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{%- include role.html type=page.role text=true description=page.description -%} diff --git a/_members/alessia-carrara.md b/_members/alessia-carrara.md new file mode 100644 index 0000000000..cb546d0928 --- /dev/null +++ b/_members/alessia-carrara.md @@ -0,0 +1,15 @@ +--- +name: Alessia Carrara +image: images/people/alessia-carrara.png +description: Student +status: alumni +role: student +aliases: + - + - +links: + home-page: + email: + github: + linkedin: +--- diff --git a/_members/anita-schurch.md b/_members/anita-schurch.md new file mode 100644 index 0000000000..7b08958c33 --- /dev/null +++ b/_members/anita-schurch.md @@ -0,0 +1,19 @@ +--- +name: Anita Schurch +image: images/people/anita-schurch.jpg +description: Assistant Professor +status: current +role: pi +aliases: + - A C Schurch + - A. C. Schürch +links: + email: a.c.schurch@umcutrecht.nl + home-page: https://aschuerch.github.io/ + orcid: 0000-0003-1894-7545 + github: aschuerch + linkedin: aschurch761a132a + twitter: AnitaSchurch +--- + +Anita's bio. diff --git a/_members/anne-chovie.md b/_members/anne-chovie.md deleted file mode 100644 index 516c6b8d10..0000000000 --- a/_members/anne-chovie.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -name: Anne Chovie -image: images/member.jpg -description: Bark Ops Engineer -role: programmer -aliases: - - A. Chovie - - A Chovie -links: - home-page: annechovie.com - email: anne@chovie.com - github: anne-chovie ---- - -Anne is a good dog. -She studied at the University of Good Dogs. -She likes pets, walkies, and treats. diff --git a/_members/felix-cited.md b/_members/felix-cited.md deleted file mode 100644 index 808f7bff01..0000000000 --- a/_members/felix-cited.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -name: Felix Cited -image: images/member.jpg -description: Treat Researcher -role: phd -group: alum -aliases: - - F. Cited - - F Cited -links: - home-page: felixcited.com - email: felix@cited.com - twitter: felixcited ---- - -Felix is a good dog. -He studied at the University of Good Dogs. -He likes pets, walkies, and treats. diff --git a/_members/gijs-teunis.md b/_members/gijs-teunis.md new file mode 100644 index 0000000000..c47ca2bac9 --- /dev/null +++ b/_members/gijs-teunis.md @@ -0,0 +1,20 @@ +--- +name: Gijs Teunis +image: images/people/gijs-teunis.jpg +description: PhD Student +status: current +role: phd +aliases: + - Gijs Teunis + - G Teunis + - G. Teunis +links: + home-page: + email: gijs.teunis@rivm.nl + orcid: + github: gidjes + gitlab: + linkedin: gijs-teunis +--- + +I’m a PhD candidate at the National Institute of Public Health and Environment (RIVM) as well as the Medical Microbiology department of the UMCU. I am researching the spread of plasmids containing antimicrobial resistance genes between the One Health domains in the Netherlands. diff --git a/_members/giulia-fornero.md b/_members/giulia-fornero.md new file mode 100644 index 0000000000..49f88cf2fc --- /dev/null +++ b/_members/giulia-fornero.md @@ -0,0 +1,14 @@ +--- +name: Giulia Fornero +image: images/people/giulia-fornero.jpg +description: Student +status: alumni +role: student +aliases: + - +links: + home-page: + email: + github: + linkedin: +--- diff --git a/_members/janetta-top.md b/_members/janetta-top.md new file mode 100644 index 0000000000..ad34c00748 --- /dev/null +++ b/_members/janetta-top.md @@ -0,0 +1,15 @@ +--- +name: Janetta Top +image: images/people/janetta_top.jpg +description: Assistant Professor +status: current +role: postdoc +aliases: + - J. Top + +links: + email: J.Top@umcutrecht.nl + orcid: + github: + linkedin: +--- diff --git a/_members/jari-koot.md b/_members/jari-koot.md new file mode 100644 index 0000000000..e7ca7ba62d --- /dev/null +++ b/_members/jari-koot.md @@ -0,0 +1,19 @@ +--- +name: Jari Koot +image: images/people/jari-koot.jpg +description: Student +role: student +status: alumni +aliases: + - Jari Koot + - J.M.A. Koot +links: + home-page: https://github.com/JariKoot + email: j.m.a.koot-2@umcutrecht.nl + gitlab: https://gitlab.com/jarikoot + github: JariKoot + linkedin: jari koot +--- + +Hey there! I'm Jari, a 20 year old Life Science student. With a passion for programming and biology. This year I'm