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bioinformatics_for_biologist_workshop [2019/11/14 20:40] – [Useful links] adminbioinformatics_for_biologist_workshop [2024/12/11 20:24] (current) – [Objectives] habil
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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.\\ \\ +====== Bioinformatics for biologist workshop ====== 
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 +===== Objectives ===== 
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 +\\ 
 +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. The following material was used in 2015 in two sections of the workshop in The University of Texas Health Science Center at San Antonio. 
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 +======   ====== 
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 ===== Design ===== ===== 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}}]]\\ \\ + 
 +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|usb_workshop.jpg}}]] 
 ===== Slides and material ===== ===== 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}}]. +  - 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 [[: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 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 [[: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}}] +  - 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?"\\ \\ + 
 + \\ **Additional resources** \\ Similar workshops and online courses are listed at "How to begin [[:bioinformatics_for_biologist_workshop|learning]] bioinformatics?" \\ 
 ===== Useful links ===== ===== Useful links =====
  
-- Salmon [[https://combine-lab.github.io/salmon/|webpage]]. It is useful for mapping and analyzing RNAseq data.\\ +- 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.\\ +- 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.\\ +- 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".\\ +- Stephen Turner's "[[http://www.gettinggeneticsdone.com/2013/04/list-of-bioinformatics-workshops-training.html|List]] of Bioinformatics Workshops and Training Resources". \\ 
-- Evelien Bunnik had a workshop on multiomics data analysis in Spring 2020 in UTHSC-SA.\\+- Evelien Bunnik had a workshop on multiomics data analysis in Spring 2020 in UTHSC-SA. \\
 - Dhireesha Kudithipudi, the director of the Neuromorphic AI Lab, organized an AI [[http://research.utsa.edu/event/aisummit1/|Summit]] at UTSA in Nov 2019. - Dhireesha Kudithipudi, the director of the Neuromorphic AI Lab, organized an AI [[http://research.utsa.edu/event/aisummit1/|Summit]] at UTSA in Nov 2019.
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 ===== Date and location ===== ===== 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.+ 
 +- 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. 
 +