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MET_2023_schedule.md

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+---
+layout: tutorial_page
+permalink: /MET_2023_schedule
+title: Metabolomics
+header1: Workshop Pages for Students
+header2: Metabolomics 2023 Schedule
+image: /site_images/CBW_metabolomics_icon.jpg
+home: https://bioinformaticsdotca.github.io/MET_2023
+---
+
+| | **Day 1** | | **Day 2** |  
+| :---: | :---: | :---: | :---: |  
+| | **Monday, June 15** | | **Tuesday, June 16** | 
+|	10:00	|	Welcome (Rachade)	|	10:00	|	Module 4: Backgrounder in Statistics (Jeff Xia)	|
+|	10:45	|	Module 1: Introduction to Metabolomics (David Wishart)	|	11:30	|	<font color="green">Break</font>|
+|	12:30	|	<font color="green">Break</font>|	12:00	|	Module 5: MetaboAnalyst (Jeff Xia)	|
+|	13:00	|	Module 2: Metabolite Identification (David Wishart)	|	14:30	|	<font color="green">Break</font>	|
+|	14:30	|	<font color="green">Break</font>|	15:00	|	Module 5 Lab: Metabolomic Data Analysis using MetaboAnalyst 4.0 (Xia, Wishart, Chong, Berjanskii)	|
+|	15:00	|	Module 2 Lab: Compound ID & Quantification (Wishart, Xia, Berjanskii, Chong, Yamamoto)	|	16:30	|	<font color="green">Break</font>|
+|	16:30	|	<font color="green">Break</font>|	17:00	|	Module 5 Lab: Continued (Xia, Wishart, Berjanskii, Chong, Yamamoto)	|
+|	17:00	|	Module 3 Lecture: Databases for Chemical, Spectral and Biological Data (David Wishart)	|	18:30	|	Module 6: Future of Metabolomics	|
+|	18:30	|	(Optional) Spectral Processing & Functional Analysis until 8pm	|	19:00	|	Survey & Closing Remarks	|

README.md

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-# MET_2023
+# MET_2023

laptop_setup.md

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+---
+layout: tutorial_page
+permalink: /metabolomics_2019_laptop_setup
+title: Metabolomics Laptop Setup Instructions
+header1: Workshop Pages for Students
+header2: Informatics and Statistics for Metabolomics 2019
+image: /site_images/CBW_metabolomics_icon.jpg
+home: https://bioinformaticsdotca.github.io/metabolomics_2019
+---
+
+## Programs to Install
+
+1) A robust internet browser such as Firefox or Safari (Internet Explorer and Chrome are not recommended because of Java issues).
+
+2) A PDF viewer (Adobe Acrobat or equivalent).  
+
+
+
+If you are interested to perform the raw spectra analysis using R on your own, then also install:
+
+3) Install the most recent version of R for your operating system by following the links from http://www.r-project.org/  
+
+4) Download and install the most recent version of R Studio desktop from http://www.rstudio.com/.  
+
+5) Visit the MetaboAnalystR page and complete Step 1 and Step 2: https://github.com/xia-lab/MetaboAnalystR
+
+
+
+If you bring your own raw spectral data, then you will also need to install:  
+
+6) [Proteowizard MS convert](http://proteowizard.sourceforge.net/user_installation.shtml).
+
+

