! ¿Listos para mañana? 🇲🇽https://t.co/UUhX5RMSut\nSchedulehttps://t.co/BZTD7wGskI\nMaterialshttps://t.co/Oz2ingGije#rstats #teaching @Bioconductor Thanks to @lcgunam @ccg_unam @LIIGH_UNAM\nSoIBio @RConsortium@WINTERGENOMICS pic.twitter.com/YQxmnTNwQa\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) July 29, 2018 Community building Unlike the US and Europe, where many universities have Computational Biology and Biostatistics Departments that gather experts in the field, in Mexico and Latin America experts in Biostatistics and Computational Biology are often spread across the country. The benefits of having Computational Biology and Biostatistics Departments are plenty: for example, experts can interact and work together on a specific problem, and researchers from other disciplines can easily find support and establish collaborations. The goal of CDSB is to create a virtual department where experts in Biostatistics and Computational Biology can discuss ideas and help each other across all stages of their careers.\nThe first event organized by CDSB, LatAmBioc2018 included talks where both participants and speakers could start a dialogue and motivate each other by showcasing their work. As keynote invited speakers we had Daniel Piñero, who talked about population genetics of maize in Mexico; Alejandro Ponce-Mendoza, who showed elegant shiny apps to visualize ecological data along with maps; Teresa Ortiz, who talked about gender biases among R programmers; and Benilton Carvalho, who showed the development of personalized medicine in Brazil.\nWe are having a great presentation from the founder of @RLadiesCDMX, @TeresaOM, about getting rid of gender biases among the #rstats community. #LatAmBioc18 @CDSBMexico #womeninSTEM pic.twitter.com/TPdDzHVdqC\n\u0026mdash; Alejandro Reyes (@areyesq) August 2, 2018 The LatAmBioc2018 poster session was designed to encourage interdisciplinary collaborations. We invited people to contribute bioinformatic problems that would benefit from advice from experts such as the participants of LatAmBioc2018. We were happy to see that this event helped to create new collaborations.\nHere, we are presenting the basic structure and some examples with the framework -Winterflow- using @nextflowio, @Docker, #mk and #git pic.twitter.com/Ktn9o01X2Z\n\u0026mdash; Winter Genomics (@wintergenomics) August 2, 2018 A LatAm Bioconductor community Anecdotally, some of us felt that Latin Americans were not fully represented in the Bioconductor Developers Meetings (see Leonardo Collado Torres’s blog post). As scientists, we like our statements to be supported by data: the map below shows the affiliations, when available, of the contributors of the latest package submissions to the Bioconductor project. (These data were scraped using the Github API.) Although biases such as Mexican contributors with affiliations abroad might not have been considered, it is clear that only a few contributions come from Latin American countries.\nIn hopes of filling this gap, we gathered a diverse team of instructors, including Martin Morgan, Benilton Carvalho and Selene L. Fernandez-Valverde, who taught participants how to develop R/Bioconductor packages. The main idea was to turn Bioconductor software users into Bioconductor software developers.\nLet\u0026#39;s estimate Pi! Rcpp exercise! Rcpp sugar! Now I\u0026#39;m hungry, I want pie @benilton @CDSBMexico #rstats #CDSBMexico #TIBMexico2018 🍰👩💻 pic.twitter.com/2OeGWr35r3\n\u0026mdash; Alejandra Medina-Rivera (@AleMedinaRivera) August 1, 2018 How to debug R code with Martin Morgan :D @CDSBMexico\n\u0026mdash; Semiramis (@semiramis_cj) August 1, 2018 Participants attended lectures from Monday to Wednesday. Before the workshop, co-organizer Daniela Ledezma received and coordinated R package development proposals. On Wednesday afternoon, the participants formed teams and chose problems from Daniela’s curated list. They worked on their projects on Thursday and Friday, and we were very pleased with the final products: most teams wrote documented R packages that are available through GitHub. Two interesting examples are the prototype of the regulonDB package, which enables users to query RegulonDB within an R interphase, and rGriffin, an R interphase to inquire regulatory networks (for details, check their contributed blog post).\nParticipants are gathering to work in collaborative projects targeting specific questions. The objetive is write a fully documented #rstats package by Friday. @CDSBMexico #LatAmBioc18 pic.twitter.com/vDAvuOothC\n\u0026mdash; Alejandro Reyes (@areyesq) August 1, 2018 #CDSBMexico package developers course attendants presenting their projects #TIBs2018 #rstats @CDSBMexico pic.twitter.com/ST44hCsLT6\n\u0026mdash; Alejandra Medina-Rivera (@AleMedinaRivera) August 3, 2018 We are looking forward to seeing how the participants keep developing their R packages and collaborating through CSDB.\nOverachievers We felt that the goals of the workshop were reached programmers from all over Latin America worked together and wrote new R packages, which hopefully will be submitted to Bioconductor soon.\nWe also had the chance to enjoy some good Mexican food and hang out with colleagues in less formal settings, such as lunches and group outings. To celebrate the conclusion of the workshop, we had an improvised party in a bar that played Latin American music. As any good party should, it ended up quite late. Some of us went to bed at 4am, but we woke up energized to keep CSDB going. Even now, two months on, we are excited to continue developing a strong community of bioinformatic developers in Latin America.\nIn #mexico, we don\u0026#39;t only know how to do #Science and good #Bioinformatics but also how to eat! Tacos during #TIBMexico2018 and @qBio18 @AlexielMedyna @licloona1487 something great is happening here 😊 pic.twitter.com/bC7ycfIA9n\n\u0026mdash; Ana B Villaseñor-Altamirano (@AnaBetty2304) August 2, 2018 Thank you The LatAmBioc2018 would not have been possible without the time and support from the instructors, presenters, organizers and our sponsors CCG-UNAM, LCG-UNAM, LIIGH-UNAM, Winter Genomics, R Consortium and SoIBio.\n","date":1536891202,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1536891202,"objectID":"bb8026c23d4c8cd6757e48069b6e2648","permalink":"http://comunidadbioinfo.github.io/post/a-recap-of-cdsb-2018-the-start-of-a-community/","publishdate":"2018-09-14T02:13:22Z","relpermalink":"/post/a-recap-of-cdsb-2018-the-start-of-a-community/","section":"post","summary":"Organizing an event is a lot of work, much more than you plan for it. But harvesting the fruits of a successful event makes the workload worth it.\nIn July, we kicked off the first Bioconductor Latin American Developers Workshop 2018 (LatAmBioc2018). The main goals of this meeting were to encourage the development of the Bioconductor project in Mexico and to start a community of Mexican bioinformatic software developers – the Community of Bioinformatic Software Developers (CDSB, from its acronym in Spanish).","tags":null,"title":"A recap of CDSB 2018: the start of a community","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":" This blog post was written by ME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth.\nIn this blog post we will describe the package rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) that was one of the projects developed during the TIB2018-BCDW. We hope to continue developing Griffin and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). If you have ideas, suggestions or bugs, please contact us via rGriffin GitHub repo.\n The problem Boolean networks allow us to give a mechanistic explanation to how cell types emerge from regulatory networks. However, inferring the regulatory network and its functions is complex problem, as the available information is often incomplete. rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) uses available biological information (regulatory interactions, cell types, mutants) codified as a set of restrictions and returns the Boolean Networks that satisfy that restrictions. This Boolean networks can then be used to study the biological system.\nThe rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) package is an R connector to Griffin (Gene Regulatory Interaction Formulator For Inquiring Networks), a java library for inference and analysis of Boolean Network models. Griffin takes as inputs biologically meaningful constraints and turns them into a symbolic representation. Using a SAT engine, Griffin explores the Boolean Network search space, finding all satisfying assignments that are compatible with the specified constraints. The rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) package includes a number of functions to interact with the BoolNet package.\n A small example Let us suppose a cell, we know that this cell has three proteins called a, b and c. We know that a activates b and that b and c inhibit each other. We also suspect that b and c may have positive self-regulatory loops. We can add this interactions to the table as “OPU” (optional, positive, unambiguous). This dataframe is the topology of the network.\n Source Target Interaction a b + b c - c b - b b OPU c c OPU Suppose we also have some information of what cell types have been observed. For example, there is a cell type that expresses b, but not a or c and an other cell type that expresses c, but not a or b. There might exist a third cell type that has not been fully characterized where we know that the cell expresses no a or c but we have NO information on b. This dataframe is the attractors of the network.\n a b c 0 1 0 0 0 1 0 * 0 We can then use this information to create a query. rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) can include other types of information like transition between cell type, cycles, transitions between cell types or mutant cell types.\n## Install using: # devtools::install_github(\u0026#39;mar-esther23/rgriffin\u0026#39;) ## Note that the package depends on rJava library(\u0026#39;rGriffin\u0026#39;) ## Loading required package: rJava genes = c(\u0026#39;a\u0026#39;,\u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;) inter = data.frame(source=c(\u0026#39;a\u0026#39;,\u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;, \u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;), target=c(\u0026#39;b\u0026#39;, \u0026#39;c\u0026#39;, \u0026#39;b\u0026#39;, \u0026#39;b\u0026#39;, \u0026#39;c\u0026#39;), type=c(\u0026#39;+\u0026#39;,\u0026#39;-\u0026#39;,\u0026#39;-\u0026#39;,\u0026#39;OPU\u0026#39;,\u0026#39;OPU\u0026#39;), stringsAsFactors = F ) q = create.gquery.graph(inter, genes) attr = data.frame(a=c(0,\u0026#39;*\u0026#39;,0), b=c(0,1,0), c=c(0,0,1), stringsAsFactors = F ) q = add.gquery.attractors(q, attr) Then we can use Griffin to find the networks that behave according with our biological information.\nnets = run.gquery(q) nets ## [1] \u0026quot;targets,factors\\na,false\\nb,((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [2] \u0026quot;targets,factors\\na,false\\nb,(((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [3] \u0026quot;targets,factors\\na,false\\nb,((((((!a\u0026amp;b)\u0026amp;!c)|((!a\u0026amp;b)\u0026amp;c))|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [4] \u0026quot;targets,factors\\na,false\\nb,((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [5] \u0026quot;targets,factors\\na,false\\nb,((((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;!b)\u0026amp;c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; There are multiple options to integrate BoolNet and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). The function get.net.topology() can obtain the topology with interaction signs of a BoolNet network. The function attractor2dataframe() can be used to export a BoolNet attractor as a dataframe that rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) can use. The function run.gquery() includes the option return=’BoolNet’, that return the inferred networks as BoolNet networks.\n History The development of Griffin began in 2013 as a PAPIIT (Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica) project to solve the inference of Boolean Network models for the Arabidopsis thaliana root stem cell niche. It continued in 2015 with support of Conacyt grant 221341.\nIn January, 2017 we organized a course in C3-UNAM to teach biologist how to use Griffin. We received two main comments: the input format was too complicated and it was uncomfortable to use the output with other packages. After some consideration we decided to create an R wrapper that could export and import BoolNet networks. We selected BoolNet as it has an good documentation and the package BoolFilter had been designed to work with it.\nThe development of rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) began during the EOBM 2017 in CUIB. For the following year we continued developing rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) as our schedules allowed. There were multiple challenges during the development: defining user-friendly inputs, using Rjava, and structuring the package. In August 2018, we attended the TIB2018-BCDW where we received valuable guidance from Martin Morgan and Benilton S Carvalho. It was during this workshop that the first version of rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) was finished.\n Acknowledgments Here you can find the tweet about the original blog post:\nCheck our first contributed blog post: R Gene Regulatory Interaction Formulator For Inquiring Networkshttps://t.co/9azbElGZGH\nME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth\nThx @mt_morgan @benilton!#CDSBMexico #TIB2018 #LatAmBioc18 #rstats #TIB #blog pic.twitter.com/TbJv37fkWQ\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) August 21, 2018 This blog post was made possible thanks to:\n blogdown (Xie, Hill, and Thomas, 2017) devtools (Wickham, Hester, and Chang, 2018) knitcitations (Boettiger, 2017) rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) References [1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations. [2] M. Martinez-Sanchez, S. Muñoz, M. Carrillo, E. Azpeitia, et al. rGriffin: Gene Regulatory Interaction Formulator For Inquiring Networks. R package version 0.1. 2018. [3] H. Wickham, J. Hester and W. Chang. devtools: Tools to Make Developing R Packages Easier. R package version 1.13.6. 2018. URL: https://CRAN.R-project.org/package=devtools. [4] Y. Xie, A. P. Hill and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown. Reproducibility ## Session info ---------------------------------------------------------------------------------------------------------- ## setting value ## version R version 3.5.1 (2018-07-02) ## system x86_64, darwin15.6.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## tz America/New_York ## date 2018-09-13 ## Packages -------------------------------------------------------------------------------------------------------------- ## package * version date source ## backports 1.1.2 2017-12-13 cran (@1.1.2) ## base * 3.5.1 2018-07-09 local ## bibtex 0.4.2 2017-06-30 CRAN (R 3.5.0) ## BiocManager 1.30.2 2018-08-24 CRAN (R 3.5.0) ## BiocStyle * 2.9.6 2018-08-19 Bioconductor ## blogdown 0.8 2018-07-15 CRAN (R 3.5.0) ## bookdown 0.7 2018-02-18 CRAN (R 3.5.0) ## colorout * 1.2-0 2018-05-03 Github (jalvesaq/colorout@c42088d) ## compiler 3.5.1 2018-07-09 local ## datasets * 3.5.1 2018-07-09 local ## devtools * 1.13.6 2018-06-27 CRAN (R 3.5.0) ## digest 0.6.16 2018-08-22 CRAN (R 3.5.0) ## evaluate 0.11 2018-07-17 CRAN (R 3.5.0) ## graphics * 3.5.1 2018-07-09 local ## grDevices * 3.5.1 2018-07-09 local ## htmltools 0.3.6 2017-04-28 cran (@0.3.6) ## httr 1.3.1 2017-08-20 CRAN (R 3.5.0) ## jsonlite 1.5 2017-06-01 CRAN (R 3.5.0) ## knitcitations * 1.0.8 2017-07-04 CRAN (R 3.5.0) ## knitr 1.20 2018-02-20 cran (@1.20) ## lubridate 1.7.4 2018-04-11 CRAN (R 3.5.0) ## magrittr 1.5 2014-11-22 cran (@1.5) ## memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) ## methods * 3.5.1 2018-07-09 local ## plyr 1.8.4 2016-06-08 cran (@1.8.4) ## R6 2.2.2 2017-06-17 CRAN (R 3.5.0) ## Rcpp 0.12.18 2018-07-23 CRAN (R 3.5.1) ## RefManageR 1.2.0 2018-04-25 CRAN (R 3.5.0) ## rGriffin * 0.1 2018-09-13 Github (mar-esther23/rgriffin@04cdc39) ## rJava * 0.9-10 2018-05-29 CRAN (R 3.5.0) ## rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0) ## rprojroot 1.3-2 2018-01-03 cran (@1.3-2) ## stats * 3.5.1 2018-07-09 local ## stringi 1.2.4 2018-07-20 CRAN (R 3.5.0) ## stringr 1.3.1 2018-05-10 CRAN (R 3.5.0) ## tools 3.5.1 2018-07-09 local ## utils * 3.5.1 2018-07-09 local ## withr 2.1.2 2018-03-15 CRAN (R 3.5.0) ## xfun 0.3 2018-07-06 CRAN (R 3.5.0) ## xml2 1.2.0 2018-01-24 CRAN (R 3.5.0) ## yaml 2.2.0 2018-07-25 CRAN (R 3.5.0) ","date":1534801528,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1534801528,"objectID":"775aa6c081b2122a77b89ae3a9a4cefc","permalink":"http://comunidadbioinfo.github.io/post/r-gene-regulatory-interaction-formulator-for-inquiring-networks/","publishdate":"2018-08-20T21:45:28Z","relpermalink":"/post/r-gene-regulatory-interaction-formulator-for-inquiring-networks/","section":"post","summary":"This blog post was written by ME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth.\nIn this blog post we will describe the package rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) that was one of the projects developed during the TIB2018-BCDW. We hope to continue developing Griffin and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). If you have ideas, suggestions or bugs, please contact us via rGriffin GitHub repo.","tags":null,"title":"R Gene Regulatory Interaction Formulator For Inquiring Networks","type":"post"},{"authors":null,"categories":null,"content":"If you want to sponsor us please get in touch: cdsbmexico@gmail.com. Thank you!\nWhy you should support us? CDSB and TIBs are workshops held yearly in Cuernavaca, Morelos, Mexico in a week chosen such that students, faculty, and industry employees across the country are more likely to be able to travel and attend the workshops. Workshop participants come from all over the country (and abroad) representing a unique opportunity to reach budding bioinformatics talent from many states without having to travel to them. From 2010 to 2019, participants came from an average of 18/32 (56%) different Mexican states and 4 countries, with a mean of 80 students and 49 academia or industry employees per event. The workshop organizers and core instructors are seasoned veterans that have received positive reviews from participants across the years. By sponsoring these workshops you will have the opportunity to help train and recruit talent for your institution. The workshops are jointly organized by the National Bioinformatics Node (NNB in Spanish) and the Community of Bioinformatics Software Developers (CDSB in Spanish) with the logistical support by the Mexican Bioinformatics Network (RMB in Spanish). All events follow a code of conduct designed to foster a welcoming environment for everyone involved.\nSponsor levels PLATINUM LEVEL $5,000 USD or more\n The option to present directly or show a promotional video for 5 minutes in all of the workshops: TIB workshops and CDSB.\n Recognition as a sponsor in the videos made prior to and during the event.\n A total of two full registrations as a courtesy for any of the workshops of the event.\n Opportunity to request a blog post written by the event organizers on your website.\n Includes all items offered to gold level sponsors.\n GOLD LEVEL $2,500 USD or more\n Recognition as a sponsor in a promotional item that will be given to participants.\n You will be allowed a display exhibition module during the event where you will be able to interact directly with participants during breaks.\n A full registration as a courtesy for any of the workshops of the event.\n Includes all items offered to silver level sponsors.\n SILVER LEVEL $1,000 USD or more\n Recognition as a sponsor in our event website.\n Recognition as a sponsor in all social media posts.\n Opportunity to distribute a promotional flyer that you provide us in the welcome package of each participant.\n DONATIONS IN KIND The organizations or institutions that wish to be sponsors with donations in kind (the donations CANNOT include publicity of the sponsor), can do so by providing the following services or items:\n Photography service during the event.\n Video service during the event.\n Cafeteria items: coffee, cookies, fruit, sugar, napkins, etc.\n Water containers or bottles without publicity from the company providing them.\n Exterior furniture: carp, chairs, tables.\n Office items: pens, pencils, board markers, post-it, blank paper.\n Items for cleaning: soap, paper, trash bags, antibacterial gel.\n Any other item can be evaluated.\n The donations in kind will be recognized similar to the levels described above based on the estimated amount in cash these donations correspond to.\n","date":1525882018,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525882018,"objectID":"26e20bd4d757aceb087cbd0fb1152851","permalink":"http://comunidadbioinfo.github.io/niveles-de-patrocinio/","publishdate":"2018-05-09T16:06:58Z","relpermalink":"/niveles-de-patrocinio/","section":"","summary":"If you want to sponsor us please get in touch: cdsbmexico@gmail.com. Thank you!\nWhy you should support us? CDSB and TIBs are workshops held yearly in Cuernavaca, Morelos, Mexico in a week chosen such that students, faculty, and industry employees across the country are more likely to be able to travel and attend the workshops. Workshop participants come from all over the country (and abroad) representing a unique opportunity to reach budding bioinformatics talent from many states without having to travel to them.","tags":null,"title":"Become our sponsor","type":"page"},{"authors":["CDSB"],"categories":null,"content":"The Community of Software Developers in Bioinformatics (CDSB) is committed to providing a welcoming and free experience harassment for all, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race , ethnicity, religion (or lack thereof) or technology options. We do not tolerate harassment of participants of the conference in any way. Language and sexual images are not suitable for any place of the conference, including lectures, workshops, parties, Twitter and other online media. Workshop participants who violate these rules may be punished or expelled from the event at the discretion of the organizers of the workshop.\nThis code of conduct applies to all participants, including staff and leadership of CDSB, and applies to all modes of interaction, both in person and online, including project repositories CDSB GitHub and CDSB GitHub, forum discussions CDSB, Slack channels and Twitter.\nCDSB participants accept:\n Be considered in speech and actions, actively seek to recognize and respect the boundaries of others in attendance. Refrain from behaviors and degrading expressions, discriminatory or harassing. Harassment includes, but is not limited to: deliberate intimidation; stalking; unwanted photo or recording; sustained or deliberate interruption of the talks and other events; inappropriate physical contact; use of sexual imagery or discriminatory comments or jokes; and unwanted sexual attention. If you feel someone has harassed or treated him inappropriately, please report in person to any member of the organizing committee of the workshop. Take care of each other. Contact a member of the organizing committee of the workshop if you notice a dangerous situation, someone in distress or violations of this code of conduct, even if they seem inconsequential. Use your full name and not an alias in Slack and other internal communication channels such that we can create a secure environment and enforce the code of conduct. Need help?\nIf you have any questions or concerns, talk to Heladia Salgado, Alejandro Reyes, Alejandra Medina-Rivera or Leonardo Collado Torres.\nIf any of the assistants engages in bullying behavior, the workshop organizers can take any legal action we deem appropriate, including, among others, warn the accused or ask the offender to leave the workshop. (If you feel you have been unjustly accused of violating this code of conduct, you must contact the organizing committee of the workshop with a brief description of your complaint).\nWe welcome your comments on this and all other aspects of CDSB events, and we thank you for working with us to make it a safe, pleasant and friendly experience for all involved.\nThis code of conduct was adapted from unconf rOpenSci 2018\u0026rsquo;s code of conduct which is licensed under CC BY-SA 4.0. Please review the page for more information about the license and attribution.