doing my internship at the UMC Utrecht. +Currently I'm working on a metagenomics pipeline that creates a visualization of WGS data. I think it's very important to document all my work and to make use of a reproducible workflow. diff --git a/_members/jesse-kerkvliet.md b/_members/jesse-kerkvliet.md new file mode 100644 index 0000000000..011cc24dbd --- /dev/null +++ b/_members/jesse-kerkvliet.md @@ -0,0 +1,21 @@ +--- +name: Jesse Kerkvliet +image: images/people/jesse-kerkvliet.jpg +description: PhD Student +status: current +role: phd +aliases: + - J Kerkvliet + - J. Kerkvliet + - J J Kerkvliet + - J.J. Kerkvliet +links: + home-page: + email: j.j.kerkvliet@umcutrecht.nl + orcid: + github: jessekerkvliet + linkedin: jesse-kerkvliet +--- + +I'm a PhD Candidate in the Medical Microbiology department, interested in the way (antibiotic resistance) genes spread throughout the environment. I develop research software to track these genes on mobile DNA, like plasmids and tranposons, in environental (metagenomics-)samples. Currently, I am developping a workflow tool to identify antibiotic resistance genes and several types of mobile DNA anticipiating to compare these mobile resistome data between samples. + diff --git a/_members/julian-paganini.md b/_members/julian-paganini.md new file mode 100644 index 0000000000..d633adb4b3 --- /dev/null +++ b/_members/julian-paganini.md @@ -0,0 +1,24 @@ +--- +name: Julian Paganini +image: images/people/julian-paganini.jpg +description: PhD Student +status: current +role: phd +aliases: + - Julian Paganini + - J Paganini + - J. Paganini + - J A Paganini + - J. A. Paganini +links: + home-page: + email: j.a.paganini@umcutrecht.nl + orcid: 0000-0003-1414-8105 + github: jpaganini + gitlab: jpaganini + linkedin: julian-paganini +--- + +I’m a PhD candidate at the University Medical Center of Utrecht, currently working for the Medical Microbiology Department. + +I’m interested in understanding how antibiotic resistance develops and spreads across bacteria. I apply and develop bioinformatic tools to study multi-drug resistant E. coli, focusing on the study of plasmids and other mobile-genetic elements. diff --git a/_members/lisa-vader.md b/_members/lisa-vader.md new file mode 100644 index 0000000000..140d07d5d7 --- /dev/null +++ b/_members/lisa-vader.md @@ -0,0 +1,17 @@ +--- +name: Lisa Vader +image: images/people/lisa-vader.jpg +description: Student +status: alumni +role: student +aliases: + - +links: + home-page: + email: + orcid: + github: + linkedin: +--- + +Lisa's bio. diff --git a/_members/malbert-rogers.md b/_members/malbert-rogers.md new file mode 100644 index 0000000000..78101efd0a --- /dev/null +++ b/_members/malbert-rogers.md @@ -0,0 +1,21 @@ +--- +name: Malbert Rogers +image: images/people/malbert-rogers.jpg +description: Support Bioinformatician +status: current +role: programmer +aliases: + - Malbert R. C. Rogers + - M. R. C. Rogers +links: + home-page: + email: M.R.C.Rogers-2@umcutrecht.nl + orcid: + gitlab: malbert.rogers + github: MalbertRogers + linkedin: malbert-rogers-20429794/ +--- + +I’m a Bioinformatician in the BioIT group of the Medical Microbiology Department at the UMCU. + +My main task is to provide bioinformatician support to (non-bioinformatician) researchers of our department. This also include tasks such as setup and maintenance of pipelines and provide (basic) bioinformatics education. My main area of focus at the moment is in metagenomics (microbiome) related researches. diff --git a/_members/matteo-buffoni.md b/_members/matteo-buffoni.md new file mode 100644 index 0000000000..6522efb9dc --- /dev/null +++ b/_members/matteo-buffoni.md @@ -0,0 +1,16 @@ +--- +name: Matteo Buffoni +image: images/people/matteo-buffoni.jpg +description: PhD Student +status: current +role: phd +aliases: + - Matteo Buffoni +links: + email: + orcid: + github: + linkedin: +--- + +Matteo's bio. diff --git a/_members/rodrigo-meneses.md b/_members/rodrigo-meneses.md new file mode 100644 index 0000000000..d02a2e42b2 --- /dev/null +++ b/_members/rodrigo-meneses.md @@ -0,0 +1,23 @@ +--- +name: Rodrigo Meneses +image: images/people/rodrigo-meneses.jpg +description: Support Bioinformatician +status: alumni +role: programmer +aliases: + - Rodrigo Meneses + - R. Meneses + - R Meneses +links: + home-page: https://groodri.github.io + email: rsilvame@umcutrecht.nl + orcid: 0000-0002-1632-1752 + github: groodri + linkedin: groodri +--- + +I'm a (Support) Bioinformatician in the BioIT group. + +My main tasks involve group infrastructure, analysis support and consultancy. I also participate in research projects, where I focus on coding analysis pipelines. Recently, I've been working on finding minority variants from deep population sequencing, and using tehcnologies like Snakemake, Docker & Singularity. + +I'm very interested in open science, code and data. I believe transparency leads to a more welcoming environment where scientific ideas can thrive. diff --git a/_members/sander-vermeulen.md b/_members/sander-vermeulen.md new file mode 100644 index 0000000000..9f95309849 --- /dev/null +++ b/_members/sander-vermeulen.md @@ -0,0 +1,17 @@ +--- +name: Sander Vermeulen +image: images/people/sander-vermeulen.jpg +description: Student +status: alumni +role: student +aliases: + - +links: + home-page: + email: + orcid: + github: + linkedin: +--- + +Sander's bio. diff --git a/_members/sergio-arredondo-alonso.md b/_members/sergio-arredondo-alonso.md new file mode 100644 index 0000000000..189e8eace2 --- /dev/null +++ b/_members/sergio-arredondo-alonso.md @@ -0,0 +1,17 @@ +--- +name: Sergio Arredondo-Alonso +image: images/people/sergio-arredondo-alonso.jpg +description: PhD Student +status: alumni +role: phd +aliases: + +links: + home-page: https://www.med.uio.no/imb/english/people/aca/sergioar/index.html + email: s.a.alonso@medisin.uio.no + orcid: + github: + linkedin: +--- + +Former PhD candidate, developer of mlplasmids and gplas. diff --git a/_members/upton-goode.md b/_members/upton-goode.md deleted file mode 100644 index 5f1a0c441b..0000000000 --- a/_members/upton-goode.md +++ /dev/null @@ -1,18 +0,0 @@ ---- -name: Upton O. Goode -image: images/member.jpg -description: Bone Investigator -role: pi -aliases: - - U. Goode - - U. O. Goode - - U Goode -links: - orcid: 0000-0001-8713-9213 - email: upton@ogoode.com - twitter: uptonogoode ---- - -Upton is a good dog. -He studied at the University of Good Dogs. -He likes pets, walkies, and treats. diff --git a/_members/victoria-pascal.md b/_members/victoria-pascal.md new file mode 100644 index 0000000000..9d52732beb --- /dev/null +++ b/_members/victoria-pascal.md @@ -0,0 +1,20 @@ +--- +name: Victoria Pascal Andreu +image: images/people/victoria-pascal.jpg +description: Postdoctoral Researcher +status: current +role: postdoc +aliases: + - Victoria Pascal + - V Pascal + - V. Pascal +links: + email: v.pascalandreu@umcutrecht.nl + orcid: 0000-0001-9609-9401 + github: victoriapascal + linkedin: vict%C3%B2ria-pascal +--- + +I'm a Postoctoral researcher in the BioIT group. + +I develop tools and analyse different types of omics data. I am interested on studying the role of microbes in humans health and disease. Specifically my main project focuses on vancomycin-resistant Enterococcus faecium outbreaks that happen in Dutch hospitals. For that I'm building a pipeline to understand dissemination modes of the vancomycin-resistant genes and get insights into their transmission networks. diff --git a/_members/weizhen-xu.md b/_members/weizhen-xu.md new file mode 100644 index 0000000000..6db3ca891d --- /dev/null +++ b/_members/weizhen-xu.md @@ -0,0 +1,20 @@ +--- +name: Weizhen Xu +image: images/people/weizhen-xu.jpg +description: Postdoctoral researcher +status: current +role: postdoc +aliases: + - Xu Weizhen + - W Xu + - Xu W +links: + email: w.xu@umcutrecht.nl + home-page: + orcid: 0000-0002-0826-2721 + github: weizhenxuuu + gitlab: weizhenxu + linkedin: weizhen-xu-452a89194 +--- + +I'm a postdoc with the MMB-BioIT group - I'm currently developing a pipeline for using Nanopore adaptive sequencing to enrich and detect antibiotic resistance genes and plasmids from clinical and environmental samples. I also dabble in machine learning methods. diff --git a/_posts/2019-01-07-example-post-1.md b/_posts/2019-01-07-example-post-1.md deleted file mode 100644 index 481ee33d17..0000000000 --- a/_posts/2019-01-07-example-post-1.