main_metabolomics.md

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+---
+layout: workshop_main_2day
+permalink: /MET_2023
+title: Metabolomics 2023
+header1: Workshop Pages for Students
+header2: Metabolomics 2023
+image: /site_images/CBW_metabolomics_icon.jpg
+keywords: metabolome-focused experiments, analyzing metabolomic data, metabolome
+description: Course covers many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomics databases, and exploring chemical databases. 
+instructors: David Wishart, Jeff Xia
+length: 2 days
+---
+
+# Welcome <a id="welcome"></a>
+
+[Welcome] to Informatics and Statistics for Metabolomics 2023.  
+
+The course schedule can be found [here](https://bioinformaticsdotca.github.io//MET_2023_schedule.md)
+
+Meet your faculty! [here](https://drive.google.com/open?id=12M8Ao7TP9qbpnDIZgBVu8ZbMRVKfqJBG)
+
+***
+
+# Pre-Workshop Materials <a id="preworkshop"></a>
+
+
+## Pre-workshop Lecture
+
+Pre-readings and pre-work can be found here [here](https://bioinformaticsdotca.github.io/metabolomics_2020_prework).  
+It is in your best interest to complete these before the workshop.
+
+***
+
+# Class Photo
+
+<img src="https://github.com/bioinformatics-ca/Metabolomics_2020/blob/master/Metabo_class_v2.png?raw=true" alt="Class Photo" width="750" />
+
+
+*** 
+
+# Day 1 <a id="day1"></a>
+
+##  Welcome
+
+  *<font color="#827e9c">Rachade Hmamouchi</font>* 
+
+##  Module 1: Introduction to Metabolomics 
+
+  *<font color="#827e9c">David Wishart</font>*
+
+  Access Module 1's [lecture here.](https://drive.google.com/open?id=1XaP50oi_2fpA-cMWXnQRR-pKhmGSEWyi)  
+
+##  Module 2: Metabolite Identification and Annotation 
+
+  *<font color="#827e9c">David Wishart</font>*
+
+  Access Module 2's lecture slides [here](https://drive.google.com/open?id=1mn7nzBH7Xmbh6N2kUy5k82_6p3QKDYWr) 
+  ---- Updated slides [here](https://www.dropbox.com/s/opyz1mbanu5wl4t/CBW-Metabolomics2.1-2020_Final-June12.ppt?dl=0)
+
+ ##  Module 2 LAB: Metabolite Identification and Annotation 
+
+  Access Module 2's lab practical slides [here](https://drive.google.com/open?id=12k_Ub9Mtbp6RJB1aKCxOaMZzC2qG7JkG)
+  ---- Updated slides [here](https://www.dropbox.com/s/l5tswq1b4pxig37/CBW-Metabolomics2.1-lab-2020_Final-June12_Updated.pptx?dl=0)
+
+  Follow the instructions for Module 2's lab [here](https://bioinformaticsdotca.github.io/metabolomics_2020_mod2lab)  
+
+Briefly, the lab will go over the following pre-processing workflows:  
+
+1. NMR and <a href="http://bayesil.ca/">Bayesil</a>.  
+
+2. GC-MS and <a href="http://gc-autofit.wishartlab.com/">GC-Autofit</a>.  
+
+3. LC-MS and <a href="https://dev.metaboanalyst.ca/">MetaboAnalyst</a>. 
+
+
+#### Data Set and Results Files:
+
+##### NMR (Bayesil):
+
+**Example datasets (zipped files) for Lab2**
+
+
+ - a reduced data set to run during the lab [CBW_NMR_Data.zip](https://github.com/bioinformatics-ca/Metabolomics_2020/raw/master/CBW_NMR_Data.zip)
+ - optional, could be run after the lab [8-spectra dataset](https://github.com/bioinformatics-ca/Metabolomics_2020/raw/master/CBW_NMR_set_of_8_spectra.zip)
+ - Bayesil profiling results that could be used to generate input for Metaboanalyst [CBW_NMR_result](https://github.com/bioinformaticsdotca/Metabolomics_2017/raw/master/CBW_NMR_result.zip)
+ - The 40-spectra dataset that were used to obtain the results above [CBW_NMR_full](https://github.com/bioinformatics-ca/Metabolomics_2020/raw/master/CBW_NMR_full_dataset.zip)