\n","date":1523372974,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1523372974,"objectID":"58030e5126bc3c5d4daec335fdd4c317","permalink":"http://comunidadbioinfo.github.io/codigo-de-conducta/","publishdate":"2018-04-10T15:09:34Z","relpermalink":"/codigo-de-conducta/","section":"","summary":"The Community of Software Developers in Bioinformatics (CDSB) is committed to providing a welcoming and free experience harassment for all, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race , ethnicity, religion (or lack thereof) or technology options. We do not tolerate harassment of participants of the conference in any way. Language and sexual images are not suitable for any place of the conference, including lectures, workshops, parties, Twitter and other online media.","tags":null,"title":"Code of conduct","type":"page"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/\n Level: intermediate - advanced\n Language: english\n When: July 30 - August 3, 2018\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/R-BioConductor-Developers-Workshop-2018\n Register\n Requirements Requirements prior knowledge\n Participants should have basic knowledge of programming language R: variable assignment, reading files: read.csv, read.delim, read.table; data structures: matrix, dataframe, list; data types: character, numeric, factor, logical, etc; installation and use of packages. R: know how to install packages RStudio: know how to use. Technical requirements\n Personal computer Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Introduction In recent years, biology has seen a rise in the use of technologies that enable high-throughput, quantitative, data-rich profiling of cellular states. As a result, the field now faces computational challenges to analyze such data. The R/ Bioconductor project is an open source, open development software platform that provides tools to translate complex data sets into biological knowledge.\nThis workshop is aimed at students and researchers interested in the analysis of biological data. We encourage applications from experts in diverse disciplines, including but not limited to biologists, bioinformaticians, data scientists, software engineers and programmers and R users at large. The main goals of the workshop are:\n Teach participants the principles of reproducible data science through the development of R/Bioconductor packages.\n Turn bioinformatics software users into bioinformatics software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for biological data analysis.\n Help train bioinformatics instructors that can continue to grow in their local communities.\n This workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram Materials\n Day 1: July 30, 2018 09:00 - 10:00 Inauguration in the main auditorium 10:00 - 10:30 Keynote Lecture I: From learning to using to teaching to developing R Leonardo Collado-Torres 10:30 - 11:00 Talk I: Example of Bioinformatics in Mexico Daniel Piñero 11:00 - 11:20 Coffee break 11:20 - 12:20 Creating a package Alejandro Reyes 12:20 - 12:40 Break 12:40 - 14:00 Version control with git and GitHub Selene L. Fernandez-Valverde 14:00 - 15:30 Lunch break 15:30 - 16:15 Open source software projects and collaborative development Selene L. Fernandez-Valverde 16:45 - 17:30 Package documentation Alejandro Reyes 17:30 - Welcome cocktail Day 2: July 31, 2018 9:00 - 10:00 Keynote Lecture II Martin Morgan 10:00 - 10:30 Talk II: Example of Bioinformatics in Mexico: Using R-Shiny in Agrobiodiversity Alejandro Ponce-Mendoza 10:30 - 11:00 Coffee break 11:00 - 12:15 Best practices for writing efficient functions Martin Morgan 12:15 - 13:45 Bioconductor: core package, common objects and extending classes Benilton de Sá Carvalho 13:45 - 15:30 Lunch break 15:30 - 17:30 S4 - system for object oriented programming Martin Morgan 17:30 - 18:30 Poster session Day 3: August 1, 2018 9:00 - 10:00 Collaborative project organization and introduction Daniela Ledezma-Tejeida 10:00 - 10:30 Vignette writing with markdown/BiocStyle Benilton de Sá Carvalho 10:30 - 10:50 Coffee break/Event Photo (to be confirmed) 10:50 - 11:30 Unit testing and R CMD check Martin Morgan 11:30 - 12:10 Rcpp (Adding C/C++ code to R packages) Benilton de Sá Carvalho 12:10 - 12:30 Break 12:30 - 14:00 Debugging and Parallelization Martin Morgan 14:00 - 15:30 Lunch break 15:30 - 17:30 Working on a Collaborative Project Day 4: August 2, 2018 9:00 - 10:00 Keynote Lecture IV Benilton Carvalho 10:00 - 10:30 Talk III: RLadies Community Experience Teresa Ortíz 10:30 - 11:00 Coffee break 11:00 - 14:00 Working on a Collaborative Project 14:00 - 15:30 Lunch break 15:30 - 17:30 Working on a Collaborative Project Day 5: August 3, 2018 9:00 - 10:00 Working on a Collaborative Project and recovery from La Palapa 10:00 - 10:30 Working on a Collaborative Project 10:30 - 11:00 Coffee break 11:00 - 11:30 Working on a Collaborative Project 11:30 - 12:30 Presentations of collaborative projects 12:30 - 13:00 Closing remarks and community building Instructors: Martin Morgan (Roswell Park Comprehensive Cancer Center, Buffalo, USA)\n Benilton Carvalho (University of Campinas, Campinas, Brazil)\n Selene L. Fernandez-Valverde (National Laboratory of Genomics for Biodiversity, Irapuato, Mexico)\n Organizing committee: Heladia Salgado (Center for Genomic Sciences, Cuernavaca, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA)\n Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Delfino García (Center for Genomic Sciences, Cuernavaca, Mexico)\n Daniela Ledezma-Tejeida (Center for Genomic Sciences, Cuernavaca, Mexico)\n Laura Gómez (Center for Genomic Sciences, Cuernavaca, Mexico)\n Code of Conduct Sponsors Become our sponsor\n[](http://www.soibio.org) [](http://www.ccg.unam.mx) [](http://www.lcg.unam.mx) [](http://liigh.unam.mx/) [](https://www.r-consortium.org/) [](http://wintergenomics.com/) ","date":1521722421,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1521722421,"objectID":"f3d8b475cdd776e2c7b1b09b94366e53","permalink":"http://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/","publishdate":"2018-03-22T12:40:21Z","relpermalink":"/post/r-bioconductor-developers-workshop-2018/","section":"post","summary":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/\n Level: intermediate - advanced\n Language: english\n When: July 30 - August 3, 2018\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/R-BioConductor-Developers-Workshop-2018\n Register\n Requirements Requirements prior knowledge\n Participants should have basic knowledge of programming language R: variable assignment, reading files: read.","tags":null,"title":"Latin American R/BioConductor Developers Workshop 2018","type":"post"},{"authors":["CDSB"],"categories":["Events"],"content":"The National Node of Bioinformatics (NNB-UNAM) and the Community of Bioinformatics Software Developers (CDSB) invite you to\nTIB2018: R para todos \u0026amp; Latin American R/Bioconductor Developers Workshop UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 30 to August 3, 2018\nThis year, we decided to join efforts to promote the development of skills in the programming language R, under the slogan \u0026ldquo;Learn R and do community\u0026rdquo; .\nIn the world of data analysis R and Python they are positioned as programming languages fastest growing.\nThe reasons:\n They are easy to learn\n Specialized libraries offer advanced statistics.\n Why have we chosen R?\nIt is ideal for non - programmers and has really powerful libraries.\nOur teachers are researchers, postdocs and academic technicians with extensive experience in the area of domestic and foreign institutions. Most of them are certified as Software Carpentry certified instructors, who trained in the best practices of teaching computer science research.\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network)\n Community of Bioinformatics Software Developers (CDSB)\n Workshops T1: Introduction workshop R and R Studio\n T2: Exploratory and statistical analysis of biological data using R \n T3: Workshop RNA-Seq: Exploratory analysis of genes and differential expression\n T4: Workshop NGS: Assembly and Genome Annotation\n Register\n","date":1521655946,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1521655946,"objectID":"6bce212d03df2a863760c7323774d2f4","permalink":"http://comunidadbioinfo.github.io/post/talleres-internacionales-de-bioinformatica-2018/","publishdate":"2018-03-21T18:12:26Z","relpermalink":"/post/talleres-internacionales-de-bioinformatica-2018/","section":"post","summary":"The National Node of Bioinformatics (NNB-UNAM) and the Community of Bioinformatics Software Developers (CDSB) invite you to\nTIB2018: R para todos \u0026amp; Latin American R/Bioconductor Developers Workshop UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 30 to August 3, 2018\nThis year, we decided to join efforts to promote the development of skills in the programming language R, under the slogan \u0026ldquo;Learn R and do community\u0026rdquo; .","tags":null,"title":"2018 International Workshop on Bioinformatics","type":"post"},{"authors":["CDSB"],"categories":null,"content":"See version in Spanish. This privacy notice is for those of you in Mexico.\n","date":1520961796,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1520961796,"objectID":"b47f3b94fc84cce845b30025c5b4efed","permalink":"http://comunidadbioinfo.github.io/aviso-de-privacidad/","publishdate":"2018-03-13T17:23:16Z","relpermalink":"/aviso-de-privacidad/","section":"","summary":"See version in Spanish. This privacy notice is for those of you in Mexico.","tags":null,"title":"Aviso de Privacidad para la Protección de Datos Personales","type":"page"},{"authors":["Delfino García-Alonso"],"categories":["difusion"],"content":"La Bioinformática es un área interdisciplinaria en la que convergen las tecnologías de la información y las comunicaciones con las ciencias de la vida, donde los recursos computacionales y humanos asisten al análisis de cantidades enormes de datos biológicos, para extraer de ellos información valiosa y obtener resultados con impactos beneficiosos en la salud humana o animal (González Hernández D**., 2007).**\nDesde la segunda mitad del siglo XX, la biología ha tenido una relación creciente con las ciencias de la información. Su relación se inicia debido al constante impulso del hombre por saber de qué estamos hechos, y fue por allá de 1956 con la secuenciación de la primera proteína por Margaret O. Dayhoff. A partir de entonces, con la constante producción de información biológica, la cual crecía a un ritmo lento comparado con el actual volumen de generación de datos, se creó la necesidad de recopilar y organizar toda la información generada a partir de dichos proyectos de secuenciación, surgiendo así, la primera base de datos con información biológica llamada Protein Data Bank (PDB) (Benítez Páez A, Cárdenas Brino S, 2010).\nEsa relación incipiente de las ciencias de la vida con las ciencias de la computación ha dado origen a una disciplina que ha cobrado vida en los últimos años: la bioinformática.\nLos mayores avances en la bioinformática acontecieron en años posteriores a la creación de la primera base de datos, y fue con la generación de algoritmos matemáticos para el análisis de secuencias, así como también, la creación y el impuso dado a las bases de datos y herramientas para el análisis de secuencias con un impacto a nivel global.\nAdemás, con la creación del consorcio para la ejecución del proyecto de secuenciación del genoma humano (Human Genome, HUGO), en 1993, se inició la era genómica. Siendo la decodificación del genoma humano un proyecto tan ambicioso, que otros consorcios se crearon con el fin de secuenciar los primeros genomas no virales. En 1996, S. cerevisiae fue el primer genoma eucariota secuenciado. En 1995 y 1997, respectivamente, los genomas de Haemophilus influenzae y Escherichia coli fueron los primeros genomas bacterianos publicados. Entre los años 1998 y 2000, se tuvieron los genomas secuenciados de Caenorhabditis elegans, Pseudomonas aeruginosa, Drosophila melanogaster y Arabidopsis thaliana. En el año 2003, se finalizó la secuencia definitiva del genoma humano y, este hecho se logró gracias a la proyección y explotación del potencial de la industria biotecnológica.\nComo consecuencia, todos los avances tecnológicos destinados al campo de la genómica lograron proyectar a la comunidad científica hacia la secuenciación del genoma de cualquier organismo de interés científico o económico. Hoy en día, existen más de 12,574 genomas de bacterias completamente secuenciados y más de 65,142 proyectos en curso (GOLD Database, https://gold.jgi.doe.gov/index release v.6).\nLa gran cantidad de información generada a partir de los múltiples proyectos de secuenciación hizo que las bases de datos crecieran a un ritmo acelerado y casi insostenible. Al mismo tiempo, el enorme volumen de datos conlleva a que el número de herramientas de análisis y algoritmos computacionales surjan al mismo ritmo para poder extraer un conocimiento tangible que permita dar un significado a la diversidad biológica de nuestro ecosistema.\n","date":1520369358,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1520369358,"objectID":"17187444b10eb1a3aab48aaa15a15cd1","permalink":"http://comunidadbioinfo.github.io/post/la-bioinformatica-una-disciplina-en-auge-en-el-mundo/","publishdate":"2018-03-06T20:49:18Z","relpermalink":"/post/la-bioinformatica-una-disciplina-en-auge-en-el-mundo/","section":"post","summary":"La Bioinformática es un área interdisciplinaria en la que convergen las tecnologías de la información y las comunicaciones con las ciencias de la vida, donde los recursos computacionales y humanos asisten al análisis de cantidades enormes de datos biológicos, para extraer de ellos información valiosa y obtener resultados con impactos beneficiosos en la salud humana o animal (González Hernández D**., 2007).**\nDesde la segunda mitad del siglo XX, la biología ha tenido una relación creciente con las ciencias de la información.","tags":null,"title":"Bioinformatics, a field on the rise in the world","type":"post"},{"authors":null,"categories":null,"content":"The Community of Software Developers in Bioinformatics, stems from the concern for encouraging the participation and collaboration of people specializing in Bioinformatics and Genomics, to contribute or bring in free software development internationally.\nThe Community is convinced that, through courses, workshops, conferences, and other technological means, can strengthen the skills of its members to participate in development projects software, or undertake the development of new software quality, always promoting the spirit of cooperation and integration.\nWhat do we believe in ?\n Objectivity and neutrality: Members of the community, our colleagues deserve the truth and real knowledge, we do not allow ourselves to deceive them. Innovation: We continually work to be at the forefront and inspire those around us with new ideas. We do not believe in borders: We live in a globalized world, we care about connecting with what happens beyond. Passion and perfection: We work with passion and perfection in everything we do to develop quality software. Open Collaboration: As always we invite the community to collaborate in our initiatives, we also seek to collaborate and add third-party initiatives. Our objectives:\n Create a large community of software developers in bioinformatics Create links with other communities: TIBs, SoIBio, Bioconductor Recruit talent Create content for programming courses and creating packages in R, Python, C, Perl etc. Maintain repository for sharing software made by our community via GitHub. ","date":1519319230,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1519319230,"objectID":"86648fca13531778c6f0ab5bb4d930ad","permalink":"http://comunidadbioinfo.github.io/quienes-somos/","publishdate":"2018-02-22T17:07:10Z","relpermalink":"/quienes-somos/","section":"","summary":"The Community of Software Developers in Bioinformatics, stems from the concern for encouraging the participation and collaboration of people specializing in Bioinformatics and Genomics, to contribute or bring in free software development internationally.\nThe Community is convinced that, through courses, workshops, conferences, and other technological means, can strengthen the skills of its members to participate in development projects software, or undertake the development of new software quality, always promoting the spirit of cooperation and integration.","tags":null,"title":"About us","type":"page"}] \ No newline at end of file +[{"authors":["admin"],"categories":null,"content":"Welcome to the Community of Bioinformatics Software Developers (CDSB in Spanish)!\nWe are a group interested in helping members of Latin American countries acquire the necessary skills to contribute to open source software development. R is now used by many industries and has been a long time favorite in academia. As R users grow more familiar with the language, they typically end up writing their own functions and sharing them with others via packages. These packages can be distributed via GitHub or via formal repositories like CRAN and Bioconductor. Bioconductor is a project centered around open source software for bioinformatics made with R that has been helpful to many of us. We want to improve the representation of Latin American countries in open source developer communities to make them more diverse. Thus, our main goal is to help teach Latin Americans how to make R packages and share them via GitHub, CRAN and Bioconductor.\nYou can find some of our recorded videos available on our YouTube channel.\nCDSB2022 CDSB2021 scRNAseq CDSB2021 workflows Mini courses RMB 2020-2021 CDSB2020 ","date":1685318400,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1685318400,"objectID":"2525497d367e79493fd32b198b28f040","permalink":"http://comunidadbioinfo.github.io/authors/admin/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/admin/","section":"authors","summary":"Welcome to the Community of Bioinformatics Software Developers (CDSB in Spanish)!\nWe are a group interested in helping members of Latin American countries acquire the necessary skills to contribute to open source software development. R is now used by many industries and has been a long time favorite in academia. As R users grow more familiar with the language, they typically end up writing their own functions and sharing them with others via packages.","tags":null,"title":"CDSB","type":"authors"},{"authors":["lcollado"],"categories":null,"content":" Leonardo uses R daily and contributes R packages to the Bioconductor project as part of his work at LIBD. He is interested in high-throughput genomics assays such as RNA-seq, developments in R and helping others get started in their R journey. Leonardo has been learning and teaching R since 2008 and is a co-founder of the LIBD rstats club.\n","date":1611705600,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1611705600,"objectID":"59aecbe3d862df17fbda914be3a22015","permalink":"http://comunidadbioinfo.github.io/authors/lcollado/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lcollado/","section":"authors","summary":"Leonardo uses R daily and contributes R packages to the Bioconductor project as part of his work at LIBD. He is interested in high-throughput genomics assays such as RNA-seq, developments in R and helping others get started in their R journey. Leonardo has been learning and teaching R since 2008 and is a co-founder of the LIBD rstats club.","tags":null,"title":"Leonardo Collado-Torres, PhD","type":"authors"},{"authors":["erickcufe"],"categories":null,"content":"I am a Biological Data Scientist. I am also a Scientist and Entrepreneur in training. I have a Masters degree in Biochemical Sciences at UNAM and I am currently a Ph.D. student at UNAM.\n","date":1597968000,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1597968000,"objectID":"899f8150894e1d8b384f08811787b1b5","permalink":"http://comunidadbioinfo.github.io/authors/erickcufe/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/erickcufe/","section":"authors","summary":"I am a Biological Data Scientist. I am also a Scientist and Entrepreneur in training. I have a Masters degree in Biochemical Sciences at UNAM and I am currently a Ph.D. student at UNAM.","tags":null,"title":"Erick Cuevas-Fernández, MsC","type":"authors"},{"authors":["areyes"],"categories":null,"content":"I am a Data Scientist for Early Drug Development at Novartis Institute for BioMedical Research. I develop computational strategies to translate large amounts of data into biological knowledge. I implement my analyses in documented workflows, software packages and graphic interphases. I am a contributor of software to the Bioconductor project.\n","date":1536891202,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1536891202,"objectID":"e39f632bdf1febdce36f1533983ddebd","permalink":"http://comunidadbioinfo.github.io/authors/areyes/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/areyes/","section":"authors","summary":"I am a Data Scientist for Early Drug Development at Novartis Institute for BioMedical Research. I develop computational strategies to translate large amounts of data into biological knowledge. I implement my analyses in documented workflows, software packages and graphic interphases. I am a contributor of software to the Bioconductor project.","tags":null,"title":"Alejandro Reyes, PhD","type":"authors"},{"authors":["delfinog"],"categories":null,"content":"","date":1520369358,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":1520369358,"objectID":"ea39f799b3ec580a1fb8bda0917c928d","permalink":"http://comunidadbioinfo.github.io/authors/delfinog/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/delfinog/","section":"authors","summary":"","tags":null,"title":"Delfino García-Alonso","type":"authors"},{"authors":["aescalante"],"categories":null,"content":"Con formación como Actuario por la Benemérita Universidad Autónoma de Puebla (BUAP), inicié mi camino profesional como Data Scientist hace 4 años. Actualmente, trabajo como Analytics Developer en el equipo global de Kantar, en donde hago desarrollo de software con R.\nDisfruto aplicar conocimientos en desarrollo y ciencia de datos para crear y mantener paquetes para facilitar los procesos de análisis.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"0e740809f90d8045be45c23b25a4276d","permalink":"http://comunidadbioinfo.github.io/authors/aescalante/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/aescalante/","section":"authors","summary":"Con formación como Actuario por la Benemérita Universidad Autónoma de Puebla (BUAP), inicié mi camino profesional como Data Scientist hace 4 años. Actualmente, trabajo como Analytics Developer en el equipo global de Kantar, en donde hago desarrollo de software con R.\nDisfruto aplicar conocimientos en desarrollo y ciencia de datos para crear y mantener paquetes para facilitar los procesos de análisis.","tags":null,"title":"Ángel Escalante, Actuario","type":"authors"},{"authors":["alabasti"],"categories":null,"content":"Aurora Labastida Martínez estudió la Licenciatura en Investigación Biomédica Básica y la Maestría en Ciencias Bioquímicas en la UNAM. Se dedica al análisis de datos de secuenciación masiva de ADN y ha formado parte de distintos equipos de de biólogos y programadores en instituciones públicas y privadas.\nActualmente dirige el servicio de análisis de datos OMICs Analysis, que brinda sus servicios a científicos y empresas en proyectos de metagenómica y transcriptómica.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"7f84e7c295f8352289c9fb68c64b45f4","permalink":"http://comunidadbioinfo.github.io/authors/alabasti/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/alabasti/","section":"authors","summary":"Aurora Labastida Martínez estudió la Licenciatura en Investigación Biomédica Básica y la Maestría en Ciencias Bioquímicas en la UNAM. Se dedica al análisis de datos de secuenciación masiva de ADN y ha formado parte de distintos equipos de de biólogos y programadores en instituciones públicas y privadas.\nActualmente dirige el servicio de análisis de datos OMICs Analysis, que brinda sus servicios a científicos y empresas en proyectos de metagenómica y transcriptómica.","tags":null,"title":"Aurora Labastida Martínez, M.C.","type":"authors"},{"authors":["amedina"],"categories":null,"content":"Alejandra obtained her Ph.D. in 2012 from the Biomedical Sciences Program at the National University of Mexico (UNAM). Since her Ph.D., she has been focused on developing bioinformatic tools, and strategies to study gene regulatory mechanisms, most of the developed tools are now part of the Regulatory Sequence and Analysis Tools suite (RSAT, http://rsat.eu/). Currently, using computational approaches, her research will incorporate functional genomics data into Genome Wide Association Studies (GWAS), aiming to identify variants that lead to misregulation of gene expression.