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bioinformatics_for_biologist_workshop [2018/06/25 15:25] (current)
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 +**Objectives**\\ This workshop is a practical introduction to some basic bioinformatics tools for audience with little computational skills. The participants will have hands-on experience with simple, toy-example data.\\ \\ 
 +===== Design =====
 + Each participant is expected to bring a laptop or have access to a computer during the workshop. They install [[http://​environmentalomics.org/​bio-linux/​|Bio-Linux]] on their computes, which facilitates running simple analysis on toy-example data. To save time, each participant is provided with a USB flash drive that contains necessary files for installing Bio-Linux and also some example data.\\ [[/​file/​view/​usb_workshop.jpg|{{::​usb_workshop.jpg?​nolink&​132}}]]\\ \\ 
 +===== Slides and material =====
  
 +  - Guidelines for installing BioLinux on Mac OS X or Windows using a virtual machine [{{ :​biolinux_vm.pptx|ppt}},​ {{ :​biolinux_vm.pdf|pdf}}].
 +  - The [[/​file/​view/​workshop.zip/​567529515/​workshop.zip|zipped]] folder for session 1, includes sample data, a script for installing Salmon on BioLinux, a cheat [[/​file/​view/​cheat_sheet_workshop1.txt/​567529053/​cheat_sheet_workshop1.txt|sheet]],​ etc.
 +  - The main presentation in session 1:\\ Part 1: BioLinux and Mapping RNASeq (Samlon) [{{ :​bioinformatics_for_biologists_workshop_part1_v2.pptx|ppt}},​ {{ :​bioinformatics_for_biologists_workshop_part1_v2.pdf|pdf}}]\\ ​ Part 2: R and Differential expression analysis (DESeq2) [{{ :​bioinformatics_for_biologists_workshop_part2_v2.pptx|ppt}},​ {{ :​bioinformatics_for_biologists_workshop_part2_v2.pdf|pdf}}]\\ Part 3: Finding gene homologs (Ensembl Biomart) and Pathway and network analysis (GeneMANIA & InnateDB) [{{ :​bioinformatics_for_biologists_workshop_part3_v2.pptx|ppt}},​ {{ :​bioinformatics_for_biologists_workshop_part3_v2.pdf|pdf}}]
 +  - The [[/​file/​view/​workshop2.zip/​578335687/​workshop2.zip|zipped]] folder for session 1, includes sample protein MS [[/​file/​view/​protein_MS.xlsx/​578335701/​protein_MS.xlsx|data]],​ a cheat [[/​file/​view/​cheat_sheet_workshop2.txt/​578335697/​cheat_sheet_workshop2.txt|sheet]],​ etc.
 +  - The main presentation in session 2:\\  Part 1: Pathway and functional analyses on protein MS results (String manipulation in R, InnateDB, MouseMine) [{{ :​bioinformatics_for_biologists_workshop_session2_part1.pptx|ppt}},​ {{ :​bioinformatics_for_biologists_workshop_session2_part1.pdf|pdf}}]\\ ​ Part 2: Sample size for RNA Seq experiments and DNA methylation (minfi) [{{ :​bioinformatics_for_biologists_workshop_session2_part2.pptx|ppt}},​ {{ :​bioinformatics_for_biologists_workshop_session2_part2.pdf|pdf}}]
 +\\ **Additional resources**\\ Similar workshops and online courses are listed at "How to begin [[|learning]] bioinformatics?"​\\ \\ 
 +===== Useful links =====
 +- Salmon [[https://​combine-lab.github.io/​salmon/​|webpage]]. It is useful for mapping and analyzing RNAseq data.\\ ​ - Titus Brown'​s [[https://​github.com/​ngs-docs/​2015-nov-adv-rna/​blob/​master/​README.md|tutorials]],​ more advanced RNAseq analysis using Salmon on Amazon Web Services.\\ ​ - A [[useful_tools_for_functional_and_pathway_analysis|collection]] of useful tools for functional and pathway analysis.\\ ​ - Stephen Turner'​s "​[[http://​www.gettinggeneticsdone.com/​2013/​04/​list-of-bioinformatics-workshops-training.html|List]] of Bioinformatics Workshops and Training Resources"​.\\ \\ 
 +===== Date and location =====
 + - The first session held on 20 Nov 2015 at the University of Texas Health Science Center - San Antonio.\\ ​ - The second session held on 25 March 2016 at the University of Texas Health Science Center - San Antonio.