+
+##### GCMS (GC-Autofit):
+
+**Example datasets (mzXML.zip files)**
+
+Download this file: [GC_autofit.zip](https://drive.google.com/a/bioinformatics.ca/file/d/1ZIPj5jVWYUG-LMB3-19Uy3EI9RLn_IDM/view?usp=sharing)  
+
+##### LC-MS (MetaboAnalyst):
+
+**Example datasets (mzXML.zip files)**
+
+Download this file: [ibd_data_cbw2020_updated.zip](https://github.com/bioinformatics-ca/Metabolomics_2020/blob/master/ibd_data_cbw2020_updated.zip)
+
+**Spectra processing with MetaboAnalyst (example result files)** 
+
+[- Peak Table](https://drive.google.com/open?id=10G4Vek0RAOR_Zb1CCGs9imFx1Beipvr_)
+
+[- Input for MS Peaks to Path](https://drive.google.com/open?id=1O6QCeBLJD8DWLuaDUnnVsLOyf8WwRlBw)
+
+[- Finished MetaboAnalyst spectral processing job](https://dev.metaboanalyst.ca/MetaboAnalyst/faces/Share?ID=_hkb08011a)  
+
+#### Links:
+
+ * [MetaboMiner](http://wishart.biology.ualberta.ca/metabominer/) 
+ * [rNMR](http://rnmr.nmrfam.wisc.edu/) 
+ * [BMRB Peaks Server](http://www.bmrb.wisc.edu/metabolomics/query_metab.php) 
+ * [BATMAN](http://batman.r-forge.r-project.org/) 
+ * [Bayesil](http://bayesil.ca/) 
+ * [Golm Database](http://gmd.mpimp-golm.mpg.de/) 
+ * [NIST/AMDIS](http://chemdata.nist.gov/) 
+ * [CFM-ID](http://cfmid.wishartlab.com/) 
+ * [Metlin](http://metlin.scripps.edu/upload.php/) 
+ * [MetFusion](http://msbi.ipb-halle.de/MetFusion/) 
+ * [Adduct Table](http://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator/) 
+ * [MZedDB](http://maltese.dbs.aber.ac.uk:8888/hrmet/search/genip.php) 
+ * [MWTWIN](http://www.alchemistmatt.com/mwtwin.html/) 
+ * [HighChem](http://www.highchem.com/formula-generator/) 
+ * [7GR Software](http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software/) 
+ * [MyCompoundID](http://mycompoundid.org/) 
+
+
+
+##  Module 3: Databases for Chemical, Spectral, and Biological Data  
+
+*<font color="#827e9c">David Wishart</font>*  
+
+Access Module 3's lecture [here](https://drive.google.com/file/d/1D4aP4ZJtC05X6Bcmim2K9HrEYOnPO4C8/view)  
+
+#### Links:
+
+ * [HMDB](http://hmdb.ca/) 
+ * [DrugBank](http://drugbank.ca/) 
+ * [METLIN](http://metlin.scripps.edu/) 
+ * [PubChem](http://pubchem.ncbi.nlm.nih.gov/) 
+ * [ChEBI](http://www.ebi.ac.uk/chebi/) 
+ * [ChemSpider](http://chemspider.com/) 
+ * [SDBS](http://sdbs.db.aist.go.jp/) 
+ * [BioMagResBank](http://bmrb.wisc.edu/metabolomics/) 
+ * [MMCD](http://mmcd.nmrfam.wisc.edu/) 
+ * [MassBank](http://www.massbank.jp/) 
+ * [BMRB](http://www.bmrb.wisc.edu/) 
+ * [NMRShiftDB](http://www.ebi.ac.uk/nmrshiftdb/) 
+ * [SMPDB](http://www.smpdb.ca/) 
+ * [KEGG](http://www.genome.jp/kegg/) 
+ * [Reactome](http://www.reactome.org/) 
+ * [BioCyc](http://biocyc.org/) 
+
+## (Optional) Lab Practical: Spectral Processing and Functional Analysis with MetaboAnalyst(R)
+
+ *<font color="#827e9c">Jeff Xia</font>*  
+
+This dataset was acquired using an UPLC-Q/E-ESI- in negative ionization mode. The 10 samples (per group) are a subset of a much larger study from [Lloyd-Price et al.](https://www.nature.com/articles/s41586-019-1237-9), and include fecal samples from patients with Crohn's Disease (CD, 4), healthy controls (4), and two quality controls. The [metadata](https://drive.google.com/open?id=1LK9zmXYoFG7DCPnptp3xAybUavmYqUkl) contains more sample information. Using the MetaboAnalyst [web service](https://dev.metaboanalyst.ca/) or [MetaboAnalystR](https://dev.metaboanalyst.ca/docs/RTutorial.xhtml), process one of the example datasets below.