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"11e5c4662ac478bfb20ecc7657b80649","permalink":"http://comunidadbioinfo.github.io/authors/amedina/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/amedina/","section":"authors","summary":"Alejandra obtained her Ph.D. in 2012 from the Biomedical Sciences Program at the National University of Mexico (UNAM). Since her Ph.D., she has been focused on developing bioinformatic tools, and strategies to study gene regulatory mechanisms, most of the developed tools are now part of the Regulatory Sequence and Analysis Tools suite (RSAT, http://rsat.eu/). Currently, using computational approaches, her research will incorporate functional genomics data into Genome Wide Association Studies (GWAS), aiming to identify variants that lead to misregulation of gene expression.","tags":null,"title":"Alejandra Medina Rivera, PhD","type":"authors"},{"authors":["anabva"],"categories":null,"content":"Ana B learned to program in R, currently, she uses it daily, and has given workshops, classes, and consultancies at all levels. She is co-founder of Rladies-Querétaro, uses R in her transcriptomic analysis, and has created a package in R and several web applications. She also programs in Python for her analyses, uses Django for web applications, and has experience in relational databases such as MySQL.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a61eac9bb0a7d9ac89410e86d5bff317","permalink":"http://comunidadbioinfo.github.io/authors/anabva/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/anabva/","section":"authors","summary":"Ana B learned to program in R, currently, she uses it daily, and has given workshops, classes, and consultancies at all levels. She is co-founder of Rladies-Querétaro, uses R in her transcriptomic analysis, and has created a package in R and several web applications. She also programs in Python for her analyses, uses Django for web applications, and has experience in relational databases such as MySQL.","tags":null,"title":"Ana Beatriz Villaseñor Altamirano, PhD","type":"authors"},{"authors":["andresarredondo"],"categories":null,"content":"I have participated in genomic and metagenomic analysis projects. My main interest is bioinformatics and open-source software development. I am interested in participating in activities where knowledge from different areas of knowledge is shared.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"32d79e9ff810dc74e425ea614ff831f0","permalink":"http://comunidadbioinfo.github.io/authors/andresarredondo/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/andresarredondo/","section":"authors","summary":"I have participated in genomic and metagenomic analysis projects. My main interest is bioinformatics and open-source software development. I am interested in participating in activities where knowledge from different areas of knowledge is shared.","tags":null,"title":"Andrés Arredondo Cruz, M.C.","type":"authors"},{"authors":["aponce"],"categories":null,"content":"Hi !!! I Studied Food Technology at UIA and my masters and PhD in Biotechnology and Bioengineering at CINVESTAV. I\u0026rsquo;ve have had several years in postdocs and jobs at many Institutions (ECOSUR, UNSIJ, INIFAP, CONABIO, UAM-X). I\u0026rsquo;m interested in numerical ecology, data visualization and agrobiodiversity. Finally, I practice touring bike and admire Thomas Bernhard, WG Sebald and Glenn Gould.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"a432943019f570a576c17a87326e4eaf","permalink":"http://comunidadbioinfo.github.io/authors/aponce/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/aponce/","section":"authors","summary":"Hi !!! I Studied Food Technology at UIA and my masters and PhD in Biotechnology and Bioengineering at CINVESTAV. I\u0026rsquo;ve have had several years in postdocs and jobs at many Institutions (ECOSUR, UNSIJ, INIFAP, CONABIO, UAM-X). I\u0026rsquo;m interested in numerical ecology, data visualization and agrobiodiversity. Finally, I practice touring bike and admire Thomas Bernhard, WG Sebald and Glenn Gould.","tags":null,"title":"Alejandro Ponce-Mendoza, PhD","type":"authors"},{"authors":["bcarvalho"],"categories":null,"content":"Statistician (BS, M.Sc.), biostatistician (Ph.D.) Instructor: Statistics - Regression Models; Database designer and developer: MySQL, PHP; Teacher Assistant: Biocomputing, Statistical Computing and Statistical Methods in Public Health; Developer: BioConductor - oligo, makePlatformDesign, crlmm, pdInfoBuilder. Specialties: High-throughput genotyping, microarray preprocessing, statistical modeling, gene-expression analyzes, genetic epidemiology, statistical computing, programming (R, C / C ++, MATLAB)\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"6b72e93d4828c9e878b7d78fbae5bde5","permalink":"http://comunidadbioinfo.github.io/authors/bcarvalho/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/bcarvalho/","section":"authors","summary":"Statistician (BS, M.Sc.), biostatistician (Ph.D.) Instructor: Statistics - Regression Models; Database designer and developer: MySQL, PHP; Teacher Assistant: Biocomputing, Statistical Computing and Statistical Methods in Public Health; Developer: BioConductor - oligo, makePlatformDesign, crlmm, pdInfoBuilder. Specialties: High-throughput genotyping, microarray preprocessing, statistical modeling, gene-expression analyzes, genetic epidemiology, statistical computing, programming (R, C / C ++, MATLAB)","tags":null,"title":"Benilton S Carvalho, PhD","type":"authors"},{"authors":["brettbaker"],"categories":null,"content":"Brett Baker is an assistant professor in marine science at the Marine Science Institute, University of Texas at Austin. His research seeks to understand the ecology and evolution of uncultured bacteria and archaea.\nHis laboratory leverages computational approaches to characterize the genomic diversity of marine sediments primarily. The reconstruction of uncultured genomes from his team in recent years has provided the first glimpses of the physiological capabilities of new branches on the tree of life.\nDr. Baker’s research group also uses a variety of activity-based methods to track the metabolic activity of these novel microbes in nature. His laboratory has also been instrumental in the characterization of archaea that are related to eukaryotes that have advanced our understanding of the origin of complex cellular life.\nIn 2014, he received his Ph.D. in geological sciences from the University of Michigan, where he studied the geomicrobiology of deep-sea hydrothermal plumes and estuary sediments. Prior to doing so he was a research assistant at the University of California, Berkeley for 10 years, studying the microbes associated with acid mine drainage\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"edd0bac58be7ddfc1246cd337f835205","permalink":"http://comunidadbioinfo.github.io/authors/brettbaker/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/brettbaker/","section":"authors","summary":"Brett Baker is an assistant professor in marine science at the Marine Science Institute, University of Texas at Austin. His research seeks to understand the ecology and evolution of uncultured bacteria and archaea.\nHis laboratory leverages computational approaches to characterize the genomic diversity of marine sediments primarily. The reconstruction of uncultured genomes from his team in recent years has provided the first glimpses of the physiological capabilities of new branches on the tree of life.","tags":null,"title":"Brett Baker, PhD","type":"authors"},{"authors":["carbarjon"],"categories":null,"content":"Author of regutools that was submitted to Bioconductor.\n Description from here:\n I\u0026rsquo;m (also) a graduate of the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM). My current project in MorenoLab involves the analysis of identity-by-descent genomic segments to determine the population structure of Mexico and their implications in biomedical traits using the data from the Mexican BioBank. I am also involved in other projects as the Oceanian Genome Variation Project. I like photography, surrealist paintings, and good-looking cocktails, I also love rats; one of my dreams is to have a pet rat named Bojack.\n ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"f2296ef237d3a57e44d1f4b5241a16d3","permalink":"http://comunidadbioinfo.github.io/authors/carbarjon/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/carbarjon/","section":"authors","summary":"Author of regutools that was submitted to Bioconductor.\n Description from here:\n I\u0026rsquo;m (also) a graduate of the Undergraduate Program on Genomic Sciences from the National Autonomous University of Mexico (UNAM). My current project in MorenoLab involves the analysis of identity-by-descent genomic segments to determine the population structure of Mexico and their implications in biomedical traits using the data from the Mexican BioBank. I am also involved in other projects as the Oceanian Genome Variation Project.","tags":null,"title":"Carmina Barberena-Jonas","type":"authors"},{"authors":["CitlaliGA"],"categories":null,"content":"I studied genomic sciences at UNAM. I\u0026rsquo;d worked on various projects focused on population genetics and evolution. Some of my current interests are: philosophy, programming (R, python and trying arduino), science communication ( Más ciencia por México ), I really love teaching and learning from others.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"d7f5cdb0479a508e26be441dde701091","permalink":"http://comunidadbioinfo.github.io/authors/citlaliga/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/citlaliga/","section":"authors","summary":"I studied genomic sciences at UNAM. I\u0026rsquo;d worked on various projects focused on population genetics and evolution. Some of my current interests are: philosophy, programming (R, python and trying arduino), science communication ( Más ciencia por México ), I really love teaching and learning from others.","tags":null,"title":"Citlali Gil Aguillon","type":"authors"},{"authors":["emarquezz"],"categories":null,"content":" Elisa integrates multiple omics and phenotypic data with genome-scale metabolic modeling for rational strain design and bioprocess optimization project as part of his work at CCG with Utrilla Lab. She is interested in the integration of different types of data such as RNA-seq, proteomics, Ribo-seq and fitness information, with metabolism and expression models built with thepython module COBRAme. Her objective is to make a quantitative comparison between genome and proteome reduction strategies for redirecting cellular resources to synthetic functions.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"70cf7c97cec87510b0ca1f458d7daccc","permalink":"http://comunidadbioinfo.github.io/authors/emarquezz/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/emarquezz/","section":"authors","summary":"Elisa integrates multiple omics and phenotypic data with genome-scale metabolic modeling for rational strain design and bioprocess optimization project as part of his work at CCG with Utrilla Lab. She is interested in the integration of different types of data such as RNA-seq, proteomics, Ribo-seq and fitness information, with metabolism and expression models built with thepython module COBRAme. Her objective is to make a quantitative comparison between genome and proteome reduction strategies for redirecting cellular resources to synthetic functions.","tags":null,"title":"Elisa Márquez Zavala, MsC Candidate","type":"authors"},{"authors":["eveliacoss"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"18efa430de6ac5b9f6cde704726f6236","permalink":"http://comunidadbioinfo.github.io/authors/eveliacoss/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/eveliacoss/","section":"authors","summary":"","tags":null,"title":"Evelia Lorena Coss Navarrete, PhD","type":"authors"},{"authors":["hsalgado"],"categories":null,"content":"Bioinformatician. I am interested in disseminating and supporting the teaching of bioinformatics in Mexico and LA ( @swcarpentry, @ComunidadBioInfo and NNB)\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"2fe4b6df35220a9de4414e4c7c7e01d0","permalink":"http://comunidadbioinfo.github.io/authors/hsalgado/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/hsalgado/","section":"authors","summary":"Bioinformatician. I am interested in disseminating and supporting the teaching of bioinformatics in Mexico and LA ( @swcarpentry, @ComunidadBioInfo and NNB)","tags":null,"title":"Heladia Salgado Osorio","type":"authors"},{"authors":["jemilianosf"],"categories":null,"content":"Author of regutools that was submitted to Bioconductor.\n regrnalab member.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"3fa59542a2f5d63ef66e1d561c6ce2ea","permalink":"http://comunidadbioinfo.github.io/authors/jemilianosf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/jemilianosf/","section":"authors","summary":"Author of regutools that was submitted to Bioconductor.\n regrnalab member.","tags":null,"title":"Jesus Emiliano Sotelo-Fonseca","type":"authors"},{"authors":["joseovando"],"categories":null,"content":"","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"220e663aba981e28ff4b8ac28dc8163b","permalink":"http://comunidadbioinfo.github.io/authors/joseovando/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/joseovando/","section":"authors","summary":"","tags":null,"title":"José Antonio Ovando Ricárdez, M.C.","type":"authors"},{"authors":["josschavezf"],"categories":null,"content":"During my PhD project, in the Computational Genomics Laboratory at IBT-UNAM, I focused on the study of bacterial transcriptional regulators through evolution. Additionally, I gained experience in writing R/Bioconductor packages and teaching R.\nCurrently, I\u0026rsquo;m a Postdoctoral Fellow in the Department of Personalized Medicine of the Icahn School of Medicine at Mount Sinai, in New York City. My main interest is bioinformatics and the development of open source software for the analysis of single cell and spatial transcriptomics.\nBesides my research project, I enjoy teaching R and participating in activities that help expand the community of software developers in Latin America.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"72e346927b1c9c105a022174b2388839","permalink":"http://comunidadbioinfo.github.io/authors/josschavezf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/josschavezf/","section":"authors","summary":"During my PhD project, in the Computational Genomics Laboratory at IBT-UNAM, I focused on the study of bacterial transcriptional regulators through evolution. Additionally, I gained experience in writing R/Bioconductor packages and teaching R.\nCurrently, I\u0026rsquo;m a Postdoctoral Fellow in the Department of Personalized Medicine of the Icahn School of Medicine at Mount Sinai, in New York City. My main interest is bioinformatics and the development of open source software for the analysis of single cell and spatial transcriptomics.","tags":null,"title":"Joselyn C. Chávez-Fuentes, Ph.D","type":"authors"},{"authors":["lgomez"],"categories":null,"content":" Laura enjoys teaching bioinformatic courses. Her research interest are focused on genomic variation and its link with human diseases. She has wide experience with R, python and other programming languages oriented to solve biological questions.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"d813a570ce60c36151b5f8193458aba5","permalink":"http://comunidadbioinfo.github.io/authors/lgomez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/lgomez/","section":"authors","summary":"Laura enjoys teaching bioinformatic courses. Her research interest are focused on genomic variation and its link with human diseases. She has wide experience with R, python and other programming languages oriented to solve biological questions.","tags":null,"title":"Laura Gómez-Romero, PhD","type":"authors"},{"authors":["mirnavrl"],"categories":null,"content":"I am an evolutionary ecologist who seeks to understand microbial life, what are the ecological and evolutionary factors that shape microbial populations, as well as understanding the dynamics of their genomes in the light of evolution.\nI’m currently an associate professor at the UNAM Institute of Marine and Limnology Sciences, where I study the microbial life of the ocean. My work explores questions about biogeography, evolution, ecology, and physiology of microorganisms. I use computational and experimental approaches to answer these questions and my main interest is to understand the factors that determine the distribution of microbial species in the ocean, what are the genomic bases of adaptation leading to speciation, what is their role in the Earth’s biogeochemistry and how they interact with other organisms within the ecosystem.\nI did my PhD at the Institute of Ecology UNAM, where I studied the evolution of bacteria using comparative and population genomics. For this research, I isolated bacteria from the pools of Cuatro Ciénegas and looked for genes associated with local adaptation. During my first postdoc, I studied the interaction between plants, insects and microbes, using transcriptomic tools and 16s RNA amplicone libraries.\nDuring my postdoc at the microbial ecology lab at the University of Texas at Austin, my research focused on the discovery of new lineages and metabolic pathways of ocean microorganisms through the reconstruction of genomes obtained with metagenomics.\nI like the R community, I am co-organizer of R-Ladies Xalapa and San Cristobal, and also part of the board team of the Community of Software Developers in Bioinformatics (CDSB). Currently, I am working on my first R package called Rbims that it\u0026rsquo;s focused on the analysis of metabolism.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"482d2e9e74e0afb6c3d37a6acd27d032","permalink":"http://comunidadbioinfo.github.io/authors/mirnavrl/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mirnavrl/","section":"authors","summary":"I am an evolutionary ecologist who seeks to understand microbial life, what are the ecological and evolutionary factors that shape microbial populations, as well as understanding the dynamics of their genomes in the light of evolution.\nI’m currently an associate professor at the UNAM Institute of Marine and Limnology Sciences, where I study the microbial life of the ocean. My work explores questions about biogeography, evolution, ecology, and physiology of microorganisms.","tags":null,"title":"Mirna Vázquez Rosas Landa, PhD","type":"authors"},{"authors":["mramos"],"categories":null,"content":" Marcel has written or contributed to over 9 packages in Bioconductor and CRAN. He is interested in Bioconductor data classes and representations for the analysis of multi-omic and multi-modal data. He is the developer of the MultiAssayExperiment package, currently in the top 10% most downloaded in Bioconductor. Marcel also has teaching appointments at the CUNY School of Public Health on introductory topics in Biostatistics, R, and SAS.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b6f8733c519ba6fcbff7526bca2a4081","permalink":"http://comunidadbioinfo.github.io/authors/mramos/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mramos/","section":"authors","summary":"Marcel has written or contributed to over 9 packages in Bioconductor and CRAN. He is interested in Bioconductor data classes and representations for the analysis of multi-omic and multi-modal data. He is the developer of the MultiAssayExperiment package, currently in the top 10% most downloaded in Bioconductor. Marcel also has teaching appointments at the CUNY School of Public Health on introductory topics in Biostatistics, R, and SAS.","tags":null,"title":"Marcel Ramos Perez, MPH","type":"authors"},{"authors":["mteresa"],"categories":null,"content":"I am a data analyst with experience in ecology and marketing, I currently work in Kantar where I do software development with R.\nI also enjoy teaching, I teach statistic courses to master students in Data Science and to bachelors in Mathematics and Actuarial Sciences at ITAM. Lastly, I love R, I am co-organizer of R-Ladies CDMX and I regularly give short courses in R.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b92f6a30b831499900664c8e88fb5510","permalink":"http://comunidadbioinfo.github.io/authors/mteresa/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mteresa/","section":"authors","summary":"I am a data analyst with experience in ecology and marketing, I currently work in Kantar where I do software development with R.\nI also enjoy teaching, I teach statistic courses to master students in Data Science and to bachelors in Mathematics and Actuarial Sciences at ITAM. Lastly, I love R, I am co-organizer of R-Ladies CDMX and I regularly give short courses in R.","tags":null,"title":"Maria Teresa Ortiz, MA","type":"authors"},{"authors":["mtmorgan"],"categories":null,"content":"Dr. Morgan spent 10 years as an Assistant Professor and Associate then at Washington State University, before joining the Fred Hutchinson Cancer Research Center in 2005. At the Hutch, Dr. Morgan worked on the Bioconductor project for the analysis and comprehension of high-throughput genomic data; which he has led since 2008. Dr. Morgan recently moved to Roswell Park in Buffalo Comprehensive Cancer Center, NY, where the Bioconductor project is now based.\nSpecial Interests:\n Statistical methods in computational biology Analysis and comprehension of ‘next generation’ high-throughput sequence data Integrative analysis of large-scale multiple ‘omics data sets Inference of single-cell evolutionary processes in cancer development ","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"c41a22cf279d8d85cf21b8fb94509259","permalink":"http://comunidadbioinfo.github.io/authors/mtmorgan/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/mtmorgan/","section":"authors","summary":"Dr. Morgan spent 10 years as an Assistant Professor and Associate then at Washington State University, before joining the Fred Hutchinson Cancer Research Center in 2005. At the Hutch, Dr. Morgan worked on the Bioconductor project for the analysis and comprehension of high-throughput genomic data; which he has led since 2008. Dr. Morgan recently moved to Roswell Park in Buffalo Comprehensive Cancer Center, NY, where the Bioconductor project is now based.","tags":null,"title":"Martin Morgan, PhD","type":"authors"},{"authors":["robamezquita"],"categories":null,"content":"Robert Amezquita is a Postdoctoral Fellow in the Immunotherapy Integrated Research Center (IIRC) at Fred Hutch under the mentorship of Raphael Gottardo. His current research focuses on utilizing computational approaches leveraging transcriptional and epigenomic profiling at single-cell resolution to understand how novel anti-cancer therapeutics - ranging from small molecule therapies to biologics such as CAR-T cells - affect immune response dynamics. Extending from his graduate work at Yale’s Dept. of Immunobiology, Robert’s research aims to better understand the process of immune cell differentiation under the duress of cancer as a means to inform future immunotherapies. To accomplish this, Robert works collaboratively across the Fred Hutch IIRC with experimental collaborators, extensively utilizing R and Bioconductor for data analysis.\nRobert is one of the authors of the Orchestrating Single-Cell Analysis with Bioconductor book.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"5a79396d0960df7b636f4b0d80bd4cc6","permalink":"http://comunidadbioinfo.github.io/authors/robamezquita/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/robamezquita/","section":"authors","summary":"Robert Amezquita is a Postdoctoral Fellow in the Immunotherapy Integrated Research Center (IIRC) at Fred Hutch under the mentorship of Raphael Gottardo. His current research focuses on utilizing computational approaches leveraging transcriptional and epigenomic profiling at single-cell resolution to understand how novel anti-cancer therapeutics - ranging from small molecule therapies to biologics such as CAR-T cells - affect immune response dynamics. Extending from his graduate work at Yale’s Dept. of Immunobiology, Robert’s research aims to better understand the process of immune cell differentiation under the duress of cancer as a means to inform future immunotherapies.","tags":null,"title":"Robert Amezquita, PhD","type":"authors"},{"authors":["roramirezf"],"categories":null,"content":" Ricardo uses statistics to analyze multiomics data at different scales. His research interests are focused in the study of tissue architecture and its disruption during disease. He uses single cell data and spatial technologies to achieve this.