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -title: Example post 1 -tags: - - biology - - medicine - - big data -author: Anne Chovie -member: anne-chovie ---- - -# Heading 1 - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Amet porttitor eget dolor morbi. -Est ullamcorper eget nulla facilisi etiam dignissim diam. -A pellentesque sit amet porttitor eget dolor morbi non. -Id nibh tortor id aliquet lectus proin nibh nisl. -Ipsum nunc aliquet bibendum enim facilisis gravida neque convallis a. -Tristique sollicitudin nibh sit amet commodo nulla facilisi nullam vehicula. -Facilisis leo vel fringilla est ullamcorper eget nulla facilisi etiam. -Congue eu consequat ac felis donec et odio pellentesque diam. -Ipsum nunc aliquet bibendum enim facilisis gravida neque convallis. -Urna molestie at elementum eu. -Purus faucibus ornare suspendisse sed nisi lacus sed viverra. -Feugiat scelerisque varius morbi enim nunc faucibus a pellentesque. -Dolor magna eget est lorem ipsum. -Feugiat scelerisque varius morbi enim nunc faucibus a. diff --git a/_posts/2019-12-14-example-post-2.md b/_posts/2019-12-14-example-post-2.md deleted file mode 100644 index e79c657e5d..0000000000 --- a/_posts/2019-12-14-example-post-2.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -title: Example post 2 -author: Felix Cited -member: felix-cited ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Amet porttitor eget dolor morbi. -Est ullamcorper eget nulla facilisi etiam dignissim diam. -A pellentesque sit amet porttitor eget dolor morbi non. -Id nibh tortor id aliquet lectus proin nibh nisl. -Ipsum nunc aliquet bibendum enim facilisis gravida neque convallis a. -Tristique sollicitudin nibh sit amet commodo nulla facilisi nullam vehicula. -Facilisis leo vel fringilla est ullamcorper eget nulla facilisi etiam. -Congue eu consequat ac felis donec et odio pellentesque diam. -Ipsum nunc aliquet bibendum enim facilisis gravida neque convallis. -Urna molestie at elementum eu. -Purus faucibus ornare suspendisse sed nisi lacus sed viverra. -Feugiat scelerisque varius morbi enim nunc faucibus a pellentesque. -Dolor magna eget est lorem ipsum. -Feugiat scelerisque varius morbi enim nunc faucibus a. diff --git a/_posts/2020-07-02-example-post-3.md b/_posts/2020-07-02-example-post-3.md deleted file mode 100644 index 239a7404e7..0000000000 --- a/_posts/2020-07-02-example-post-3.md +++ /dev/null @@ -1,21 +0,0 @@ ---- -title: Example post 3 -tags: biology, medicine -author: Upton O. Goode -member: upton-goode ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -A lacus vestibulum sed arcu non odio. -Libero volutpat sed cras ornare. -Natoque penatibus et magnis dis parturient montes nascetur. -Ullamcorper dignissim cras tincidunt lobortis feugiat vivamus at. -Ultricies lacus sed turpis tincidunt id. -Tellus rutrum tellus pellentesque eu tincidunt. -Amet commodo nulla facilisi nullam vehicula ipsum a. -Ultrices dui sapien eget mi proin sed libero enim. -Quam vulputate dignissim suspendisse in est. -Tortor condimentum lacinia quis vel eros donec ac. -Mauris commodo quis imperdiet massa tincidunt nunc pulvinar sapien. -Eu nisl nunc mi ipsum faucibus vitae aliquet. -Interdum posuere lorem ipsum dolor sit amet consectetur adipiscing. diff --git a/_posts/2022-01-11-post-1.md b/_posts/2022-01-11-post-1.md new file mode 100644 index 0000000000..b57a2c36b0 --- /dev/null +++ b/_posts/2022-01-11-post-1.md @@ -0,0 +1,21 @@ +--- +title: Website release +tags: + - hackathon + - website +author: Anita Schurch +member: a.c.schurch +--- + +# New website + +With many thanks to the [Lab Website Template](https://github.com/greenelab/lab-website-template), +we created our own group website during a hackathon in December. + +Have a look around and enjoy! + + + + diff --git a/_posts/2022-03-31-post-2.md b/_posts/2022-03-31-post-2.md new file mode 100644 index 0000000000..c53a0cd814 --- /dev/null +++ b/_posts/2022-03-31-post-2.md @@ -0,0 +1,31 @@ +--- +title: Hackathon +tags: + - hackathon + - dokuwiki +author: Anita Schurch +member: a.c.schurch +--- + +# Hackathon + +The third hackathon centered around documentation, for which we use, among other tools, [DokuWiki](https://www.dokuwiki.org/dokuwiki). +DokuWiki is purely text-file based and doesn't require a database. +It's syntax is straighforward which makes it a versatile tool to programmers and non-programmers alike. + + +{% capture col1 %} +{% + include figure.html + image="images/hack3.jpg" + caption="A few hackathon people" +%} +{% endcapture %} +{% capture col2 %} +{% + include figure.html + image="images/hackathonwiki.png" + caption="Example wiki entry" +%} +{% endcapture %} +{% include two-col.html col1=col1 col2=col2 %} diff --git a/blog/index.md b/blog/index.md index 89331dc258..4ca14966e8 100644 --- a/blog/index.md +++ b/blog/index.md @@ -19,9 +19,18 @@ nav: -Tweets by GreeneScientist -{:.center} - -Follow @GreeneScientist -Tweet to @GreeneScientist -{:.center} +