+
+ Full Metadata [here](https://drive.google.com/open?id=1LK9zmXYoFG7DCPnptp3xAybUavmYqUkl)    
+
+*Larger example datasets (mzXML.zip files) (Optional!! Intended only for Monday's evening session)*
+
+Download example data [here](https://drive.google.com/file/d/1VT1KOUMqvbS-To5qG0VPuUH2_4m3eNLN/view?usp=sharing) 
+
+Following spectra processing, use the [lab practical](https://drive.google.com/file/d/1BxbfJEbgqufhkBehBQgzwne3IryB9tbQ/view) and follow Protocol 9 on the resulting peak table to gain functional insights from the untargeted metabolomics data.  
+
+# Day 2 <a id="day2"></a>
+
+##  Module 4: Backgrounder in Statistics 
+
+  *<font color="#827e9c">Jeff Xia</font>*
+
+  Access Module 4's lecture [here](https://www.dropbox.com/s/6eopm1qd3yj5t9d/CBW-Metabolomics4.1-2020_final_JX.ppt?dl=0) --- Updated slides [here](https://www.dropbox.com/s/6eopm1qd3yj5t9d/CBW-Metabolomics4.1-2020_final_JX.ppt?dl=0
+) 
+
+
+##  Module 5: MetaboAnalyst 
+
+  *<font color="#827e9c">Jeff Xia</font>*
+
+  Access Module 5's lecture [here](https://www.dropbox.com/s/st0cj934b23b2ea/CBW-Metabolomics5.1-2020_final_JX.ppt?dl=0) 
+
+  To understand how to use MetaboAnalyst, please follow the 11 protocols in this [lab practical.](https://drive.google.com/file/d/1BxbfJEbgqufhkBehBQgzwne3IryB9tbQ/view)  
+
+
+#### Data Input:
+
+Critical: Before uploading your data, perform a sanity check: 
+
+* Verify that it is a data table separated by commas (.csv) or tabs (.txt); 
+* For concentration/peak intensity tables: three types of labels should be present; feature names, sample names and group labels (must directly follow sample names);
+* All measurements should be numerical values (empty for missing values); 
+* For details and screenshot instructions, [click here](http://www.metaboanalyst.ca/faces/docs/Format.xhtml)
+
+* [Data 1](https://www.metaboanalyst.ca/resources/data/human_cachexia.csv) Metabolomic concentration table of 77 urine samples from cancer patients and healthy controls. Can be used for Protocols 1-5.  
+* [Data 2](https://github.com/jsychong/MetaboAnalystR/blob/master/MetaboAnalystR_2_Supplementary_Data/iHMP2_48_metaboanalyst_input.csv) Peak intensity table of 48 fecal samples from pediatric inflammatory bowel disease patients and healthy controls. Can be used for Protocols 1-3.
+* [Data 3](https://www.metaboanalyst.ca/resources/data/mummichog_ibd.txt) Peak list of 48 fecal samples from pediatric inflammatory bowel disease patients and healthy controls. Used for Protocol 9.
+* [Data 4](https://github.com/bioinformatics-ca/Metabolomics_2020/blob/master/ibd_peak_table.csv)
+Full peak intensity table of stool samples of CD (n = 266), UC (n = 144), and non-IBD (n = 135) obtained from [Lloyd-Price et al.](https://www.nature.com/articles/s41586-019-1237-9). [Full metadata here.](https://drive.google.com/open?id=1LK9zmXYoFG7DCPnptp3xAybUavmYqUkl) Can be used for Protocols 1-3.    
+
+
+
+##  Module 6: Future of Metabolomics 
+
+*<font color="#827e9c">David Wishart</font>*
+
+Access Module 6's lecture [here](https://drive.google.com/file/d/1X_1c77pxAeDBoguV_1qSOx4WBNII5E-y/view) 
+
+***
+
+##  Survey
+
+
+please take 2min of your time Thank you [here](https://forms.gle/GFkxPRMrPjo6LhiV7)
+
+***