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"b7f51e5d62a2fbb56a24357f1535471e","permalink":"http://comunidadbioinfo.github.io/authors/roramirezf/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/roramirezf/","section":"authors","summary":"Ricardo uses statistics to analyze multiomics data at different scales. His research interests are focused in the study of tissue architecture and its disruption during disease. He uses single cell data and spatial technologies to achieve this.","tags":null,"title":"Ricardo O. Ramírez Flores, BSc","type":"authors"},{"authors":["sfernandez"],"categories":null,"content":"Selene Fernandez is a bioinformatician / genomic data scientist studying the evolution of gene regulatory mechanisms underlying the phenotypic diversity and differentiation in multicellular eukaryotes cell. She is particularly interested in the evolution of regulatory roles of non-coding RNAs.\nIn addition to her academic roles, she participates in initiatives that link scientists and the general public (such as Más Ciencia por Mexico, Clubes de Ciencia Mexico), programs to introduce researchers to computing (Software/Data Carpentry) as well as mentoring programs (Ekpapalek).\nExpertise: Analysis of high-throughput (next generation) sequencing data, transcriptomics, genome annotation, non-coding RNAs.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"809889e334034eaafacb3b24ecf1fde1","permalink":"http://comunidadbioinfo.github.io/authors/sfernandez/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/sfernandez/","section":"authors","summary":"Selene Fernandez is a bioinformatician / genomic data scientist studying the evolution of gene regulatory mechanisms underlying the phenotypic diversity and differentiation in multicellular eukaryotes cell. She is particularly interested in the evolution of regulatory roles of non-coding RNAs.\nIn addition to her academic roles, she participates in initiatives that link scientists and the general public (such as Más Ciencia por Mexico, Clubes de Ciencia Mexico), programs to introduce researchers to computing (Software/Data Carpentry) as well as mentoring programs (Ekpapalek).","tags":null,"title":"Selene L. Fernandez-Valverde, PhD","type":"authors"},{"authors":["Yalbibalderas"],"categories":null,"content":"Yalbi Balderas is interested in studying respiratory diseases through high-throughput assays such as microarrays, bulk or single cell RNA-seq. She teaches several courses of statistics and bioinformatics at UNAM.\n","date":-62135596800,"expirydate":-62135596800,"kind":"term","lang":"en","lastmod":-62135596800,"objectID":"17c7e91d920e689ef6f6a52d96486901","permalink":"http://comunidadbioinfo.github.io/authors/yalbibalderas/","publishdate":"0001-01-01T00:00:00Z","relpermalink":"/authors/yalbibalderas/","section":"authors","summary":"Yalbi Balderas is interested in studying respiratory diseases through high-throughput assays such as microarrays, bulk or single cell RNA-seq. She teaches several courses of statistics and bioinformatics at UNAM.","tags":null,"title":"Yalbi I. Balderas-Martínez, PhD","type":"authors"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":" TIB2023 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Writting R/Bioconductor packages for scRNAseq analysis as part of the National Bioinformatics Meeting Mexico 2023.\n Level: Intermediate-Advanced. Language: Spanish. Where: This workshop will be held online on Zoom. When: 07-11 August 2023, 9:00am - 5:00pm (Mexico City timezone). Registration Twitter: @CDSBMexico Facebook: @CDSBMexico GitHub: https://github.com/ComunidadBioInfo/cdsb2023 Workshop webpage: https://comunidadbioinfo.github.io/cdsb2023 Calendar What are you going to learn? In recent years, the generation of scRNAseq data has become very important in biomedical research; however, the tools needed for its analysis are still under development.\nIn this workshop, we will review the existing statistical tools to analyze scRNAseq data using Bioconductor, how to document your analysis and check some tools for interpreting results.\nAt the same time, you will learn the crucial steps to develop an R package and some good practices for code generation. With the integration of these tools, you will have the opportunity to create your first package and contribute to the developers community.\nWho is it for? This course is aimed at people who want to learn how to develop packets to analyze scRNAseq data using R/Bioconductor tools.\nPre-requirements This workshop is Advanced, so you’ll need some background knowledge:\n Basic knowledge of RNAseq. Basic knowledge of RStudio: Rscripts creation, RStudio console management, display space management. Intermediate knowledge of R: Managing variables, reading files, creating and managing data frames and lists. Generation of graphs. How to install packages from CRAN and Bioconductor. Technical requirements\n Computer with at least 8Gb of memory. Access to a Linux terminal. Have R and RStudio installed in their latest version. Instructors Instructors\n Dra. Joselyn Cristina Chávez Fuentes: Postdoctoral Fellow at Icahn School of Medicine at Mount Sinai. Dra. Yalbi Balderas Martínez: Investigator at Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Dr. Leonardo Collado Torres: Investigator at Lieber Institute for Brain Development. M.C. Erick Cuevas Fernández: PhD Student at Universidad Nacional Autónoma de México. Dra. Mirna Vázquez Rosas Landa: Associate Professor at Instituto de Ciencias de Mar y Limnología de la UNAM. Dra. Alejandra Medina Rivera: Associate Professor at Laboratorio Internacional de Investigación de Medicina Genómica, UNAM. Invited speakers\n Dra. Evelia Lorena Coss Navarrete M.C. José Antonio Ovando Ricárdez M.C. Andrés Arredondo Cruz TAs\n M. C. Diego Ramírez M. C. Luis Alberto Meza Program Day 1: scRNAseq analysis workflow Part I\n Presentation of the CDSB. Structure and importing of data. Quality control. Normalization. Day 2: scRNAseq analysis workflow Part II\n Selection of highly variable genes. Dimension reduction. Clustering. Marker genes. Annotation of cellular types. Day 3: Writting R/Bioconductor packages Part I\n New features of RStudio, Quarto. Version control with GitHub and RStudio. Troubleshooting with Rstudio package versions. Infrastructure of an R/Bioconductor package. Talk: Converting your analysis workflow into an R/Bioconductor package. Documentation of functions. Social session: Getting to know the community. Day 4: Writting R/Bioconductor packages Part II\n Design of tests. Vignettes. Compilation and installation of packages. Collaborative projects Part I. Day 5: Collaborative projects\n Collaborative projects Part II. Projects presentation. Closure. Looking forward to see you!\nOrganizers \n \n \nWith the support of: \n","date":1685318400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1685318400,"objectID":"348b5ffa3ea6e0f92da60aa48f0a0841","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2023-workshop/","publishdate":"2023-05-29T00:00:00Z","relpermalink":"/post/cdsb-2023-workshop/","section":"post","summary":"TIB2023 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Writting R/Bioconductor packages for scRNAseq analysis as part of the National Bioinformatics Meeting Mexico 2023.","tags":null,"title":"CDSB Workshop 2023: Writting R/Bioconductor packages for scRNAseq analysis.","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":" TIB2022 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Advanced analysis of metagenomes. Creating workflows with R/Bioconductor as part of the National Bioinformatics Meeting Mexico 2022.\n Level: Advanced. Language: Spanish. Where: This workshop will be held online on Zoom. When: 01-05 August 2022, 9:00am - 5:00pm (Mexico City timezone). Registration Twitter: @CDSBMexico Facebook: @CDSBMexico GitHub: https://github.com/ComunidadBioInfo/cdsb2022 Workshop webpage: https://comunidadbioinfo.github.io/cdsb2022 Calendar What are you going to learn? In recent years metagenomics has gained importance for discovering new groups of microorganisms and metabolic pathways. In this workshop, we will review the latest methods for analyzing metagenomic data, using free software tools and specialized R packages freely available via Bioconductor.\nDuring this workshop, you will learn to reconstruct genomes from metagenomes using different free software tools. We will review different binning and metabolic prediction strategies, and we will identify areas of opportunity for software development in metagenomics; you will also learn how to document your code using RMarkdown.\nWho is it for? This course is designed for people who want to learn how to reconstruct genomes from metagenomes, make metabolic predictions, and contribute to the development of bioinformatics tools in this area. Participants who wish to register for the workshop must know Linux, R, NGS sequence quality analysis, and metagenomic assembly.\nPre-requirements Basic knowledge of metagenome sequencing and assembly Know what reads are. Quality control of NGS sequences. Assembly of metagenomes. Basic knowledge of RStudio. Technical requirements\n Computer with at least 8Gb of memory. Access to a Linux terminal. Have R and RStudio installed in their latest version. Instructors Instructors\n Dra. Mirna Vázquez Rosas Landa: Estancia Postdoctoral en la Universidad de Texas en Austin. Dra. Joselyn Chávez Fuentes: Estancia Postdoctoral en Icahn School of Medicine at Mount Sinai. M.C. Erick Cuevas Fernández: Estudiante de Doctorado en la Universidad Nacional Autónoma de México. Dra. Alejandra Medina Rivera: Investigadora Asociada en el Laboratorio Internacional de Investigación de Medicina Genómica, UNAM. Dra. Yalbi Balderas Martínez: Investigadora en el Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas. Invited speakers\n Dr. Brett Baker Dra. Valerie De Anda Dr. Leonardo Collado-Torres Program Day 1: Generating reports and workflows with R markdown\n Presentation to CDSB. Talk: The latest version of the tree of life. Version control with GitHub and RStudio. Report generation with R markdown. Day 2: Reconstruction of genomes\n Talk: Turning your analysis flow into a R/Bioconductor package. Talk: Bioconductor packages related to metagenomics. Reconstruction of genomes. Day 3: Metabolic reconstruction and phylogenetic inference\n Taxonomic assignment. Analysis of metabolic pathways. MEBs Social session: Building the community. Day 4:\n Collaborative metagenome projects. Day 5:\n Collaborative metagenome projects. Project presentation. Closure. Looking forward to see you!\nOrganizers \n \n \n \nWith the support of: \n \n","date":1652227200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1652227200,"objectID":"6464941fee83bdd045edd7b665505eba","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2022-workshops/","publishdate":"2022-05-11T00:00:00Z","relpermalink":"/post/cdsb-2022-workshops/","section":"post","summary":"TIB2022 RMB NNB CCG-UNAM Community of Software Developers in Bioinformatics (CDSB) We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing the summer workshop Advanced analysis of metagenomes. Creating workflows with R/Bioconductor as part of the National Bioinformatics Meeting Mexico 2022.","tags":null,"title":"CDSB Workshop 2022: Advanced analysis of metagenomes. Creating workflows with R/Bioconductor.","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing two week-long workshops this summer as part of the National Bioinformatics Meeting Mexico 2021. These are:\n Workflows with RStudio and creating shiny apps Analysis of scRNA-seq data with Bioconductor These workshops will be held online on August 9 to 13, 2021 and you can register here.\nWe are looking forward to seeing you soon!\nThis summer CDSB organizes 2 workshops as part of the National Bioinformatics Meeting Mexico 2021\nJoin us! #rstats @Bioconductor\n🗓️ August 2-13\n🙏🏽 @codeforsociety @RConsortium\nOrg @RBioinformatica@nnb_unam\nRegisterhttps://t.co/UJ1FAnxp52https://t.co/tTwX0RAm0K pic.twitter.com/mUZ7DeSudB\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) July 2, 2021 ","date":1623974400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1623974400,"objectID":"709dff01ba882fe0e12abc52adb04759","permalink":"http://comunidadbioinfo.github.io/post/cdsb-2021-workshops/","publishdate":"2021-06-18T00:00:00Z","relpermalink":"/post/cdsb-2021-workshops/","section":"post","summary":"We are delighted to announce that CDSB, along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG), is organizing two week-long workshops this summer as part of the National Bioinformatics Meeting Mexico 2021. These are:\n Workflows with RStudio and creating shiny apps Analysis of scRNA-seq data with Bioconductor These workshops will be held online on August 9 to 13, 2021 and you can register here.","tags":null,"title":"Workshops CDSB 2021: RStudio workflows and scRNA-seq with Bioconductor","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"We are delighted to announce that Code for Science and Society has selected our application for their first cohort of Event Fund grant recipients as announced on January 25, 2021. The CS\u0026amp;S Event Fund program is made possible through award number GBMF8449 from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF8449).\nThanks to this support, CDSB along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG) will be able to carry out a series of short courses throughout 2021 (including one event from December 2020) that will end with the National Bioinformatics Meeting 2021 that will be composed of 6 week-long courses.\nIf you are interested in taking part in the short courses, please check the RMB website for how to register.\nFelicidades @ErickCuevasF y @josschavezf1 por completar el primer mini curso de R de este ciclo ^^\nSon organizados por la CDSB y @RBioinformatica @nnb_unam con apoyo de @codeforsociety y @MooreFound\nEl resto del calendario propuesto está disponible acá #rstatsES https://t.co/Gx1WHdnKgp\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) December 19, 2020 As stated in our application, our goals are:\n Over the years, the workshops organized by NNB-CCG and, more recently, with the support of RMB have helped introduce an average of 40 participants per workshop every year into the world of open-source data analysis applied to bioinformatics. Many students, researchers, and industry members have found these workshops highly valuable to acquire skills at relatively low costs that empower them to succeed in the world of biological data. There are now participants who attend the introductory workshops one year and come back the next year for either other introductory workshops or those focusing on advanced material, which is where the CDSB steps in.\nCDSB has fostered the inclusion and collaboration of Latin American participants in the R and Bioconductor communities in the past three years. During the summer, one week CDSB courses (2018, 2019, and 2020) focused on developing advanced R programming skills. Supplemented by a Slack workspace, CDSB has set up the foundation for an inclusive community that supports and fosters collaboration, respect, and community building, as noted at https://www.r-consortium.org/blog/2020/03/18/cdsb-diversity-and-outreach-hotspot-in-mexico and BioC2020, JSM2020 and CDSB2020 presentations at https://speakerdeck.com/lcolladotor (CDSB2020 video about CDSB in Spanish: https://www.youtube.com/watch?v=rtP4zmbR3p4).\nWith the proposed short courses, RMB and CDSB, together with NNB-CCG, will provide a structured path to advance on software developing skills in R, and in bioinformatics, throughout the year. This will have a strong impact on integrating more members into the community. In our experience, many people in Latin America underestimate their programming abilities and avoid advanced courses that would provide them with additional skills to become tool developers. The proposed program will allow us to integrate people in different programming knowledge stages to the CDSB, reassess their programming skills, or improve them to get to the next stage. Our series of events will culminate with week-long workshops in the summer at the National Bioinformatics Meeting 2021.\n We greatly appreciate all the support and trust that has been placed on our CDSB + RMB + NNB-CCG team.\nThank you!\n⭐️ co-founder; 💫 board member\n Leonardo Collado Torres, CDSB ⭐️💫 Joselyn Chavez, CDSB 💫 Alejandro Reyes, CDSB ⭐️💫 Erick Cuevas Fernández, CDSB 💫 Irma Martínez, Education coordinator at Mexican Bioinformatics Network (RMB in Spanish), National Bioinformatics Node representative (NNB in Spanish) Alejandra Medina Rivera, CDSB ⭐️💫, President RMB Shirley Alquicira, Project Manager at RMB, NNB Yalbi Balderas, Members Committee Coordinator at RMB ","date":1611705600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1611705600,"objectID":"011746eb29b06aa44a587bebb2978d7b","permalink":"http://comunidadbioinfo.github.io/post/cs_and_s_event_fund_award/","publishdate":"2021-01-27T00:00:00Z","relpermalink":"/post/cs_and_s_event_fund_award/","section":"post","summary":"We are delighted to announce that Code for Science and Society has selected our application for their first cohort of Event Fund grant recipients as announced on January 25, 2021. The CS\u0026amp;S Event Fund program is made possible through award number GBMF8449 from the Gordon and Betty Moore Foundation (https://doi.org/10.37807/GBMF8449).\nThanks to this support, CDSB along with the Mexican Bioinformatics Network (RMB in Spanish) and the National Node of Bioinformatics at UNAM (NNB-CCG) will be able to carry out a series of short courses throughout 2021 (including one event from December 2020) that will end with the National Bioinformatics Meeting 2021 that will be composed of 6 week-long courses.","tags":["Latin American","Bioconductor","RMB","NNB"],"title":"CS\u0026S Event Fund award announcement","type":"post"},{"authors":["Erick Cuevas-Fernández, MsC"],"categories":["rstats"],"content":"By Erick Cuevas Fernández, M. Sc., Bioinformatician. Universidad Nacional Autonoma de Mexico. Universidad Autonoma del Estado de Morelos. Systems Biology and Translational Medicine Laboratory. @ErickCuevasF\nIn 2018 I heard of a workshop where Martin Morgan was performing in Mexico, at that time I had only a few months learning to use R, and I did not know who Martin Morgan was and had vague notions of Bioconductor. That year I started taking the international bioinformatics workshops.\nIt was thanks to taking the 2019 CDSB workshop that I was able to have a new international panorama of R development, know that there were events such as useR, BioC, rstudio :: global(), etc., It was highly motivated that a Mexican community was doing a effort to spread knowledge, inspire and expand the perspective of collaboration and development of free software to Mexicans. As a graduate student and with the science cuts that are becoming more frequent in Mexico, it is difficult to travel to another country to attend a workshop or a congress, due to the issue of VISA, passport, paying for a flight, accommodation, meals and registration. That is why the CDSB workshop of international quality accessible by its location and cost are valued to many Mexican students. And not only that, the same CDSB helps and promotes the application for scholarships for Mexican students in workshops and congresses for R developers in other countries.\nThis 2020 with the pandemic and the promotion of the CDSB, was that I had the opportunity to attend the BioC2020. The dedication and effort of each speaker to explain a relevant and specialized topic was amazing. The knowledge that was displayed in just one hour was shocking. Despite having been virtually, it was to admire Bioconductor\u0026rsquo;s commitment so that each exhibitor will generate interaction with all attendees. The inclusion and support of the Bioconductor community is impressive, willing to cooperate and help. Regardless of their age, nationality, gender, or grade, they all intended to help, cooperate, and share. There was a huge emotion to see Mexicans displaying their own packages, people you know physically, students like me. At the end of the workshop I finished with a feeling of happiness, enthusiasm, inspiration, wanting to learn and share.\n#BioC2020 @CDSBMexico My first BioC, I really enjoyed it a lot, opened up a universe for me. I feel responsible and enthusiastic to share what I have learned in my academic community and continue learning. I look forward to exhibiting my first first pack in BioC2021 next year pic.twitter.com/1K9dscoB1e\n\u0026mdash; Erick Cuevas (@ErickCuevasF) July 31, 2020 The CDSB 2020 workshop was no exception, the entire community transmitted that spark of enthusiasm, to expand and improve. Of course, the academic content and knowledge that was shown was a lot, such as maintaining the R sessions, working with github, choosing appropriate names for each project, quality testing the functions, debugging, workflows for handling scRNAseq data and an application of it with space expression.\nAs I think about the CDSB and the international communities that support inclusion and diversity, I think of this excerpt from the poem “sembrando” by the poet Marcos Rafael Blanco Belmonte (originally in Spanish):\n When the world sad, I contemplate, I toil and set myself a hard task\nand I know that my poor example is worth a lot\nAlthough poor and humble it seems and be\nWe must fight for all those who do not fight!\nWe must ask for all those who do not implore!\nWe must make those who do not listen hear us!\nWe must cry for all those who do not cry!\nHave to be like bees in the hive\nmake sweet honeycombs for everyone.\nHave to be like the water that goes serene\ngiving the whole world fresh streams.\nMust imitate the wind, which sows flowers\nthe same in the mountains as in the plains,\nand have to live life sowing loves,\nwith the sight and the soul always in the height.\nThe madman said and with noble melancholy\nthrough the scrublands of the mountain he continued to climb,\nand when lost in the shadows, he still repeated:\nHave to live sowing! Always sowing!\u0026hellip;\n ","date":1597968000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1597968000,"objectID":"af5db10436acf76d8d2eea5dd6c99ca4","permalink":"http://comunidadbioinfo.github.io/post/the_impact_of_cdsb_on_me/","publishdate":"2020-08-21T00:00:00Z","relpermalink":"/post/the_impact_of_cdsb_on_me/","section":"post","summary":"By Erick Cuevas Fernández, M. Sc., Bioinformatician. Universidad Nacional Autonoma de Mexico. Universidad Autonoma del Estado de Morelos. Systems Biology and Translational Medicine Laboratory. @ErickCuevasF\nIn 2018 I heard of a workshop where Martin Morgan was performing in Mexico, at that time I had only a few months learning to use R, and I did not know who Martin Morgan was and had vague notions of Bioconductor. That year I started taking the international bioinformatics workshops.","tags":["Latin American","Bioconductor"],"title":"The impact of CDSB on me","type":"post"},{"authors":["CDSB"],"categories":["rstats"],"content":"This useR!2020 session and video was organized by Laura Acion, Yanina Bellini Saibene, Paola Corrales, and Paloma Rojas Saunero. Leonardo Collado Torres coordinated the blog post submission. This blog post was originally submitted to the R Consortium blog and published there on July 7th 2020.\nOn June 19th 2020 we filmed a video for useR!2020 showcasing the communities and organizations we are involved in that are for Latin Americans or have Latin American participants. In this blog post, we wanted to highlight these initiatives and remind everyone that we are more than happy to help you launch similar initiatives in your local communities.