+
+
+
+ + diff --git a/contact/index.md b/contact/index.md index 319be8b670..4694372b94 100644 --- a/contact/index.md +++ b/contact/index.md @@ -6,26 +6,25 @@ nav: --- # Contact - -Our lab is part of the [Department of Metaphor](), at the school of [Whimsy and Caprice](). -We are located on the 13th floor of the [Center for Wit and Sagacity](). +Our lab is part of the group of [Prof. Rob Willems](https://www.umcutrecht.nl/en/Research/Researchers/Willems-Rob-RJL) of the [Department of Medical Microbiology](https://www.umcutrecht.nl/nl/over-ons-medische-microbiologie?lang=en), at the Division Laboratories, Pharmacy and Biomedical Genetics, [University Medical Center Utrecht](https://www.umcutrecht.nl/en). + {% include link.html type="email" icon="" - text="scrooge@mcduck.com" + text="" tooltip="" - link="scrooge@mcduck.com" + link="a.c.schurch@umcutrecht.nl" style="button" %} {% include link.html type="phone" icon="" - text="(555) 867-5309" + text="" tooltip="" - link="+1-555-867-5309" + link="+31887551318" style="button" %} {% @@ -34,7 +33,7 @@ We are located on the 13th floor of the [Center for Wit and Sagacity](). icon="" text="Google Maps" tooltip="Our location on Google Maps for easy navigation" - link="https://www.google.com/maps/place/That+St+%26+The+Other+St,+Porters+Lake,+NS+B3E+1H3,+Canada/@44.7389237,-63.3033296,20.78z/data=!4m5!3m4!1s0x4b5a31023bb02565:0xb9505694e83a53d7!8m2!3d44.7389353!4d-63.3030828" + link="https://goo.gl/maps/NKyMyckT54guBjvz6" style="button" %} {:.center} @@ -43,23 +42,30 @@ We are located on the 13th floor of the [Center for Wit and Sagacity](). ### Mailing Address -That St & The Other St -Porters Lake, NS B3E 1H3 -Canada +Heidelberglaan 100 +{:.center} + +3584 CX Utrecht +{:.center} + +Internal mail no. G04.614 +{:.center} + +The Netherlands {:.center} {% capture col1 %} {% include figure.html - image="images/photo.jpg" - caption="The Center for Wit and Sagacity" + image="images/robin-ooode-XusR7PXCV0o-unsplash.jpg" + caption="Utrecht by Robin Oode on Unsplash" %} {% endcapture %} {% capture col2 %} {% include figure.html - image="images/photo.jpg" - caption="Department of Metaphor" + image="images/bodi-raw-izMtCpq_RyI-unsplash.jpg" + caption="Utrecht by Bodi.raw on Unsplash" %} {% endcapture %} {% include two-col.html col1=col1 col2=col2 %} diff --git a/css/all.scss b/css/all.scss old mode 100644 new mode 100755 diff --git a/css/anchor.scss b/css/anchor.scss old mode 100644 new mode 100755 diff --git a/css/background.scss b/css/background.scss old mode 100644 new mode 100755 diff --git a/css/banner.scss b/css/banner.scss old mode 100644 new mode 100755 diff --git a/css/button.scss b/css/button.scss old mode 100644 new mode 100755 diff --git a/css/card.scss b/css/card.scss old mode 100644 new mode 100755 diff --git a/css/citation.scss b/css/citation.scss old mode 100644 new mode 100755 index 64fabcd77b..3b31932aba --- a/css/citation.scss +++ b/css/citation.scss @@ -22,22 +22,6 @@ border: none; } - .citation_image { - width: 120px; - height: 120px; - max-width: 100%; - margin-right: 40px; - flex-shrink: 0; - overflow: hidden; - box-shadow: $shadow; - - img { - object-fit: cover; - width: 100%; - height: 100%; - } - } - .citation_text { width: 0; flex-grow: 1; @@ -67,13 +51,6 @@ align-items: center; flex-direction: column; - .citation_image { - width: 200px; - height: 200px; - margin: 0; - margin-bottom: 20px; - } - .citation_text { width: 100%; } diff --git a/css/code.scss b/css/code.scss old mode 100644 new mode 100755 diff --git a/css/feature.scss b/css/feature.scss old mode 100644 new mode 100755 diff --git