no way to compare when less than two revisions

Differences

This shows you the differences between two versions of the page.


Last revision
bioinformatics_for_biologist_workshop [2018/06/25 12:25] – external edit 127.0.0.1
Line 1: Line 1:
 +**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.