\n LatinR: LatinR is a trilingual international conference on the use of R in research and development across Latin America. Since launching in 2018, our annual meetings have been a starting point for new packages, local user groups, reading clubs, R-Ladies chapters, translations, and other initiatives in the region. ConectaR: ConectaR 2019 took place during January 24-26, 2019 at the University of Costa Rica, in San José, Costa Rica. It was the first event in Central America endorsed by The R Foundation, and it was held completely in Spanish. You can find more information here. satRday: satRday is a conference about R and its applications, that happens all over the world, and it is organized by the local community. Two satRdays events happened in Latin America: in Santiago - Chile and São Paulo - Brazil. If you want to organize a satRday anywhere in Latin America, please get it touch so we can help each other! R-Ladies: R-Ladies is a global organisation that promotes gender diversity in the R community. It has 123 active chapters in 51 countries around the world, of which 49 are found across 10 Latin American countries. Some Latin Americans are part of the R-Ladies Global Team, including its leadership. COVID-19 has not stopped us, instead, we have migrated online and fostered alliances among different chapters. All in an effort to give gender minorities in the R community the opportunity to learn R in a safe and supportive environment. Join us! rOpenSci: R for open science, rOpenSci, provides free technical review of R packages to improve the quality of open source software in order to maximize readability, usability, usefulness, and minimize redundancy. Their peer-review process will soon be translated to Spanish and you can get involved! CDSB: the Community of Bioinformatics Software Developers (CDSB in Spanish) was born in 2018 with the goal of helping Latin American R users become R \u0026amp; Bioconductor developers and increase the representation of Latinx in these communities. For more information about CDSB check bit.ly/cdsbpost2020. RUGs: there are several R User Groups in Latin America, some of which are officially sponsored by the R Consortium. We believe that creating a welcoming space is crucial for keeping the ideas flowing, which allows for meaningful networking and, consequently, the development of new projects. We can help you start your own group! R4DS in Spanish + datos package: the resources to learn R in English are many, awesome, online, and free. But in Latin America few people can afford to learn English, and the resources in Spanish are few. To help solve this problem, we community-translated to Spanish the “R for Data Science” book and developed a package with the translation of all the datasets used in it: datos. The workflow to contribute to the package was designed to engage first-time contributors, and is now guiding the development of a new version in Portuguese that will be released in the next few months. #DatosDeMiércoles + #30díasdegráficos: The @R4DS_es Twitter account was created as a way to share projects like the R4DS translation and to develop initiatives to foster the Spanish-speaking R community, like #datosdemieRcoles, the Latin American cousin of #TidyTuesday. The idea is not only to use datasets that are in Spanish, but also datasets that are relevant for our Region. This initiative has been complemented with the 30 days plot challenge #30díasdegráficos. If you want to participate proposing a dataset for #datodemiéRcoles, please visit our github repo. The Carpentries: The Carpentries builds global capacity in essential data and computational skills for conducting efficient, open, and reproducible research. Building a sustainable and active community in Latin America includes several initiatives: lesson translations, instructor training, workshop coordination, and fundraising. Get in touch with us through the mailing list and the carpentries-es channel at the Carpentries Slack workspace. ReproHack: ReproHack is a growing community for researchers that are fighting the reproducibility crisis by sharing their experiences across disciplines. It is focused on organizing hackathons where participants attempt to reproduce published research from a list of proposed papers with public code and data. We are planning the first ReproHack in Spanish for October 2020 and you can get in touch with us through Twitter. AI Inclusive: AI Inclusive is an organization that promotes diversity in the AI Community. We want to bring awareness around Artificial Intelligence issues and empower the community so they can enter in the AI field, a field that is not diverse at all. In December 2019, we had our launch events in Rio de Janeiro, Brazil and San Francisco, California. Follow us and join us! Data Latam: in May 2016 we started with the first Data Latam podcast, aimed at offering an easy entry point, in Spanish, to those interested in data science. We always ask our interviewees: “How did you get where you are?”, and the diversity of stories has been enormous. Today Data Latam is a Latin American community of professionals and academics, who apply data science in their day to day work and we invite you to participate! What happens in the R Community doesn’t stay in the R Community. All the good practices of inclusive and diverse communities learned in several of the initiatives presented before, generate strong work teams within and beyond the R community. There is still a lot to be done, but what we’ve already achieved is very encouraging and provides a solid foundation for the future.\nThese initiatives are sustained by many people making a great, mostly volunteer, effort behind the scenes. Some of the challenges that the communities face are translated into multiple positives, sustained, and a lot of invisible hard work. Some of them are: finding international funding due to limited local options, translating content, joining forces across organizations, organizing regional conferences, and becoming active developers of the technology.\nThe Latin American R community is growing fast and so does the responsibility to make this growth solid and safe. Some of the future work that we, as community builders, look forward to fulfilling are: consolidating regional conferences with support of international sponsors; acquiring funding to sustain translations; amplifying the voices of regional minorities; importing educational material and work opportunities; connecting expats with their local communities; helping other groups such as RUGs and RLadies; connecting with other initiatives such as R-Forwards, Africa-R, MiR, among others; Increase our and other minorities representation in the R Core Team, the R Foundation, and the R Consortium.\nThank you! Please watch our useR! 2020 video on YouTube.\n","date":1594166400,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1594166400,"objectID":"71909b2620f5f7395bc1280acda4986a","permalink":"http://comunidadbioinfo.github.io/post/user_latin_american_community/","publishdate":"2020-07-08T00:00:00Z","relpermalink":"/post/user_latin_american_community/","section":"post","summary":"This useR!2020 session and video was organized by Laura Acion, Yanina Bellini Saibene, Paola Corrales, and Paloma Rojas Saunero. Leonardo Collado Torres coordinated the blog post submission. This blog post was originally submitted to the R Consortium blog and published there on July 7th 2020.\nOn June 19th 2020 we filmed a video for useR!2020 showcasing the communities and organizations we are involved in that are for Latin Americans or have Latin American participants.","tags":["Latin American","R Consortium"],"title":"Latin American communities and organizations: useR!2020 video","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"This blog post was submitted to the R Consortium blog where it was published on 03/18/2020.\nI have been attending R conferences since 2008, and while I’ve seen the R community grow rapidly, I generally don’t encounter as many Latin Americans (LatAm) among communities of R developers. Traditionally, a lab lead investigator invested in R or Bioconductor would teach their trainees and students these skills, becoming a local R hotspot. However, that scenario is uncommon in Mexico for several reasons. Recognizing some of these challenges and driven to promote R in our home country and LatAm, in 2017 Alejandro Reyes and I teamed up with Alejandra Medina Rivera and Heladia Salgado to eventually launch the Community of Bioinformatics Software Developers ( CDSB in Spanish) in 2018. One of our goals is to facilitate and encourage the transition from R user to R/Bioconductor developer. We have organized yearly one-week long workshops together with NNB-UNAM and RMB and just announced our 2020 workshop (August 3-7 2020 Cuernavaca, Mexico).\nIf you are fighting for change, know that even when things feel hard and progress is slow (or seems nonexistent), you are still creating and holding space for those who will come after you. Even if you can’t see it now, the impact of your work will be visible in the future.\n\u0026mdash; Jen Heemstra (@jenheemstra) March 5, 2020 Now unto our third workshop, I feel like we’ve had several success stories.\nCDSB2018 alumni wrote a blog post about their R GitHub package: rGriffin. CDSB2018 alumni secured BioC2019 travel scholarships and presented their work. Three CDSB2018 and 2019 alumni submitted the first package to Bioconductor (regutools), representing a significant percent-wise increase in the representation of LatAms in the Bioconductor developers community.\nWe have greatly benefited from the logistics and organization support by NNB-UNAM and RMB local teams, allowing us to focus on designing the workshop curriculum and inviting a diverse set of instructors, including Maria Teresa Ortiz who is an RLadiesCDMX co-founder and has been supporting us from the beginning. However, we face economic challenges as the budget for the national science foundation (CONACyT) has decreased in recent years. The support by the small R conference fund by R Consortium and other sponsors has been instrumental, as well as diversity and travel scholarships some of our instructors have secured at R conferences. We just recently revamped our sponsor page and answered the question: why should you support us?.\nHowever, while we are just getting started, one of our highlights was born by rOpenSci’s icebreaker exercise at CDSB2019. We were able to really build a sense of community and desire to perform outreach activities at our local communities. Particularly, a CDSB2018 and 19 alumni, Joselyn Chávez, volunteered to join the CDSB board. At CDSB2019 we also created an #rladies channel in our Slack where at the time we had members of 3/4 Mexico’s RLadies chapters ( Qro, Xalapa, CDMX) and now have 5/6 ( Cuerna, Monterrey), as CDSB2018 and CDSB2019 alumni have been co-founders of two chapters: Ana Beatriz Villaseñor-Altamirano for Qro and Joselyn Chávez for Cuerna.\nI am proud and excited of what we have achieved with our one-week long CDSB workshops, but also with how we used the tools we’ve learnt from other communities in order to keep interacting and communicating throughout the rest of the year. Time will tell if our efforts created a ripple that grew into a wave or if we’ll end burning out. Sustainability is a challenge, but we are greatly motivated by the impact we’ve had and can only imagine a brighter future.\nvia GIPHY\nCommunity of Bioinformatics Software Developers (CDSB): The story of a diversity and outreach hotspot in Mexico that hopes to empower local R developers - https://t.co/QMcNRUy1gl @fellgernon @andrewejaffe @LieberInstitute @lcgunam @jhubiostat @jtleek @LIBDrstats @CDSBMexico pic.twitter.com/TmZmxTRwOv\n\u0026mdash; R Consortium (@RConsortium) March 18, 2020 ","date":1584403200,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1584403200,"objectID":"81f421d9bc994ebe19c303f803f85d42","permalink":"http://comunidadbioinfo.github.io/post/csdb-story-of-a-diversity-and-outreach-hotspot-in-mexico/","publishdate":"2020-03-17T00:00:00Z","relpermalink":"/post/csdb-story-of-a-diversity-and-outreach-hotspot-in-mexico/","section":"post","summary":"This blog post was submitted to the R Consortium blog where it was published on 03/18/2020.\nI have been attending R conferences since 2008, and while I’ve seen the R community grow rapidly, I generally don’t encounter as many Latin Americans (LatAm) among communities of R developers. Traditionally, a lab lead investigator invested in R or Bioconductor would teach their trainees and students these skills, becoming a local R hotspot. However, that scenario is uncommon in Mexico for several reasons.","tags":["Bioconductor","R Consortium"],"title":"CDSB: the story of a diversity and outreach hotspot in Mexico that hopes to empower local R developers","type":"post"},{"authors":["CDSB"],"categories":["Bioconductor","Conduct"],"content":"For the English version of this statement, please go to the BioC2019 Code of Conduct website. At CDSB\u0026rsquo;s website you can find the translated Spanish version of this statement.\n","date":1583778600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1583778600,"objectID":"24b044c1d14d7d76cb54e82cf7362518","permalink":"http://comunidadbioinfo.github.io/post/bioc2019-code-of-conduct-violation-response/","publishdate":"2020-03-09T18:30:00Z","relpermalink":"/post/bioc2019-code-of-conduct-violation-response/","section":"post","summary":"For the English version of this statement, please go to the BioC2019 Code of Conduct website. At CDSB\u0026rsquo;s website you can find the translated Spanish version of this statement.","tags":null,"title":"BioC2019 Code of Conduct violation response","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"This workshop is part of the Mexican Bioinformatics Encounter (EBM in Spanish) 2020 organized by CDSB with:\n TIB2020 RMB NNB CCG-UNAM Community of Bioinformatics Software Developers (CDSB) Workshop webpage\n Level: intermediate - advanced\n Language: Spanish\n When: August 3 - August 7, 2020 (9 am to 5:30 pm, Friday until 2:30 pm)\n Where: Online through the Zoom platform. Hours are based on Mexico\u0026rsquo;s central time zone.\n Twitter: @CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/cdsb2020\n Registration\n Summary Join us for our 2020 workshop! This year we’ll teach you how to improve your skills for interacting with the R programming language with diverse strategies for organizing your code and projects. This will help you document your analyses such that they are easily to reproduce and for sharing them with your collaborators (from academia to industry). As a use case, we will learn the statistical tools needed for analyzing single cell transcriptomics (scRNA-seq) data using Bioconductor. Completing this workshop will help you in all your R projects and your analyses of biological data: all your analyses will benefit from the organization skills and the ideas behind scRNA-seq are used in many bioinformatics projects.\nvia GIPHY\nRequirements Requirements prior knowledge\n Participants should have basic to intermediate knowledge of the R programming language: variable assignment, reading files: read.csv; data structures: matrix, data.frame, list; data types: character, numeric, factor, logical, etc; installation and use of packages. Know how to use RStudio. Be interested in learning good practices for organizing your work and sharing your work with others. Be interested in learning how to analyze biological data using R/Bioconductor packages. Technical requirements\n Personal computer. Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Overview In recent years, R has become one of the most used programming languages for data science. The explosion in data available in many fields has increased the demand for data analysts, which is the case in Bioinformatics. R users start by learning how to use the tools others have openly shared with the international community. These R users acquire skills as they continue to analyze data and might even start to interact with R software developers through community websites such as RStudio Community, Bioconductor Support or via Twitter using the #rstats hashtag. Eventually some R users will want to write their own functions and organize their code across several projects. It is at this point that it’s useful to learn how to organize your code in order to make your life as an R programmer easier, such that you spend more time on your projects instead of remembering where your code is or what you did a few weeks ago. In order to practice these concepts, we will review the most recent methods for analyzing single cell RNA sequencing (scRNA-seq) data using R packages specialized for this goal that are freely available through Bioconductor.\nThe instructors of this workshop have participated at CDSB since its foundation and have gone to conferences such as BioC2019 and rstudio::conf(2020), among others. In recent years we taught how to make R and Bioconductor packages, which are of great use for sharing code with others. Recently, CDSB alumni sent their first R package to Bioconductor, which represented a huge percent increase of Latin American representation in the Bioconductor developers community, thus demonstrating that participating at a CDSB workshop has an impact beyond the one week workshop. For 2020 we will have an applied focus while maintaining our goals at CDSB which are:\n Turn (bioinformatics) software users into (bioinformatics) software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for (biological) data analysis.\n Help train users that can become local instructors and continue to grow their local communities.\n The scRNA-seq portion of the workshop will be based on the book Orchestrating Single Cell Analysis with Bioconductor that was published by Nature Methods ( DOI) and is among the most publicized papers in 2020.\nThis workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram 9 am to 5:30 pm on Mexico\u0026rsquo;s central time zone (Friday we end at 2:30 pm) with breaks and time to eat. The detailed schedule and the Zoom links will be provided to those participants that register for the event through the private CDSB Google Calendar. For more schedule details check the CDSB2020 workshop GitHub repository.\nEvery day we will have a help session from 8 to 9 am for those that need help installing the required software for the workshop.\nDay 1\n EBM2020 inauguration Welcome to CDSB Participants self introductions Workflow around RStudio projects: Introduction to the project-oriented workflow. Working with projects against scripts. Creating a project. Using safe paths. How should I name my file? Day 2\n Using Git and GitHub. Modifying the R startup files. Writing and documenting functions. Debugging R code. Day 3\n Good practice for configuring and maintain workspaces. Remote picture / video. Installing R packages from source. General overview of single cell RNA-seq (scRNA-seq) data processing Community-building activities Overview of the scRNA-seq material Day 4\n Introduction to scRNA-seq Introduction to scRNA-seq with Bioconductor Data infrastructure and data import Quality control Data normalization Day 5\n Feature selection Dimension reduction Clustering and differential gene expression analysis spatialLIBD: analyzing data from the Visium assay by 10x Genomics Workshop evaluation Closing ceremony and CDSB reminders Instructors Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Querétaro, Mexico) Alejandra recently presented a keynote at the Women in Data Science event in Mexico City.\n Alejandro Reyes (Data Scientist, Novartis, Basel, Switzerland). Alejandro recently worked on the regutools project with CDSB alumni that was published at Oxford Bioinformatics.\n Joselyn Chávez (IBT-UNAM, Cuernavaca, Morelos, Mexico). Joselyn presented her work at BioC2019 thanks to a travel award, attended rstudio::conf(2020) thanks to a diversity scholarship where she took the What They Forgot to Teach You about R workshop, and recently was part of the first R package submission to Bioconductor by CDSB alumni. She initially was a CDSB2018 student.\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, MD, USA). Leonardo recently published a pre-print on spatial transcriptomics using 10xGenomics Visium data.\n Marcel Ramos Perez (Roswell Park Comprehensive Cancer Center and CUNY School of Public Health, USA). Marcel is part of the Bioconductor Core Team and is the author of many Bioconductor packages including MultiAssayExperiment.\n Maria Teresa Ortiz (CONABIO and ITAM, Mexico). Teresa presented at rstudio::conf(2020) her work on fast counting algorithms for Mexican presidential elections.\n Organizing committee Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Querétaro, Mexico)\n Alejandro Reyes (Data Scientist, Novartis, Basel, Switzerland)\n Joselyn Chávez (IBT-UNAM, Cuernavaca, Morelos, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, MD, USA)\n Code of Conduct Sponsors Become our sponsor\nPlatinum level Gold level Silver level \n \nOrganizers CDSB is a node of the Mexican Bioinformatics Network (RMB in Spanish) and jointly organizes the yearly workshop with the National Node of Bioinformatics (NNB).\n \n \n \n \nWith support from:\n \n \n","date":1583415000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1583415000,"objectID":"eebba06807993bba897a7d43257f8aeb","permalink":"http://comunidadbioinfo.github.io/post/cdsb2020-building-workflows-with-rstudio-and-scrnaseq-with-bioconductor/","publishdate":"2020-03-05T13:30:00Z","relpermalink":"/post/cdsb2020-building-workflows-with-rstudio-and-scrnaseq-with-bioconductor/","section":"post","summary":"This workshop is part of the Mexican Bioinformatics Encounter (EBM in Spanish) 2020 organized by CDSB with:\n TIB2020 RMB NNB CCG-UNAM Community of Bioinformatics Software Developers (CDSB) Workshop webpage\n Level: intermediate - advanced\n Language: Spanish\n When: August 3 - August 7, 2020 (9 am to 5:30 pm, Friday until 2:30 pm)","tags":null,"title":"CDSB Workshop 2020: Building workflows with RStudio and Bioconductor for single cell RNA-seq analysis","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":" A couple years ago we started the Community of Bioinformatics Software Developers (CDSB in Spanish) as because we were concerned with the very low representation of Latin Americans in the Bioconductor community, and the R community in general. For the full story check this this blog post.\n Since we started CDSB, part of our goal been to help Bioconductor users transition into developers. To achieve this, we organized one week long courses in Mexico at low cost during the summers of 2018 and 2019 in partnership with the TIBs leadership (NNB-UNAM) and RMB. We plan to continue organizing these courses: except a 2020 announcement next week!\nWhile these workshops allow us to reach up to 40 students in person for a week, we have been borrowing methods from others to try to interact more frequently and help throughout this process 1. But we now went a bit further.\nIn 2018, CDSB students worked on R/Bioconductor packages for two days during our workshop. One of them, Joselyn Chávez, picked up the regutools project and continued working on it with advice from Heladia Salgado. We eventually set up meetings where Alejandro Reyes and myself would advice Joselyn, Carmina Barberena-Jonas and Jesus Emiliano Sotelo-Fonseca on how to best proceed.\nI just sent @Bioconductor\u0026#39;s 2020 conf deadline reminders to @CDSBMexico @LieberInstitute @GenomicsAtJHU @LatinR_Conf @rOpenSci @jhubiostat 🗓️\nIt\u0026#39;s the conf that started my #rstats career \u0026amp; I highly recommend it!\nBioC usage intro https://t.co/8NaV68vUsAhttps://t.co/ATzkKs7c04 pic.twitter.com/km8vRfyHcY\n\u0026mdash; 🇲🇽 Leonardo Collado-Torres (@lcolladotor) February 21, 2020 We’ve known for months that the deadline for BioC2020 talk/poster proposals was March 3rd. So we designed a plan that would allow them to submit regutools prior to that deadline, then submit a proposal to present it (as well as submit proposals to present their own research projects) in order to increase their likelihood of getting a BioC2020 travel scholarship.\nAnd we were able to accomplish this plan! Well, at least the part under their and our control. That is, check out the regutools Bioconductor submission. Thus we are incredibly excited to announce that the CDSB website now has a “Bioconductor Developers Alumni” section!\nWe are also thrilled to announce that the RegulonDB team has given us the go ahead signal to write a manuscript about regutools. So you’ll soon see a pre-print about it.\n via GIPHY Though I personally really hope that Joselyn, Carmina, Emiliano and many other CDSB alumni will be able to go to BioC2020 and other R conferences.\nWe couldn’t have gotten this far without all the support we’ve received over the years. So I would like to thank all our previous sponsors 2, colleagues who’ve encouraged us to keep going, and CDSB alumni like Joselyn, Carmina, and Emiliano who believed in our ideas and spent their own time making them a reality.\n via GIPHY I leave you here with a short introduction to regutools.\nregutools The goal of regutools is to provide an R interface for extracting and processing data from RegulonDB. This package was created as a collaboration by members of the Community of Bioinformatics Software Developers (CDSB in Spanish).\nFor more details, please check the documentation website or the Bioconductor package landing page here.\nInstallation You can install the released version of regutools from Bioconductor with:\nif (!requireNamespace(\u0026quot;BiocManager\u0026quot;, quietly = TRUE)) install.packages(\u0026quot;BiocManager\u0026quot;) BiocManager::install(\u0026quot;regutools\u0026quot;) ## Check that you have a valid Bioconductor installation BiocManager::valid() And the development version from GitHub with:\n## Since the package is currently going through the Bioconductor ## revision process, you need to use this code instead: BiocManager::install(\u0026quot;ComunidadBioinfo/regutools\u0026quot;) Example This is a basic example which shows you how to use regutools. For more details, please check the vignette.