a/css/figure.scss b/css/figure.scss old mode 100644 new mode 100755 diff --git a/css/footer.scss b/css/footer.scss old mode 100644 new mode 100755 diff 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diff --git a/css/theme.scss b/css/theme.scss old mode 100644 new mode 100755 diff --git a/css/tooltip.scss b/css/tooltip.scss old mode 100644 new mode 100755 diff --git a/css/two-col.scss b/css/two-col.scss old mode 100644 new mode 100755 diff --git a/css/util.scss b/css/util.scss old mode 100644 new mode 100755 diff --git a/custom_js/partydates.js b/custom_js/partydates.js new file mode 100644 index 0000000000..f983786ca4 --- /dev/null +++ b/custom_js/partydates.js @@ -0,0 +1 @@ +partydates = '[{"month":12,"day":1},{"month":10,"day":18},{"month":12,"day":9}]'; diff --git a/custom_js/partyscript.js b/custom_js/partyscript.js new file mode 100644 index 0000000000..ea024f78d2 --- /dev/null +++ b/custom_js/partyscript.js @@ -0,0 +1,35 @@ +var partydates = '["1-12","18-10","14-4","18-1","27-12","8-11","7-9","20-12"]'; +$(document).ready( + function(){ + var today = new Date(); + var month = today.getMonth()+1; + var day = today.getDate(); + var md = day+"-"+month; + + if (partydates.includes(md)){ + $(".portrait").each(function(){ + var img =$(this).find("img").attr("src"); + var partyimg = img.replace(".jpg","_party.jpg"); + + if (checkFileExist(partyimg)){ + $(this).find("img").attr('src',partyimg); + } + + }); + + } + +}); + + +function checkFileExist(urlToFile) { + var xhr = new XMLHttpRequest(); + xhr.open('HEAD', urlToFile, false); + xhr.send(); + + if (xhr.status == "404") { + return false; + } else { + return true; + } +} diff --git a/favicons/android.png b/favicons/android.png index f1c5e5f28e..ae5cfcc61a 100644 Binary files a/favicons/android.png and b/favicons/android.png differ diff --git a/favicons/favicon.png b/favicons/favicon.png index f1c5e5f28e..ae5cfcc61a 100644 Binary files a/favicons/favicon.png and b/favicons/favicon.png differ diff --git a/favicons/ios.png b/favicons/ios.png index c96c21bd25..ae5cfcc61a 100644 Binary files a/favicons/ios.png and b/favicons/ios.png differ diff --git a/images/.DS_Store b/images/.DS_Store new file 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/dev/null +++ b/images/plasmidEC_logo_2.svg @@ -0,0 +1,152 @@ + + + + diff --git a/images/rect3728.png b/images/rect3728.png new file mode 100644 index 0000000000..182bb5e983 Binary files /dev/null and b/images/rect3728.png differ diff --git a/images/research_picture.jpg b/images/research_picture.jpg new file mode 100644 index 0000000000..0734413f66 Binary files /dev/null and b/images/research_picture.jpg differ diff --git a/images/robin-ooode-XusR7PXCV0o-unsplash.jpg b/images/robin-ooode-XusR7PXCV0o-unsplash.jpg new file mode 100644 index 0000000000..2f5ad5538d Binary files /dev/null and b/images/robin-ooode-XusR7PXCV0o-unsplash.jpg differ diff --git a/images/tools_picture.png b/images/tools_picture.png new file mode 100644 index 0000000000..db31aa9cf1 Binary files /dev/null and b/images/tools_picture.png differ diff --git a/images/tourmaline_icon.svg b/images/tourmaline_icon.svg new file mode 100644 index 0000000000..3e47ed848e --- /dev/null +++ b/images/tourmaline_icon.svg @@ -0,0 +1 @@ + \ No newline at end of file diff --git a/images/utrecht.jpg b/images/utrecht.jpg new file mode 100644 index 0000000000..2e921f1e02 Binary files /dev/null and b/images/utrecht.jpg differ diff --git a/index.md b/index.md index 985bac5788..18230c908d 100644 --- a/index.md +++ b/index.md @@ -2,40 +2,23 @@ title: Home --- -# Your Lab Slogan +# MMB-BioIT -[Lab Website Template](https://github.com/greenelab/lab-website-template) is an easy-to-use, flexible website template for [labs](https://www.greenelab.com/), with automatic citations, GitHub tag imports, pre-built components, and more. -Spend less time reinventing the wheel, and more time running your lab. +The Medical Microbiology bioinformatics (MMB-BioIT) team from the University Medical Center Utrecht (UMCU) consists of researchers with different scientifical backgrounds. Our efforts are dedicated to develop and use bioinformatic tools that facilitate data analysis on large amounts of DNA sequences, including whole genome sequences (WGS), taxonomic profiling using 16S rRNA gene sequencing and metagenomic sequencing. -{% - include link.html - type="github" - icon="" - text="See the template on GitHub" - link="greenelab/lab-website-template" - style="button" -%} -{% - include link.html - type="docs" - icon="" - text="See the documentation" - link="https://github.com/greenelab/lab-website-template/wiki" - style="button" -%} -{:.center} {% include section.html full=true %} -{% include banner.html image="images/banner.jpg" %} +{% include figure.html + image="images/UMCU-1.jpg" +%} {% include section.html %} # Highlights {% capture text %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. +Test. The worldwide emergence of antibiotic resistant bacteria causing difficult to treat infections highlights the importance to track their local and global transmission. Using WGS or metagenomic sequences, different bioinformatic tools are used to group these bacteria based on the core and/or accessory genome, including mobile genetic elements encoding e.g. antibiotic resistance genes. In addition, we developed tools to reconstruct plasmids based on short read sequences in order to determine transmission patterns of mobile genetic elements. [See what we've published →](research) {:.center} @@ -43,30 +26,43 @@ Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliqu {% include feature.html - image="images/photo.jpg" + image="images/research_picture.jpg" + link="research" + headline="Population Genetics" + text=text +%} + +{% capture text %} +A microbiome is a collective polymicrobial community, or ‘microbiota’, including bacteria, archaea, algae, protozoa, fungi, and viruses. Over the last decades research has shown that microbiome composition can be linked to health and disease. In our group we perform microbiome analysis on taxonomic level using 16S rRNA or metagenomic sequencing. The latter can also be used to analyze metabolic pathways encoded by bacteria. (image generated by DALL-E) + +{:.center} +{% endcapture %} + +{% + include feature.html + image="images/microbiome.png" link="research" - headline="Our Research" + headline="Microbiome analysis" text=text %} {% capture text %} -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. +The mission of our team is that the developed tools and analyzed data are released to enable reproducible computational biology analyses following the FAIR (Findable, Accessible, Interoperable and Reusable) principles. Find more about our tools in the link below. -[See our resources →](resources) +[See our tools →](tools) {:.center} {% endcapture %} {% include feature.html - image="images/photo.jpg" - link="resources" - headline="Our Resources" + image="images/tools_picture.png" + link="tools" + headline="Our Tools" text=text %} {% capture text %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. +We are a group of enthusiastic scientists with different interests and backgrounds that work in close collaboration with experimentalists and clinicians. [Meet our team →](team) {:.center} @@ -74,11 +70,11 @@ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor i {% include feature.html - image="images/photo.jpg" + image="images/group.jpg" link="team" headline="Our Team" text=text %} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. +{% include twitter.html %} + diff --git a/research/index.md b/research/index.md index f4fd10752b..20825b3cc1 100644 --- a/research/index.md +++ b/research/index.md @@ -7,10 +7,7 @@ nav: # Research -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. +Our research interest is to find patterns in DNA sequencing data and to apply this knowledge to the genomic epidemiology of organisms causing infectious diseases. We are interested in the genomics of plasmids and other mobile genetic elements. Our group provides bioinformatics support for a medical microbiology department of an academic hospital. We design, write and maintain pipelines and databases for genomic or metagenomic analyses, carry out or advise on analysis of high-throughput sequencing data and provide bioinformatics education and consultation. {% include section.html %} diff --git a/team/index.md b/team/index.md index 9473b64631..eb47d44c84 100644 --- a/team/index.md +++ b/team/index.md @@ -4,88 +4,101 @@ nav: order: 3 tooltip: About our team --- - +{% include party.html %} # Team -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. - {% include section.html %} {% include list.html data="members" component="portrait" - filters="role: pi" + filters="role: pi, status: current" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: programmer, status: current" %} {% include list.html data="members" component="portrait" - filters="role: phd" + filters="role: postdoc, status: current" %} {% include list.html data="members" component="portrait" - filters="role: programmer" + filters="role: phd, status: current" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: student, status: current" %} {:.center} {% include section.html background="images/banner.jpg" dark=true%} -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. {% include section.html %} -## Join - -#### Post Dogtoral Researcher -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - -- 3+ (dog) years experience managing bone portfolios -- Strong desire to learn tricks and go on walkies -- Aptitude to sit and stay - -{% include link.html type="external" link="https://google.com/" text="Apply Now" icon="" style="button" %} -{:.center} +# Alumni {% include section.html %} -## Funding - -Our work is made possible by funding from several organizations. +{% + include list.html + data="members" + component="portrait" + filters="role: pi, status: alumni" + style="small" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: programmer, status: alumni" + style="small" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: postdoc, status: alumni" + style="small" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: phd, status: alumni" + style="small" +%} +{% + include list.html + data="members" + component="portrait" + filters="role: student, status: alumni" + style="small" +%} {:.center} -{% - include gallery.html - style="square" +{% include section.html background="images/banner.jpg" dark=true%} - image1="images/photo.jpg" - link1="https://nasa.gov/" - tooltip1="Cool Foundation" - image2="images/photo.jpg" - link2="https://nasa.gov/" - tooltip2="Cool Institute" +{% include section.html %} - image3="images/photo.jpg" - link3="https://nasa.gov/" - tooltip3="Cool Initiative" +## Join + +We have no open positions at the moment. - image4="images/photo.jpg" - link4="https://nasa.gov/" - tooltip4="Cool Foundation" +{% include link.html type="external" link="https://google.com/" text="Apply Now" icon="" style="button" %} +{:.center} - image5="images/photo.jpg" - link5="https://nasa.gov/" - tooltip5="Cool Institute" +{% include section.html %} - image6="images/photo.jpg" - link6="https://nasa.gov/" - tooltip6="Cool Initiative" -%} diff --git a/tools/index.md b/tools/index.md index 763e1cadf1..73ce3bd611 100644 --- a/tools/index.md +++ b/tools/index.md @@ -5,23 +5,33 @@ nav: tooltip: Software, datasets, and more --- -# Tools +# Tools & Education + +Hello fellow scientist! Welcome to our ‘Tools and Education’ section! + +In MMBioIT we actively develop tools for bacterial genomics, focusing on providing software that is easy to install and use. We strongly believe in transparent and collaborative science, and therefore all our tools are completely open-source. We encourage you to try our tools and, if you dare, suggest improvements for them. + +Are you a wet-labber? Are you interested in learning bioinformatics? Then you should check our Education section! You will find free courses to improve your bioinformatics skills. -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. {% include search-info.html %} {% include section.html %} -## Featured +# Tools + +## Whole Genome Sequencing + +{% include list.html component="card" data="tools" filters="group: wgs" %} + +{% include section.html %} + +## Metagenomics -{% include list.html component="card" data="tools" filters="group: featured" %} +{% include list.html component="card" data="tools" filters="group: metagenomics" %} {% include section.html %} -## More +# Educational resources -{% include list.html component="card" data="tools" filters="group: more" style="small" %} +{% include list.html component="card" data="tools" filters="group: education" %}