\nlibrary(\u0026#39;regutools\u0026#39;) ## basic example code ## Connect to the RegulonDB database if necessary if(!exists(\u0026#39;regulondb_conn\u0026#39;)) regulondb_conn \u0026lt;- connect_database() ## snapshotDate(): 2019-10-29 ## Build a regulondb object e_coli_regulondb \u0026lt;- regulondb( database_conn = regulondb_conn, organism = \u0026quot;E.coli\u0026quot;, database_version = \u0026quot;1\u0026quot;, genome_version = \u0026quot;1\u0026quot; ) ## Get the araC regulators araC_regulation \u0026lt;- get_gene_regulators( e_coli_regulondb, genes = c(\u0026quot;araC\u0026quot;), format = \u0026quot;multirow\u0026quot;, output.type = \u0026quot;TF\u0026quot; ) ## Summarize the araC regulation get_regulatory_summary(e_coli_regulondb, araC_regulation) ## regulondb_result with 3 rows and 7 columns ## TF Regulated_genes_per_TF Percent Activator Repressor Dual ## \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; \u0026lt;factor\u0026gt; ## 1 AraC 1 33.3333333333333 0 0 1 ## 2 CRP 1 33.3333333333333 1 0 0 ## 3 XylR 1 33.3333333333333 0 1 0 ## Regulated_genes ## \u0026lt;factor\u0026gt; ## 1 araC ## 2 araC ## 3 araC Citation Below is the citation output from using citation('regutools') in R. Please run this yourself to check for any updates on how to cite regutools.\ncitation(\u0026#39;regutools\u0026#39;) ## ## Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J, ## Salgado H, Collado-Torres L, Reyes A (2020). _regutools: an R package ## for data extraction from RegulonDB_. doi: 10.18129/B9.bioc.regutools ## (URL: https://doi.org/10.18129/B9.bioc.regutools), ## https://github.com/comunidadbioinfo/regutools - R package version ## 0.99.0, \u0026lt;URL: http://www.bioconductor.org/packages/regutools\u0026gt;. ## ## Chávez J, Barberena-Jonas C, Sotelo-Fonseca JE, Alquicira-Hernandez J, ## Salgado H, Collado-Torres L, Reyes A (2020). \u0026quot;Programmatic access to ## bacterial regulatory networks with regutools.\u0026quot; _bioRxiv_. doi: ## 10.1101/xxxyyy (URL: https://doi.org/10.1101/xxxyyy), \u0026lt;URL: ## https://doi.org/10.1101/xxxyyy\u0026gt;. ## ## To see these entries in BibTeX format, use \u0026#39;print(\u0026lt;citation\u0026gt;, ## bibtex=TRUE)\u0026#39;, \u0026#39;toBibtex(.)\u0026#39;, or set ## \u0026#39;options(citation.bibtex.max=999)\u0026#39;. Reproducibility information options(width = 120) sessioninfo::session_info() ## ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── ## setting value ## version R version 3.6.2 (2019-12-12) ## os macOS Catalina 10.15.2 ## system x86_64, darwin15.6.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz America/New_York ## date 2020-02-29 ## ## ─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── ## package * version date lib source ## acepack 1.4.1 2016-10-29 [1] CRAN (R 3.6.0) ## AnnotationDbi 1.48.0 2019-10-29 [1] Bioconductor ## AnnotationFilter 1.10.0 2019-10-29 [1] Bioconductor ## AnnotationHub 2.18.0 2019-10-29 [1] Bioconductor ## askpass 1.1 2019-01-13 [1] CRAN (R 3.6.0) ## assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) ## backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.0) ## base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.6.0) ## Biobase 2.46.0 2019-10-29 [1] Bioconductor ## 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VariantAnnotation 1.32.0 2019-10-29 [1] Bioconductor ## vctrs 0.2.3 2020-02-20 [1] CRAN (R 3.6.0) ## withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) ## xfun 0.12 2020-01-13 [1] CRAN (R 3.6.0) ## XML 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.0) ## xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0) ## XVector 0.26.0 2019-10-29 [1] Bioconductor ## yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.0) ## zlibbioc 1.32.0 2019-10-29 [1] Bioconductor ## ## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library As always, thank you rOpenSci unconf 2018!↩︎\n Sponsors are listed on each year’s workshop announcement. If you would like to sponsor our 2020 workshop, please get in touch with us. Thanks!!↩︎\n ","date":1582995600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1582995600,"objectID":"7b80692a9a96c383e026445e7bf8f537","permalink":"http://comunidadbioinfo.github.io/post/from-bioconductor-users-to-developers-our-first-community-submission/","publishdate":"2020-02-29T17:00:00Z","relpermalink":"/post/from-bioconductor-users-to-developers-our-first-community-submission/","section":"post","summary":"A couple years ago we started the Community of Bioinformatics Software Developers (CDSB in Spanish) as because we were concerned with the very low representation of Latin Americans in the Bioconductor community, and the R community in general. For the full story check this this blog post.\n Since we started CDSB, part of our goal been to help Bioconductor users transition into developers. To achieve this, we organized one week long courses in Mexico at low cost during the summers of 2018 and 2019 in partnership with the TIBs leadership (NNB-UNAM) and RMB.","tags":["Bioconductor","Developer Alumni"],"title":"From Bioconductor users to developers: our first community submission","type":"post"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/building-tidy-tools-CDSB-runconf-2019/\n Level: intermediate - advanced\n Language: Spanish^[If you speak English but not Spanish please let us know so we can plan accordingly.]\n When: July 29 - August 2, 2019\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/tidy-tools-CDSB-runconf-2019\n Registration\n Requirements Requirements prior knowledge\n Participants should have basic to intermediate knowledge of the R programming language: variable assignment, reading files: read.csv, read.delim, read.table; data structures: matrix, dataframe, list; data types: character, numeric, factor, logical, etc; installation and use of packages. R: know how to install packages RStudio: know how to use. Technical requirements\n Personal computer. Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Overview In recent years, R has become one of the most used programming languages for data science. The explosion in data available in many fields has increased the demand for data analysts, which is the case in Bioinformatics. R users start by learning how to use the tools others have openly shared with the international community. These R users acquire skills as they continue to analyze data and might even start to interact with R software developers through community websites such as RStudio Community, Bioconductor Support or via Twitter using the #rstats hashtag. Eventually some R users will want to write their own functions and share them online with others. They can do so via creating their own R packages and sharing them via repositories likes CRAN and Bioconductor or simply via GitHub. In this workshop participants will work through the Building Tidy Tools rstudio::conf 2019 workshop and then build their own R packages by collaborating with each other, similar to what was done at rOpenSci unconf18.\nThis workshop is aimed at students and researchers interested in data analysis that have experience using R. We encourage applications from experts in diverse disciplines, including but not limited to biologists, bioinformaticians, data scientists, software engineers and programmers and R users at large. The main goals of the workshop are:\n Teach participants the principles of reproducible data science through the development of R/Bioconductor packages.\n Turn (bioinformatics) software users into (bioinformatics) software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for (biological) data analysis.\n Help train users that can become local instructors and continue to grow their local communities.\n This workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram Overall TIB2019 program (registration, sessions and breaks) is available here.\n Day 1: July 29, 2019 08:00-09:00 Registration 09:00-09:30 TIB2019 Inauguration 09:30-10:00 Welcome to CDSB: the history of our community and where we are going. Code of conduct review Leonardo Collado-Torres 10:00-10:30 Why make an R package? Alejandro Reyes 10:30-11:00 Preliminaries Leonardo Collado-Torres 11:00-11:30 Coffee break 11:30-12:30 Packages Leonardo Collado-Torres 12:30-14:00 Testing Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 API Design Leonardo Collado-Torres 17:30-18:30 Welcome cocktail Day 2: July 30, 2019 09:00-11:00 Functional Programing Leonardo Collado-Torres 11:00-11:30 Coffee break 11:30-14:00 Errors Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 Object Oriented Programming Alejandro Reyes Day 3: July 31, 2019 09:00-11:00 Tidy Evaluation Leonardo Collado-Torres 11:00-11:30 Group picture 11:30-12:00 Coffee break 12:00-14:00 Document and Share Leonardo Collado-Torres 14:00-15:30 Break 15:30-17:30 Introduction to GitHub Alejandra Medina-Rivera Day 4: August 1, 2019 09:00-09:30 Introduction to runconf Leonardo Collado-Torres 09:30-11:00 Community building activities 11:00-11:30 Coffee break 11:30-12:00 Voting and selection of projects to work on 12:00-14:00 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz 14:00-15:30 Break 15:30-17:30 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz Day 5: August 2, 2019 09:00-09:15 (optional) change project 09:15-11:00 Working on a Collaborative Project Alejandra Medina-Rivera, Alejandro Reyes, Leonardo Collado-Torres and Maria Teresa Ortiz 11:00-11:30 Coffee break 11:30-12:00 Workshop evaluation 12:00-12:30 Prepare presentations of the collaborative project 12:30-13:00 Presentations of collaborative projects 13:00-13:30 Closing remarks and community participation opportunities 13:30-14:00 TIB2019 Closing Ceremony Building Tidy Tools Charlotte Wickham and Hadley Wickham were the instructors of the original version of this workshop at rstudio::conf 2019. They have kindly shared their materials with us, which we will translate to Spanish.\n This is a two-day hands on workshop for those who have embraced the tidyverse and now want to expand it to meet their own needs. We\u0026rsquo;ll discuss API design, functional programming tools, the basics of object design in S3, and the tidy eval system for NSE.\nLearn efficient workflows for developing high-quality R functions, using the set of conventions codified by a package. You\u0026rsquo;ll also learn workflows for unit testing, which helps ensure that your functions do exactly what you think they do. Master the art of writing functions that do one thing well and can be fluently combined together to solve more complex problems.We\u0026rsquo;ll cover common function writing pitfalls and how to avoid them.\nLearn how to write collections of functions that work well together, and adhere to existing conventions so they\u0026rsquo;re easy to pick up for newcomers.\nYou should take this workshop if you have experience programming in R and want to learn how to tackle larger scale problems. You\u0026rsquo;ll get the most from it if you\u0026rsquo;re already familiar with functions and are comfortable with R’s basic data structures (vectors, matrices, arrays, lists, and data frames).\n Instead of two days, we will teach this workshop in two and a half days such that we can give you more time to digest the material and work through an introduction to Git and GitHub.\nCDSB runconf R unconference events (runconf) typically involve two stages and an optional third one. First, participants create issues weeks ahead of the runconf where they share ideas that they can work through in collaboration with others during the two days of the runconf. In the second stage, participants meet each other and get to know each other through some icebreakers. They then work together for two days on the projects that received the most votes. This is where participants get to learn skills from each other and get a taste of developing open source software in a collaborative environment. At the end, everyone shares their work with the whole group. In the third and final stage, runconf attendees might continue to interact with each other to further polish the packages they worked on during the runconf event, start new collaborations and/or write blog posts about their experience.\nThere are many blog posts about rOpenSci unconf events. A recent runconf was the chirunconf which you can read more about on this blog post by Sharla Gelfand.\nIf you are attending our workshop, we will ask you to propose at least one R package idea by creating a GitHub Issue in our GitHub repository for the workshop. If you want some inspiration, take a look at rOpenSci unconf18\u0026rsquo;s GitHub repository. You will need to get familiarized with all the proposal before the workshop starts.\nInstructors: Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA). Leonardo attended rstudio::conf 2019 thanks to a diversity scholarship where he took the original Building Tidy Tools workshop. He also attended rOpenSci unconf 2018.\n Maria Teresa Ortiz (CONABIO and ITAM, Mexico)\n Organizing committee: Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Delfino García (Center for Genomic Sciences, Cuernavaca, Mexico)\n Heladia Salgado (Center for Genomic Sciences, Cuernavaca, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA)\n Code of Conduct Sponsors Become our sponsor\n ","date":1554471000,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554471000,"objectID":"02b4e7b64a3fd0ff1397bdcb98b6a6ef","permalink":"http://comunidadbioinfo.github.io/post/building-tidy-tools-cdsb-runconf-2019/","publishdate":"2019-04-05T13:30:00Z","relpermalink":"/post/building-tidy-tools-cdsb-runconf-2019/","section":"post","summary":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/building-tidy-tools-CDSB-runconf-2019/\n Level: intermediate - advanced\n Language: Spanish^[If you speak English but not Spanish please let us know so we can plan accordingly.]\n When: July 29 - August 2, 2019\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/tidy-tools-CDSB-runconf-2019\n Registration","tags":null,"title":"CDSB Workshop 2019: How to Build and Create Tidy Tools","type":"post"},{"authors":["CDSB"],"categories":["Events"],"content":"The National Node of Bioinformatics (NNB-UNAM), the Mexican Bioinformatics Network (RMB) and the Community of Bioinformatics Software Developers (CDSB) invite you to Bioinformatics Mexican Meeting 2019 composed by\nInternational Bioinformatics Workshops (TIB2019) \u0026amp;\nCDSB Workshop: How To Build and Create Tidy Tools UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 29 to August 9, 2019\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network) Community of Bioinformatics Software Developers (CDSB) Mexican Bioinformatics Network (RMB) thanks to the:\n Center for Genomic Sciences (CCG-UNAM) Undergrad on Genomic Sciences (LCG-UNAM) For information on how to register, check the TIB2019 website.\nWorkshops Each workshop is a week long.\nFrom July 29 to August 2, 2019\n T1: Introduction workshop R and RStudio\n T2. Introduction to Genome Assembly and Annotation\n T3. Comparative genomics with microbes: pangenomics and phyloinformatics\n CDSB Workshop 2019: How to Build and Create Tidy Tools\nFrom August 5 to August 9, 2019\n T4. Tutoring for the assembly and annotation of your genome of choice\n T5: Introduction to programming with Python\nInterested in becoming our sponsor?\n","date":1554465600,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554465600,"objectID":"d0685a87782c0a6f951997e458175085","permalink":"http://comunidadbioinfo.github.io/post/talleres-internacionales-de-bioinformatica-2019/","publishdate":"2019-04-05T12:00:00Z","relpermalink":"/post/talleres-internacionales-de-bioinformatica-2019/","section":"post","summary":"The National Node of Bioinformatics (NNB-UNAM), the Mexican Bioinformatics Network (RMB) and the Community of Bioinformatics Software Developers (CDSB) invite you to Bioinformatics Mexican Meeting 2019 composed by\nInternational Bioinformatics Workshops (TIB2019) \u0026amp;\nCDSB Workshop: How To Build and Create Tidy Tools UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 29 to August 9, 2019\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network) Community of Bioinformatics Software Developers (CDSB) Mexican Bioinformatics Network (RMB) thanks to the:","tags":null,"title":"Bioinformatics Mexican Meeting 2019","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"Last year the Community of Bioinformatics Software Developers (CDSB in Spanish) organized a one week workshop designed to train R users how to write R packages and ideally contribute them to Bioconductor. The workshop itself was a success as described in our summary post about the event. However, we didn’t want to stop there. We formed CDSB and teamed up with TIB (“Talleres Internacionales de Bioinformática”) from NNB-UNAM with the goal of simulating the BioC yearly meeting where attendees can learn R, mature as R users and become R developers. We also organized this workshop because we want to see more Latin Americans at BioC.\nBioC2019 application process Time passed since our 2018 workshop as everyone continued on their regular jobs and training programs. BioC2019 was then announced and with it were announced the application guidelines for:\n Presenting a talk or poster Applying for a travel award Proposing a workshop Basically, those applying for a travel award had to:\n Create a website or upload their CV to a publicly available website Answer in about 150 words or less How have you participated in the Bioconductor project in the past? Answer in about 150 words or less What do you hope to get out of the conference? Write a scientific abstract of 300 words or less for the talk/poster proposal^[Or propose a workshop, but that’s too much to ask from those just starting their BioC journeys. It’s more appropriate for BioC veterans.]. The whole process, while designed to be welcoming, can be a bit daunting if this is your first time applying and if English is not your native language. Thus, when we reminded our community members about BioC2019 we offered our help for this application process.\nHelping CDSB members Given their experience with Bioconductor, Alejandro Reyes and Leonardo Collado Torres volunteer to help CDSB members. The reminder blog post and individually contacting some CDSBMexico 2018 attendees helped find and motivate members to apply. Simply encouraging them and telling them that they had a realistic chance made a big difference, that is, believing in them and the work that we’ve done already as a community. There were many emails, Slack message channels and documents shared, but ultimately the clean version of the process was the following.\n A CSDB member expressed interest in BioC2019 to a CDSB volunteer (Alejandro or Leonardo). A CSDB volunteer reminded them of the BioC2019 application process and clarified any rule questions they had. If appropriate, the CDSB volunteer also explained some options for creating websites hosted on GitHub. The CDSB member wrote their draft answers to the two questions, plus their draft abstract, in a Google Doc that they shared with the CDSB volunteers with edit permissions. Similarly, the CDSB member created a draft website. All CDSB volunteers provided suggestions on how to present their information more clearly to the application reviewers keeping in mind what the CDSB member wanted to express about themselves or their work. The CDSB member made modifications and if appropriate asked for another round of feedback. Basically, the CDSB volunteers passed on the best practices they know for filling out these applications and writing abstracts, including here some timely advice from Wolfgang Huber ( a longtime Bioconductor Project contributor).\nThe generic paper abstract\n1. Why is it important? (1)\n2. What is \u0026quot;it\u0026quot;? (1)\n3. But what is the problem with it? (1)\n4. What did you do about the problem? (1)\n5. What was your result? (n)\n6. What are some wider implications? (1)\n(in parentheses: number of sentences)\n\u0026mdash; Wolfgang Huber 🇺🇦 (@wolfgangkhuber) February 22, 2019 The end result In the end, three CDSB members went through the whole process and created their websites:\n Ana Beatriz Villaseñor-Altamirano César Miguel Valdez Córdova Joselyn Chavez They all submitted their applications for the BioC2019 travel award before the deadline expired on March 15th 2019, something that we emphasized they should do!\nA couple of weeks passed, and on April 2nd we were delighted to report that all three of them got 10 minute talks 🎙and travel awards ✈️approved. This is an enormous win for CDSB and a huge morale boost 🎉🥳.\nThank you @Bioconductor!! Today 4 of our members got travel scholarships, talks and workshops approved. 6 total will attend #bioc2019 Please welcome them!@AnaBetty2304 @josschavezf1 @cmvaldezcordova @doctor_calvo @areyesq @fellgernon#rstats #diversityhttps://t.co/apxYxSpE5Z pic.twitter.com/tmSYbZvi7B\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) April 3, 2019 We cannot hide our excitement about these news and are looking forward to seeing them at BioC2019! We hope that all of them will have a great experience 🙌🏽😃\nA word from our CDSB members going to BioC2019 Like we’ve said, this is just the beginning and we want to keep helping others in years to come. We thus asked Ana, César and Joselyn to share a few words to future CDSB members on the BioC2019 travel award application process and the feedback they got from CDSB volunteers.\nAna The application process for BioC2019 and the travel award is not so difficult at the end but when I read the requirements for the first time I was overwhelmed, I had never published a web page before and I needed it to cover one of the requirements that asked for a personal website or public CV! It crossed my mind that I would not apply but Leo and Alejandro cheered me up, supported and guided me to create my own website (now I do webpages in R for anything that I can, hehe). They also helped me with the remaining requirements and at the end, I was able to enjoy the application process, I truly appreciate all the assistance they provided me and I can’t wait to meet them in NY. Without a doubt, Leo and Alejandro are accessible and inspiring bioinformaticians and people, as a consequence CDSB is a friendly and engaged community with the aim to impulse Mexican bioinformatic development to the world.\n César When I attended CDSB Mexico 2018, the last thing I imagined was that the process would culminate in me receiving a travel scholarship for BioC2019; Impostor syndrome is absolutely real. When talking about my master’s thesis with both Alejandro and Leo, they encouraged me to go all the way with its code and try and make a contribution to the Bioconductor project in the process. Said task seemed insurmountable in the beginning. However, after attending CDSB Mexico 2018, my perspective changed significantly. A deciding factor in me taking the plunge to actually go through with the contribution and consequent conference application was the overwhelmingly constructive support I received from the community at every stage in the process, from my original idea, all the way up to the conference’s application. Along the process, I noticed that even when we often expect to have an absolutely perfect product (a personal webpage, an online CV or an r package and all that it entails) from the get-go, this is rarely the way in which things happen. Cliché as it may sound, Rome wasn’t built in a day. Being able to shift my mindset and recognize the incremental nature of contributing has definitely set a precedent for how i’ll be handling most career oriented endeavors from now on; hopefully with continued contributions to the Bioconductor project and the open-source domain! If there’s anything I have to say to future applicants and CDSB members is just that: Do it! Reach out! Apply while embracing the community that’s there for you! With a little luck and elbow grease, things might just go your way, as they did for me.\n Joselyn When Alejandro Reyes and Leonardo Collado told me about applying to BioC2019 I felt nervous. I did not consider to submit my work and even less to apply for a scholarship before receiving their e-mail. They gave me all their trust and support through the process. Now I have been elected and feel very excited with this huge opportunity. I realize how warm the CDSBMexico community can be and that is possible to be part of meetings like BioC2019, all you have to do is let go of the fear to do it.\n ","date":1554418247,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1554418247,"objectID":"784b67641b4e5219388330c21faded47","permalink":"http://comunidadbioinfo.github.io/post/path-from-cdsbmexico-2018-to-bioc2019/","publishdate":"2019-04-04T22:50:47Z","relpermalink":"/post/path-from-cdsbmexico-2018-to-bioc2019/","section":"post","summary":"Last year the Community of Bioinformatics Software Developers (CDSB in Spanish) organized a one week workshop designed to train R users how to write R packages and ideally contribute them to Bioconductor. The workshop itself was a success as described in our summary post about the event. However, we didn’t want to stop there. We formed CDSB and teamed up with TIB (“Talleres Internacionales de Bioinformática”) from NNB-UNAM with the goal of simulating the BioC yearly meeting where attendees can learn R, mature as R users and become R developers.","tags":["Bioconductor","Applications"],"title":"The path from CDSBMexico 2018 to BioC2019","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":"About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America. The National Bioinformatics Node ( NNB-UNAM in Spanish) has organized workshops in bioinformatics and R since 2006 and more frequently since 2010. Last year, 2018, there were five simultaneous one week workshops:\n Introduction to R and RStudio\n Exploratory data analysis (EDA) of biological data with R\n EDA of RNA-seq data and differential expression studies\n Genome assembly and annotation from high-throughput sequencing data\n And our Latin American R/Bioconductor Developers Workshop\n Overall it was a success as described in A recap of CDSB 2018: the start of a community. However, we are not done yet! 💪🏽As we have stated several times, our goal is to turn R users into developers and to increase the representation of Mexicans and Latin Americans at other R events.\nBioC2019 The one R event that we followed as a guide last year is the Bioconductor yearly meeting, or BioC. This year, BioC2019 will be held during June 24 to 27 at New York City in the United States. If you are an academic the registration fee is 300 USD prior to May 24th. As of today (Feb 28th), a round trip from Mexico City on June 23 to 28th is about 320-410 USD1. The accommodation options listed start at 118 USD plus tax a night. As you can see, these numbers add up fairly fast which is a limiting factor for scientists from Mexico (and Latin American in general) to attend BioC2019.\nTravel scholarships However, we want to remind you that there are travel scholarships available! And we, CDSB, want to help you! 🙌🏽\nAll the details about the travel scholarship and different types of submission proposals are available on the BioC2019 website. But let us summarize the process for you.\n You have to apply for either a talk, poster or workshop.\n You need a professional website, GitHub profile or your CV to be available online.\n You need to answer two questions:\n How have you participated in the Bioconductor project in the past?\n What do you hope to get out of the conference?\n For a talk or poster proposal you have a maximum of 300 words while workshop proposals involve filling out a template.\nThis is quite a bit of work, but the payoff is immense! You will compete for the opportunity to travel basically for free: free registration and hotel, plus $500 for travel expenses. This can be a career changing opportunity as it was the case for L. Collado-Torres (see his keynote slides) and others.\nGet started on your scholarship application! We know that many of us have a tendency to do things at the last minute. However, we hope 🙏🏽 that you start your application materials as soon as you can. Remember that the deadline is March 15th and no exceptions are made.\nWebsite If you don’t have a professional website, we recommend that you make one following Emily Zabor’s tutorial. This is the tutorial that one of your fellow CDSBMexico 2018 attendees used to create his website: joseaia.github.io. Alternatively, check out the Chromebook Data Science: intro to R course (available for free if you can’t afford it) which includes a lesson that walks you through this process.\nBioconductor project participation Next, we know that each of you worked at least in one R package during CDSBMexico 2018 such as rGriffin (check the blog post). Maybe you even submitted your package to Bioconductor. At least, you met and interacted with longtime Bioconductor members such as Martin Morgan and Benilton Carvalho. Since then, you might have worked on other R packages, shiny applications, etc. You might have also answered questions on the Bioconductor support website, reported bugs or opened issues in existing packages, joined the developers mailing list, joined the Bioconductor Slack workspace, etc. Ultimately, you could potentially present a poster or give a talk about the package you worked on last summer, but you’ll need to coordinate with your team members and/or lab principal investigator.\nBenefitting from BioC2019 As for what you hope to get out of the conference, well, we will remind you that BioC has different workshops that can help you advance your R skills and knowledge. Furthermore, there’ll be scientific talks from excellent bioinformatics researchers. Then, once you return from the conference, you can spread the knowledge you acquired in a variety of ways: implementing it on your work, teaching at your local university or research institute, participating in the Bioconductor community (Slack, the support website, contributing an R package, etc), presenting at a local R meetup, and participating in other forums. You can also benefit personally from attending the conference by networking with other users and developers that will attend it. From it, you might start new collaborations, find about graduate school programs, find potential postdoc advisors, among other opportunities. Hey, you might help us out with future CDSBMexico events!\nCDSBMexico hands on help If you need help directly, please get in touch with us via the CDSBMexico Slack workspace. If you either don’t remember the Slack workspace or you couldn’t attend CDSBMexico 2018, please get in touch with us via Twitter at twitter.com/CDSBMexico.\nWe understand that not many will be able to attend BioC2019, so keep an eye open for CDSBMexico 2019! We are hoping to announce our plans soon.\n","date":1551414287,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1551414287,"objectID":"b19c492880b141146c5a943d45932d51","permalink":"http://comunidadbioinfo.github.io/post/cdsbmexico-remember-to-apply-for-bioc2019-travel-scholarships/","publishdate":"2019-03-01T04:24:47Z","relpermalink":"/post/cdsbmexico-remember-to-apply-for-bioc2019-travel-scholarships/","section":"post","summary":"About 10 months ago we announced our plans to start a new community of R/Bioconductor developers in Mexico and Latin America. The National Bioinformatics Node ( NNB-UNAM in Spanish) has organized workshops in bioinformatics and R since 2006 and more frequently since 2010. Last year, 2018, there were five simultaneous one week workshops:\n Introduction to R and RStudio\n Exploratory data analysis (EDA) of biological data with R","tags":null,"title":"CDSBMexico: remember to apply for BioC2019 travel scholarships","type":"post"},{"authors":["Alejandro Reyes, PhD"],"categories":["rstats"],"content":"Organizing an event is a lot of work, much more than you plan for it. But harvesting the fruits of a successful event makes the workload worth it.\nIn July, we kicked off the first Bioconductor Latin American Developers Workshop 2018 (LatAmBioc2018). The main goals of this meeting were to encourage the development of the Bioconductor project in Mexico and to start a community of Mexican bioinformatic software developers – the Community of Bioinformatic Software Developers (CDSB, from its acronym in Spanish).\n \nThe program of the workshop included talks, posters and lessons sessions as well as a two-day hands-on development hackathon. We had over 30 participants with strong quantitative background and experience in R programming from several LatAm countries.\nExcited about #CDSBMexico? It starts tomorrow! ¿Listos para mañana? 🇲🇽https://t.co/UUhX5RMSut\nSchedulehttps://t.co/BZTD7wGskI\nMaterialshttps://t.co/Oz2ingGije#rstats #teaching @Bioconductor Thanks to @lcgunam @ccg_unam @LIIGH_UNAM\nSoIBio @RConsortium@WINTERGENOMICS pic.twitter.com/YQxmnTNwQa\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) July 29, 2018 Community building Unlike the US and Europe, where many universities have Computational Biology and Biostatistics Departments that gather experts in the field, in Mexico and Latin America experts in Biostatistics and Computational Biology are often spread across the country. The benefits of having Computational Biology and Biostatistics Departments are plenty: for example, experts can interact and work together on a specific problem, and researchers from other disciplines can easily find support and establish collaborations. The goal of CDSB is to create a virtual department where experts in Biostatistics and Computational Biology can discuss ideas and help each other across all stages of their careers.\nThe first event organized by CDSB, LatAmBioc2018 included talks where both participants and speakers could start a dialogue and motivate each other by showcasing their work. As keynote invited speakers we had Daniel Piñero, who talked about population genetics of maize in Mexico; Alejandro Ponce-Mendoza, who showed elegant shiny apps to visualize ecological data along with maps; Teresa Ortiz, who talked about gender biases among R programmers; and Benilton Carvalho, who showed the development of personalized medicine in Brazil.\nWe are having a great presentation from the founder of @RLadiesCDMX, @TeresaOM, about getting rid of gender biases among the #rstats community. #LatAmBioc18 @CDSBMexico #womeninSTEM pic.twitter.com/TPdDzHVdqC\n\u0026mdash; Alejandro Reyes (@areyesq) August 2, 2018 The LatAmBioc2018 poster session was designed to encourage interdisciplinary collaborations. We invited people to contribute bioinformatic problems that would benefit from advice from experts such as the participants of LatAmBioc2018. We were happy to see that this event helped to create new collaborations.\nHere, we are presenting the basic structure and some examples with the framework -Winterflow- using @nextflowio, @Docker, #mk and #git pic.twitter.com/Ktn9o01X2Z\n\u0026mdash; Winter Genomics (@wintergenomics) August 2, 2018 A LatAm Bioconductor community Anecdotally, some of us felt that Latin Americans were not fully represented in the Bioconductor Developers Meetings (see Leonardo Collado Torres’s blog post). As scientists, we like our statements to be supported by data: the map below shows the affiliations, when available, of the contributors of the latest package submissions to the Bioconductor project. (These data were scraped using the Github API.) Although biases such as Mexican contributors with affiliations abroad might not have been considered, it is clear that only a few contributions come from Latin American countries.\nIn hopes of filling this gap, we gathered a diverse team of instructors, including Martin Morgan, Benilton Carvalho and Selene L. Fernandez-Valverde, who taught participants how to develop R/Bioconductor packages. The main idea was to turn Bioconductor software users into Bioconductor software developers.\nLet\u0026#39;s estimate Pi! Rcpp exercise! Rcpp sugar! Now I\u0026#39;m hungry, I want pie @benilton @CDSBMexico #rstats #CDSBMexico #TIBMexico2018 🍰👩💻 pic.twitter.com/2OeGWr35r3\n\u0026mdash; Alejandra Medina-Rivera (@AleMedinaRivera) August 1, 2018 How to debug R code with Martin Morgan :D @CDSBMexico\n\u0026mdash; Semiramis (@semiramis_cj) August 1, 2018 Participants attended lectures from Monday to Wednesday. Before the workshop, co-organizer Daniela Ledezma received and coordinated R package development proposals. On Wednesday afternoon, the participants formed teams and chose problems from Daniela’s curated list. They worked on their projects on Thursday and Friday, and we were very pleased with the final products: most teams wrote documented R packages that are available through GitHub. Two interesting examples are the prototype of the regulonDB package, which enables users to query RegulonDB within an R interphase, and rGriffin, an R interphase to inquire regulatory networks (for details, check their contributed blog post).\nParticipants are gathering to work in collaborative projects targeting specific questions. The objetive is write a fully documented #rstats package by Friday. @CDSBMexico #LatAmBioc18 pic.twitter.com/vDAvuOothC\n\u0026mdash; Alejandro Reyes (@areyesq) August 1, 2018 #CDSBMexico package developers course attendants presenting their projects #TIBs2018 #rstats @CDSBMexico pic.twitter.com/ST44hCsLT6\n\u0026mdash; Alejandra Medina-Rivera (@AleMedinaRivera) August 3, 2018 We are looking forward to seeing how the participants keep developing their R packages and collaborating through CSDB.\nOverachievers We felt that the goals of the workshop were reached programmers from all over Latin America worked together and wrote new R packages, which hopefully will be submitted to Bioconductor soon.\nWe also had the chance to enjoy some good Mexican food and hang out with colleagues in less formal settings, such as lunches and group outings. To celebrate the conclusion of the workshop, we had an improvised party in a bar that played Latin American music. As any good party should, it ended up quite late. Some of us went to bed at 4am, but we woke up energized to keep CSDB going. Even now, two months on, we are excited to continue developing a strong community of bioinformatic developers in Latin America.\nIn #mexico, we don\u0026#39;t only know how to do #Science and good #Bioinformatics but also how to eat! Tacos during #TIBMexico2018 and @qBio18 @AlexielMedyna @licloona1487 something great is happening here 😊 pic.twitter.com/bC7ycfIA9n\n\u0026mdash; Ana B Villaseñor-Altamirano (@AnaBetty2304) August 2, 2018 Thank you The LatAmBioc2018 would not have been possible without the time and support from the instructors, presenters, organizers and our sponsors CCG-UNAM, LCG-UNAM, LIIGH-UNAM, Winter Genomics, R Consortium and SoIBio.\n","date":1536891202,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1536891202,"objectID":"bb8026c23d4c8cd6757e48069b6e2648","permalink":"http://comunidadbioinfo.github.io/post/a-recap-of-cdsb-2018-the-start-of-a-community/","publishdate":"2018-09-14T02:13:22Z","relpermalink":"/post/a-recap-of-cdsb-2018-the-start-of-a-community/","section":"post","summary":"Organizing an event is a lot of work, much more than you plan for it. But harvesting the fruits of a successful event makes the workload worth it.\nIn July, we kicked off the first Bioconductor Latin American Developers Workshop 2018 (LatAmBioc2018). The main goals of this meeting were to encourage the development of the Bioconductor project in Mexico and to start a community of Mexican bioinformatic software developers – the Community of Bioinformatic Software Developers (CDSB, from its acronym in Spanish).","tags":null,"title":"A recap of CDSB 2018: the start of a community","type":"post"},{"authors":["Leonardo Collado-Torres, PhD"],"categories":["rstats"],"content":" This blog post was written by ME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth.\nIn this blog post we will describe the package rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) that was one of the projects developed during the TIB2018-BCDW. We hope to continue developing Griffin and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). If you have ideas, suggestions or bugs, please contact us via rGriffin GitHub repo.\n The problem Boolean networks allow us to give a mechanistic explanation to how cell types emerge from regulatory networks. However, inferring the regulatory network and its functions is complex problem, as the available information is often incomplete. rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) uses available biological information (regulatory interactions, cell types, mutants) codified as a set of restrictions and returns the Boolean Networks that satisfy that restrictions. This Boolean networks can then be used to study the biological system.\nThe rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) package is an R connector to Griffin (Gene Regulatory Interaction Formulator For Inquiring Networks), a java library for inference and analysis of Boolean Network models. Griffin takes as inputs biologically meaningful constraints and turns them into a symbolic representation. Using a SAT engine, Griffin explores the Boolean Network search space, finding all satisfying assignments that are compatible with the specified constraints. The rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) package includes a number of functions to interact with the BoolNet package.\n A small example Let us suppose a cell, we know that this cell has three proteins called a, b and c. We know that a activates b and that b and c inhibit each other. We also suspect that b and c may have positive self-regulatory loops. We can add this interactions to the table as “OPU” (optional, positive, unambiguous). This dataframe is the topology of the network.\n Source Target Interaction a b + b c - c b - b b OPU c c OPU Suppose we also have some information of what cell types have been observed. For example, there is a cell type that expresses b, but not a or c and an other cell type that expresses c, but not a or b. There might exist a third cell type that has not been fully characterized where we know that the cell expresses no a or c but we have NO information on b. This dataframe is the attractors of the network.\n a b c 0 1 0 0 0 1 0 * 0 We can then use this information to create a query. rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) can include other types of information like transition between cell type, cycles, transitions between cell types or mutant cell types.\n## Install using: # devtools::install_github(\u0026#39;mar-esther23/rgriffin\u0026#39;) ## Note that the package depends on rJava library(\u0026#39;rGriffin\u0026#39;) ## Loading required package: rJava genes = c(\u0026#39;a\u0026#39;,\u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;) inter = data.frame(source=c(\u0026#39;a\u0026#39;,\u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;, \u0026#39;b\u0026#39;,\u0026#39;c\u0026#39;), target=c(\u0026#39;b\u0026#39;, \u0026#39;c\u0026#39;, \u0026#39;b\u0026#39;, \u0026#39;b\u0026#39;, \u0026#39;c\u0026#39;), type=c(\u0026#39;+\u0026#39;,\u0026#39;-\u0026#39;,\u0026#39;-\u0026#39;,\u0026#39;OPU\u0026#39;,\u0026#39;OPU\u0026#39;), stringsAsFactors = F ) q = create.gquery.graph(inter, genes) attr = data.frame(a=c(0,\u0026#39;*\u0026#39;,0), b=c(0,1,0), c=c(0,0,1), stringsAsFactors = F ) q = add.gquery.attractors(q, attr) Then we can use Griffin to find the networks that behave according with our biological information.\nnets = run.gquery(q) nets ## [1] \u0026quot;targets,factors\\na,false\\nb,((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [2] \u0026quot;targets,factors\\na,false\\nb,(((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [3] \u0026quot;targets,factors\\na,false\\nb,((((((!a\u0026amp;b)\u0026amp;!c)|((!a\u0026amp;b)\u0026amp;c))|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [4] \u0026quot;targets,factors\\na,false\\nb,((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; ## [5] \u0026quot;targets,factors\\na,false\\nb,((((((!a\u0026amp;b)\u0026amp;!c)|((a\u0026amp;!b)\u0026amp;!c))|((a\u0026amp;!b)\u0026amp;c))|((a\u0026amp;b)\u0026amp;!c))|((a\u0026amp;b)\u0026amp;c))\\nc,(!b\u0026amp;c)\\n\u0026quot; There are multiple options to integrate BoolNet and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). The function get.net.topology() can obtain the topology with interaction signs of a BoolNet network. The function attractor2dataframe() can be used to export a BoolNet attractor as a dataframe that rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) can use. The function run.gquery() includes the option return=’BoolNet’, that return the inferred networks as BoolNet networks.\n History The development of Griffin began in 2013 as a PAPIIT (Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica) project to solve the inference of Boolean Network models for the Arabidopsis thaliana root stem cell niche. It continued in 2015 with support of Conacyt grant 221341.\nIn January, 2017 we organized a course in C3-UNAM to teach biologist how to use Griffin. We received two main comments: the input format was too complicated and it was uncomfortable to use the output with other packages. After some consideration we decided to create an R wrapper that could export and import BoolNet networks. We selected BoolNet as it has an good documentation and the package BoolFilter had been designed to work with it.\nThe development of rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) began during the EOBM 2017 in CUIB. For the following year we continued developing rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) as our schedules allowed. There were multiple challenges during the development: defining user-friendly inputs, using Rjava, and structuring the package. In August 2018, we attended the TIB2018-BCDW where we received valuable guidance from Martin Morgan and Benilton S Carvalho. It was during this workshop that the first version of rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) was finished.\n Acknowledgments Here you can find the tweet about the original blog post:\nCheck our first contributed blog post: R Gene Regulatory Interaction Formulator For Inquiring Networkshttps://t.co/9azbElGZGH\nME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth\nThx @mt_morgan @benilton!#CDSBMexico #TIB2018 #LatAmBioc18 #rstats #TIB #blog pic.twitter.com/TbJv37fkWQ\n\u0026mdash; ComunidadBioInfo (@CDSBMexico) August 21, 2018 This blog post was made possible thanks to:\n blogdown (Xie, Hill, and Thomas, 2017) devtools (Wickham, Hester, and Chang, 2018) knitcitations (Boettiger, 2017) rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) References [1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.8. 2017. URL: https://CRAN.R-project.org/package=knitcitations. [2] M. Martinez-Sanchez, S. Muñoz, M. Carrillo, E. Azpeitia, et al. rGriffin: Gene Regulatory Interaction Formulator For Inquiring Networks. R package version 0.1. 2018. [3] H. Wickham, J. Hester and W. Chang. devtools: Tools to Make Developing R Packages Easier. R package version 1.13.6. 2018. URL: https://CRAN.R-project.org/package=devtools. [4] Y. Xie, A. P. Hill and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown. Reproducibility ## Session info ---------------------------------------------------------------------------------------------------------- ## setting value ## version R version 3.5.1 (2018-07-02) ## system x86_64, darwin15.6.0 ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## tz America/New_York ## date 2018-09-13 ## Packages -------------------------------------------------------------------------------------------------------------- ## package * version date source ## backports 1.1.2 2017-12-13 cran (@1.1.2) ## base * 3.5.1 2018-07-09 local ## bibtex 0.4.2 2017-06-30 CRAN (R 3.5.0) ## BiocManager 1.30.2 2018-08-24 CRAN (R 3.5.0) ## BiocStyle * 2.9.6 2018-08-19 Bioconductor ## blogdown 0.8 2018-07-15 CRAN (R 3.5.0) ## bookdown 0.7 2018-02-18 CRAN (R 3.5.0) ## colorout * 1.2-0 2018-05-03 Github (jalvesaq/colorout@c42088d) ## compiler 3.5.1 2018-07-09 local ## datasets * 3.5.1 2018-07-09 local ## devtools * 1.13.6 2018-06-27 CRAN (R 3.5.0) ## digest 0.6.16 2018-08-22 CRAN (R 3.5.0) ## evaluate 0.11 2018-07-17 CRAN (R 3.5.0) ## graphics * 3.5.1 2018-07-09 local ## grDevices * 3.5.1 2018-07-09 local ## htmltools 0.3.6 2017-04-28 cran (@0.3.6) ## httr 1.3.1 2017-08-20 CRAN (R 3.5.0) ## jsonlite 1.5 2017-06-01 CRAN (R 3.5.0) ## knitcitations * 1.0.8 2017-07-04 CRAN (R 3.5.0) ## knitr 1.20 2018-02-20 cran (@1.20) ## lubridate 1.7.4 2018-04-11 CRAN (R 3.5.0) ## magrittr 1.5 2014-11-22 cran (@1.5) ## memoise 1.1.0 2017-04-21 CRAN (R 3.5.0) ## methods * 3.5.1 2018-07-09 local ## plyr 1.8.4 2016-06-08 cran (@1.8.4) ## R6 2.2.2 2017-06-17 CRAN (R 3.5.0) ## Rcpp 0.12.18 2018-07-23 CRAN (R 3.5.1) ## RefManageR 1.2.0 2018-04-25 CRAN (R 3.5.0) ## rGriffin * 0.1 2018-09-13 Github (mar-esther23/rgriffin@04cdc39) ## rJava * 0.9-10 2018-05-29 CRAN (R 3.5.0) ## rmarkdown 1.10 2018-06-11 CRAN (R 3.5.0) ## rprojroot 1.3-2 2018-01-03 cran (@1.3-2) ## stats * 3.5.1 2018-07-09 local ## stringi 1.2.4 2018-07-20 CRAN (R 3.5.0) ## stringr 1.3.1 2018-05-10 CRAN (R 3.5.0) ## tools 3.5.1 2018-07-09 local ## utils * 3.5.1 2018-07-09 local ## withr 2.1.2 2018-03-15 CRAN (R 3.5.0) ## xfun 0.3 2018-07-06 CRAN (R 3.5.0) ## xml2 1.2.0 2018-01-24 CRAN (R 3.5.0) ## yaml 2.2.0 2018-07-25 CRAN (R 3.5.0) ","date":1534801528,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1534801528,"objectID":"775aa6c081b2122a77b89ae3a9a4cefc","permalink":"http://comunidadbioinfo.github.io/post/r-gene-regulatory-interaction-formulator-for-inquiring-networks/","publishdate":"2018-08-20T21:45:28Z","relpermalink":"/post/r-gene-regulatory-interaction-formulator-for-inquiring-networks/","section":"post","summary":"This blog post was written by ME Martinez-Sanchez, S Muñoz, M Carrillo, E Azpeitia, D Rosenblueth.\nIn this blog post we will describe the package rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018) that was one of the projects developed during the TIB2018-BCDW. We hope to continue developing Griffin and rGriffin (Martinez-Sanchez, Muñoz, Carrillo, Azpeitia, et al., 2018). If you have ideas, suggestions or bugs, please contact us via rGriffin GitHub repo.","tags":null,"title":"R Gene Regulatory Interaction Formulator For Inquiring Networks","type":"post"},{"authors":null,"categories":null,"content":"If you want to sponsor us please get in touch: cdsbmexico@gmail.com. Thank you!\nWhy you should support us? CDSB and TIBs are workshops held yearly in Cuernavaca, Morelos, Mexico in a week chosen such that students, faculty, and industry employees across the country are more likely to be able to travel and attend the workshops. Workshop participants come from all over the country (and abroad) representing a unique opportunity to reach budding bioinformatics talent from many states without having to travel to them. From 2010 to 2019, participants came from an average of 18/32 (56%) different Mexican states and 4 countries, with a mean of 80 students and 49 academia or industry employees per event. The workshop organizers and core instructors are seasoned veterans that have received positive reviews from participants across the years. By sponsoring these workshops you will have the opportunity to help train and recruit talent for your institution. The workshops are jointly organized by the National Bioinformatics Node (NNB in Spanish) and the Community of Bioinformatics Software Developers (CDSB in Spanish) with the logistical support by the Mexican Bioinformatics Network (RMB in Spanish). All events follow a code of conduct designed to foster a welcoming environment for everyone involved.\nSponsor levels PLATINUM LEVEL $5,000 USD or more\n The option to present directly or show a promotional video for 5 minutes in all of the workshops: TIB workshops and CDSB.\n Recognition as a sponsor in the videos made prior to and during the event.\n A total of two full registrations as a courtesy for any of the workshops of the event.\n Opportunity to request a blog post written by the event organizers on your website.\n Includes all items offered to gold level sponsors.\n GOLD LEVEL $2,500 USD or more\n Recognition as a sponsor in a promotional item that will be given to participants.\n You will be allowed a display exhibition module during the event where you will be able to interact directly with participants during breaks.\n A full registration as a courtesy for any of the workshops of the event.\n Includes all items offered to silver level sponsors.\n SILVER LEVEL $1,000 USD or more\n Recognition as a sponsor in our event website.\n Recognition as a sponsor in all social media posts.\n Opportunity to distribute a promotional flyer that you provide us in the welcome package of each participant.\n DONATIONS IN KIND The organizations or institutions that wish to be sponsors with donations in kind (the donations CANNOT include publicity of the sponsor), can do so by providing the following services or items:\n Photography service during the event.\n Video service during the event.\n Cafeteria items: coffee, cookies, fruit, sugar, napkins, etc.\n Water containers or bottles without publicity from the company providing them.\n Exterior furniture: carp, chairs, tables.\n Office items: pens, pencils, board markers, post-it, blank paper.\n Items for cleaning: soap, paper, trash bags, antibacterial gel.\n Any other item can be evaluated.\n The donations in kind will be recognized similar to the levels described above based on the estimated amount in cash these donations correspond to.\n","date":1525882018,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1525882018,"objectID":"26e20bd4d757aceb087cbd0fb1152851","permalink":"http://comunidadbioinfo.github.io/niveles-de-patrocinio/","publishdate":"2018-05-09T16:06:58Z","relpermalink":"/niveles-de-patrocinio/","section":"","summary":"If you want to sponsor us please get in touch: cdsbmexico@gmail.com. Thank you!\nWhy you should support us? CDSB and TIBs are workshops held yearly in Cuernavaca, Morelos, Mexico in a week chosen such that students, faculty, and industry employees across the country are more likely to be able to travel and attend the workshops. Workshop participants come from all over the country (and abroad) representing a unique opportunity to reach budding bioinformatics talent from many states without having to travel to them.","tags":null,"title":"Become our sponsor","type":"page"},{"authors":["CDSB"],"categories":null,"content":"The Community of Software Developers in Bioinformatics (CDSB) is committed to providing a welcoming and free experience harassment for all, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race , ethnicity, religion (or lack thereof) or technology options. We do not tolerate harassment of participants of the conference in any way. Language and sexual images are not suitable for any place of the conference, including lectures, workshops, parties, Twitter and other online media. Workshop participants who violate these rules may be punished or expelled from the event at the discretion of the organizers of the workshop.\nThis code of conduct applies to all participants, including staff and leadership of CDSB, and applies to all modes of interaction, both in person and online, including project repositories CDSB GitHub and CDSB GitHub, forum discussions CDSB, Slack channels and Twitter.\nCDSB participants accept:\n Be considered in speech and actions, actively seek to recognize and respect the boundaries of others in attendance. Refrain from behaviors and degrading expressions, discriminatory or harassing. Harassment includes, but is not limited to: deliberate intimidation; stalking; unwanted photo or recording; sustained or deliberate interruption of the talks and other events; inappropriate physical contact; use of sexual imagery or discriminatory comments or jokes; and unwanted sexual attention. If you feel someone has harassed or treated him inappropriately, please report in person to any member of the organizing committee of the workshop. Take care of each other. Contact a member of the organizing committee of the workshop if you notice a dangerous situation, someone in distress or violations of this code of conduct, even if they seem inconsequential. Use your full name and not an alias in Slack and other internal communication channels such that we can create a secure environment and enforce the code of conduct. Need help?\nIf you have any questions or concerns, talk to Heladia Salgado, Alejandro Reyes, Alejandra Medina-Rivera or Leonardo Collado Torres.\nIf any of the assistants engages in bullying behavior, the workshop organizers can take any legal action we deem appropriate, including, among others, warn the accused or ask the offender to leave the workshop. (If you feel you have been unjustly accused of violating this code of conduct, you must contact the organizing committee of the workshop with a brief description of your complaint).\nWe welcome your comments on this and all other aspects of CDSB events, and we thank you for working with us to make it a safe, pleasant and friendly experience for all involved.\nThis code of conduct was adapted from unconf rOpenSci 2018\u0026rsquo;s code of conduct which is licensed under CC BY-SA 4.0. Please review the page for more information about the license and attribution.\n","date":1523372974,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1523372974,"objectID":"58030e5126bc3c5d4daec335fdd4c317","permalink":"http://comunidadbioinfo.github.io/codigo-de-conducta/","publishdate":"2018-04-10T15:09:34Z","relpermalink":"/codigo-de-conducta/","section":"","summary":"The Community of Software Developers in Bioinformatics (CDSB) is committed to providing a welcoming and free experience harassment for all, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race , ethnicity, religion (or lack thereof) or technology options. We do not tolerate harassment of participants of the conference in any way. Language and sexual images are not suitable for any place of the conference, including lectures, workshops, parties, Twitter and other online media.","tags":null,"title":"Code of conduct","type":"page"},{"authors":["CDSB"],"categories":["Events","rstats"],"content":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/\n Level: intermediate - advanced\n Language: english\n When: July 30 - August 3, 2018\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/R-BioConductor-Developers-Workshop-2018\n Register\n Requirements Requirements prior knowledge\n Participants should have basic knowledge of programming language R: variable assignment, reading files: read.csv, read.delim, read.table; data structures: matrix, dataframe, list; data types: character, numeric, factor, logical, etc; installation and use of packages. R: know how to install packages RStudio: know how to use. Technical requirements\n Personal computer Minimum 8GB RAM, a mouse and sufficient disk space for text files and image files. Administrator privileges to install and run utilities such as RStudio. Introduction In recent years, biology has seen a rise in the use of technologies that enable high-throughput, quantitative, data-rich profiling of cellular states. As a result, the field now faces computational challenges to analyze such data. The R/ Bioconductor project is an open source, open development software platform that provides tools to translate complex data sets into biological knowledge.\nThis workshop is aimed at students and researchers interested in the analysis of biological data. We encourage applications from experts in diverse disciplines, including but not limited to biologists, bioinformaticians, data scientists, software engineers and programmers and R users at large. The main goals of the workshop are:\n Teach participants the principles of reproducible data science through the development of R/Bioconductor packages.\n Turn bioinformatics software users into bioinformatics software developers.\n Foster the exchange of expertise and establish multidisciplinary collaborations.\n Create a community of Latin American scientists committed to the development of software and computational pipelines for biological data analysis.\n Help train bioinformatics instructors that can continue to grow in their local communities.\n This workshop is part of a long-term project to create a community of developers from Latin America. We hope to hold regular meetings in the future (similar to BioC, EuroBioc and BioCAsia) where attendees present their own software contributions. To provide a welcoming environment please follow our code of conduct.\nProgram Materials\n Day 1: July 30, 2018 09:00 - 10:00 Inauguration in the main auditorium 10:00 - 10:30 Keynote Lecture I: From learning to using to teaching to developing R Leonardo Collado-Torres 10:30 - 11:00 Talk I: Example of Bioinformatics in Mexico Daniel Piñero 11:00 - 11:20 Coffee break 11:20 - 12:20 Creating a package Alejandro Reyes 12:20 - 12:40 Break 12:40 - 14:00 Version control with git and GitHub Selene L. Fernandez-Valverde 14:00 - 15:30 Lunch break 15:30 - 16:15 Open source software projects and collaborative development Selene L. Fernandez-Valverde 16:45 - 17:30 Package documentation Alejandro Reyes 17:30 - Welcome cocktail Day 2: July 31, 2018 9:00 - 10:00 Keynote Lecture II Martin Morgan 10:00 - 10:30 Talk II: Example of Bioinformatics in Mexico: Using R-Shiny in Agrobiodiversity Alejandro Ponce-Mendoza 10:30 - 11:00 Coffee break 11:00 - 12:15 Best practices for writing efficient functions Martin Morgan 12:15 - 13:45 Bioconductor: core package, common objects and extending classes Benilton de Sá Carvalho 13:45 - 15:30 Lunch break 15:30 - 17:30 S4 - system for object oriented programming Martin Morgan 17:30 - 18:30 Poster session Day 3: August 1, 2018 9:00 - 10:00 Collaborative project organization and introduction Daniela Ledezma-Tejeida 10:00 - 10:30 Vignette writing with markdown/BiocStyle Benilton de Sá Carvalho 10:30 - 10:50 Coffee break/Event Photo (to be confirmed) 10:50 - 11:30 Unit testing and R CMD check Martin Morgan 11:30 - 12:10 Rcpp (Adding C/C++ code to R packages) Benilton de Sá Carvalho 12:10 - 12:30 Break 12:30 - 14:00 Debugging and Parallelization Martin Morgan 14:00 - 15:30 Lunch break 15:30 - 17:30 Working on a Collaborative Project Day 4: August 2, 2018 9:00 - 10:00 Keynote Lecture IV Benilton Carvalho 10:00 - 10:30 Talk III: RLadies Community Experience Teresa Ortíz 10:30 - 11:00 Coffee break 11:00 - 14:00 Working on a Collaborative Project 14:00 - 15:30 Lunch break 15:30 - 17:30 Working on a Collaborative Project Day 5: August 3, 2018 9:00 - 10:00 Working on a Collaborative Project and recovery from La Palapa 10:00 - 10:30 Working on a Collaborative Project 10:30 - 11:00 Coffee break 11:00 - 11:30 Working on a Collaborative Project 11:30 - 12:30 Presentations of collaborative projects 12:30 - 13:00 Closing remarks and community building Instructors: Martin Morgan (Roswell Park Comprehensive Cancer Center, Buffalo, USA)\n Benilton Carvalho (University of Campinas, Campinas, Brazil)\n Selene L. Fernandez-Valverde (National Laboratory of Genomics for Biodiversity, Irapuato, Mexico)\n Organizing committee: Heladia Salgado (Center for Genomic Sciences, Cuernavaca, Mexico)\n Leonardo Collado-Torres (Lieber Institute for Brain Development, Baltimore, USA)\n Alejandra Medina-Rivera (International Laboratory for Human Genome Research, Juriquilla, Mexico)\n Alejandro Reyes (Dana-Farber Cancer Institute, Boston, USA)\n Delfino García (Center for Genomic Sciences, Cuernavaca, Mexico)\n Daniela Ledezma-Tejeida (Center for Genomic Sciences, Cuernavaca, Mexico)\n Laura Gómez (Center for Genomic Sciences, Cuernavaca, Mexico)\n Code of Conduct Sponsors Become our sponsor\n[](http://www.soibio.org) [](http://www.ccg.unam.mx) [](http://www.lcg.unam.mx) [](http://liigh.unam.mx/) [](https://www.r-consortium.org/) [](http://wintergenomics.com/) ","date":1521722421,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1521722421,"objectID":"f3d8b475cdd776e2c7b1b09b94366e53","permalink":"http://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/","publishdate":"2018-03-22T12:40:21Z","relpermalink":"/post/r-bioconductor-developers-workshop-2018/","section":"post","summary":"Community of Bioinformatics Software Developers Workshop webpage: https://comunidadbioinfo.github.io/post/r-bioconductor-developers-workshop-2018/\n Level: intermediate - advanced\n Language: english\n When: July 30 - August 3, 2018\n Where: Auditorium of the Center for Genomic Sciences, Cuernavaca, Mexico\n Twitter: #CDSBMexico\n Facebook: @CDSBMexico\n GitHub: https://github.com/ComunidadBioInfo/R-BioConductor-Developers-Workshop-2018\n Register\n Requirements Requirements prior knowledge\n Participants should have basic knowledge of programming language R: variable assignment, reading files: read.","tags":null,"title":"Latin American R/BioConductor Developers Workshop 2018","type":"post"},{"authors":["CDSB"],"categories":["Events"],"content":"The National Node of Bioinformatics (NNB-UNAM) and the Community of Bioinformatics Software Developers (CDSB) invite you to\nTIB2018: R para todos \u0026amp; Latin American R/Bioconductor Developers Workshop UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 30 to August 3, 2018\nThis year, we decided to join efforts to promote the development of skills in the programming language R, under the slogan \u0026ldquo;Learn R and do community\u0026rdquo; .\nIn the world of data analysis R and Python they are positioned as programming languages fastest growing.\nThe reasons:\n They are easy to learn\n Specialized libraries offer advanced statistics.\n Why have we chosen R?\nIt is ideal for non - programmers and has really powerful libraries.\nOur teachers are researchers, postdocs and academic technicians with extensive experience in the area of domestic and foreign institutions. Most of them are certified as Software Carpentry certified instructors, who trained in the best practices of teaching computer science research.\nThe workshops are organized by:\n NNB-UNAM, Mexican node EMBNet (European Molecular Biology network)\n Community of Bioinformatics Software Developers (CDSB)\n Workshops T1: Introduction workshop R and R Studio\n T2: Exploratory and statistical analysis of biological data using R \n T3: Workshop RNA-Seq: Exploratory analysis of genes and differential expression\n T4: Workshop NGS: Assembly and Genome Annotation\n Register\n","date":1521655946,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1521655946,"objectID":"6bce212d03df2a863760c7323774d2f4","permalink":"http://comunidadbioinfo.github.io/post/talleres-internacionales-de-bioinformatica-2018/","publishdate":"2018-03-21T18:12:26Z","relpermalink":"/post/talleres-internacionales-de-bioinformatica-2018/","section":"post","summary":"The National Node of Bioinformatics (NNB-UNAM) and the Community of Bioinformatics Software Developers (CDSB) invite you to\nTIB2018: R para todos \u0026amp; Latin American R/Bioconductor Developers Workshop UNAM Center for Genomic Sciences (CCG-UNAM) in Cuernavaca Morelos, Mexico. From July 30 to August 3, 2018\nThis year, we decided to join efforts to promote the development of skills in the programming language R, under the slogan \u0026ldquo;Learn R and do community\u0026rdquo; .","tags":null,"title":"2018 International Workshop on Bioinformatics","type":"post"},{"authors":["CDSB"],"categories":null,"content":"See version in Spanish. This privacy notice is for those of you in Mexico.\n","date":1520961796,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1520961796,"objectID":"b47f3b94fc84cce845b30025c5b4efed","permalink":"http://comunidadbioinfo.github.io/aviso-de-privacidad/","publishdate":"2018-03-13T17:23:16Z","relpermalink":"/aviso-de-privacidad/","section":"","summary":"See version in Spanish. This privacy notice is for those of you in Mexico.","tags":null,"title":"Aviso de Privacidad para la Protección de Datos Personales","type":"page"},{"authors":["Delfino García-Alonso"],"categories":["difusion"],"content":"La Bioinformática es un área interdisciplinaria en la que convergen las tecnologías de la información y las comunicaciones con las ciencias de la vida, donde los recursos computacionales y humanos asisten al análisis de cantidades enormes de datos biológicos, para extraer de ellos información valiosa y obtener resultados con impactos beneficiosos en la salud humana o animal (González Hernández D**., 2007).**\nDesde la segunda mitad del siglo XX, la biología ha tenido una relación creciente con las ciencias de la información. Su relación se inicia debido al constante impulso del hombre por saber de qué estamos hechos, y fue por allá de 1956 con la secuenciación de la primera proteína por Margaret O. Dayhoff. A partir de entonces, con la constante producción de información biológica, la cual crecía a un ritmo lento comparado con el actual volumen de generación de datos, se creó la necesidad de recopilar y organizar toda la información generada a partir de dichos proyectos de secuenciación, surgiendo así, la primera base de datos con información biológica llamada Protein Data Bank (PDB) (Benítez Páez A, Cárdenas Brino S, 2010).\nEsa relación incipiente de las ciencias de la vida con las ciencias de la computación ha dado origen a una disciplina que ha cobrado vida en los últimos años: la bioinformática.\nLos mayores avances en la bioinformática acontecieron en años posteriores a la creación de la primera base de datos, y fue con la generación de algoritmos matemáticos para el análisis de secuencias, así como también, la creación y el impuso dado a las bases de datos y herramientas para el análisis de secuencias con un impacto a nivel global.\nAdemás, con la creación del consorcio para la ejecución del proyecto de secuenciación del genoma humano (Human Genome, HUGO), en 1993, se inició la era genómica. Siendo la decodificación del genoma humano un proyecto tan ambicioso, que otros consorcios se crearon con el fin de secuenciar los primeros genomas no virales. En 1996, S. cerevisiae fue el primer genoma eucariota secuenciado. En 1995 y 1997, respectivamente, los genomas de Haemophilus influenzae y Escherichia coli fueron los primeros genomas bacterianos publicados. Entre los años 1998 y 2000, se tuvieron los genomas secuenciados de Caenorhabditis elegans, Pseudomonas aeruginosa, Drosophila melanogaster y Arabidopsis thaliana. En el año 2003, se finalizó la secuencia definitiva del genoma humano y, este hecho se logró gracias a la proyección y explotación del potencial de la industria biotecnológica.\nComo consecuencia, todos los avances tecnológicos destinados al campo de la genómica lograron proyectar a la comunidad científica hacia la secuenciación del genoma de cualquier organismo de interés científico o económico. Hoy en día, existen más de 12,574 genomas de bacterias completamente secuenciados y más de 65,142 proyectos en curso (GOLD Database, https://gold.jgi.doe.gov/index release v.6).\nLa gran cantidad de información generada a partir de los múltiples proyectos de secuenciación hizo que las bases de datos crecieran a un ritmo acelerado y casi insostenible. Al mismo tiempo, el enorme volumen de datos conlleva a que el número de herramientas de análisis y algoritmos computacionales surjan al mismo ritmo para poder extraer un conocimiento tangible que permita dar un significado a la diversidad biológica de nuestro ecosistema.\n","date":1520369358,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1520369358,"objectID":"17187444b10eb1a3aab48aaa15a15cd1","permalink":"http://comunidadbioinfo.github.io/post/la-bioinformatica-una-disciplina-en-auge-en-el-mundo/","publishdate":"2018-03-06T20:49:18Z","relpermalink":"/post/la-bioinformatica-una-disciplina-en-auge-en-el-mundo/","section":"post","summary":"La Bioinformática es un área interdisciplinaria en la que convergen las tecnologías de la información y las comunicaciones con las ciencias de la vida, donde los recursos computacionales y humanos asisten al análisis de cantidades enormes de datos biológicos, para extraer de ellos información valiosa y obtener resultados con impactos beneficiosos en la salud humana o animal (González Hernández D**., 2007).**\nDesde la segunda mitad del siglo XX, la biología ha tenido una relación creciente con las ciencias de la información.","tags":null,"title":"Bioinformatics, a field on the rise in the world","type":"post"},{"authors":null,"categories":null,"content":"The Community of Software Developers in Bioinformatics, stems from the concern for encouraging the participation and collaboration of people specializing in Bioinformatics and Genomics, to contribute or bring in free software development internationally.\nThe Community is convinced that, through courses, workshops, conferences, and other technological means, can strengthen the skills of its members to participate in development projects software, or undertake the development of new software quality, always promoting the spirit of cooperation and integration.\nWhat do we believe in ?\n Objectivity and neutrality: Members of the community, our colleagues deserve the truth and real knowledge, we do not allow ourselves to deceive them. Innovation: We continually work to be at the forefront and inspire those around us with new ideas. We do not believe in borders: We live in a globalized world, we care about connecting with what happens beyond. Passion and perfection: We work with passion and perfection in everything we do to develop quality software. Open Collaboration: As always we invite the community to collaborate in our initiatives, we also seek to collaborate and add third-party initiatives. Our objectives:\n Create a large community of software developers in bioinformatics Create links with other communities: TIBs, SoIBio, Bioconductor Recruit talent Create content for programming courses and creating packages in R, Python, C, Perl etc. Maintain repository for sharing software made by our community via GitHub. ","date":1519319230,"expirydate":-62135596800,"kind":"page","lang":"en","lastmod":1519319230,"objectID":"86648fca13531778c6f0ab5bb4d930ad","permalink":"http://comunidadbioinfo.github.io/quienes-somos/","publishdate":"2018-02-22T17:07:10Z","relpermalink":"/quienes-somos/","section":"","summary":"The Community of Software Developers in Bioinformatics, stems from the concern for encouraging the participation and collaboration of people specializing in Bioinformatics and Genomics, to contribute or bring in free software development internationally.\nThe Community is convinced that, through courses, workshops, conferences, and other technological means, can strengthen the skills of its members to participate in development projects software, or undertake the development of new software quality, always promoting the spirit of cooperation and integration.","tags":null,"title":"About us","type":"page"}] \ No newline at end of file