introduction to genepattern

Introduction to GenePattern Rehan Akbani rakbani@mdanderson.org - PowerPoint PPT Presentation

Jun 16, 2023 •279 likes •395 views

Introduction to GenePattern Rehan Akbani rakbani@mdanderson.org Overview What is GenePattern and why do I care? 1. How do I convert my script into a GenePattern module? 2. How do I create customized GenePattern pipelines? 3. How do I share

  1. Introduction to GenePattern Rehan Akbani rakbani@mdanderson.org

  2. Overview What is GenePattern and why do I care? 1. How do I convert my script into a GenePattern module? 2. How do I create customized GenePattern pipelines? 3. How do I share my software/data with others? 4. How do I make my research reproducible using GenePattern? 5.

  3. What is GenePattern and why do I care?  GenePattern (GP) is server software created by the Broad Institute  What does it do? Browser based client side 1. Allows interoperability between software tools ( modules ) 2. Modules can be heterogeneous; using different languages and libraries 3. Easily converts a module into a web service 4. Allows the creation of workflows ( pipelines ) 5. Modules/pipelines can be called directly from Java, Matlab or R 6. Modules/pipelines can easily be shared 7. Allows reproducible research 8.

  4. What is GenePattern and why do I care?  TCGA will be using a GenePattern/Firehose pipeline to perform their monthly analysis runs (branded under NIH/NCI)  GP will allow MDACC GDAC Analysis group to easily share tools internally  GP server at Broad (free registration required): http://genepattern.broadinstitute.org/  MDACC local GP server behind firewall: http://mdadqsgdac1.mdanderson.edu:8080/gp/

  5. How do I convert my script into a GP module? Analysis Modules 1. Non-interactive, command line based  Runs on the GP server  Visualization Module 2. Can be interactive  Runs on client’s machine using Java applets 

  6. How do I convert my script into a GP module?  Write a command line tool using any language  Read/write input/output files from the current working directory  Write messages to standard error and standard output  Read module data files from <libdir>  Read and write standard GenePattern file formats (e.g. gct, res, odf)  Use command line parameter flags, instead of location  Avoid absolute pathnames  Ref: http://www.broadinstitute.org/cancer/software/genepattern/tutorial/ gp_programmer.html#_Writing_Modules_for_GenePattern

  7. How do I convert my script into a GP module?  Install your module into GP (if you have access rights) e.g. invocation: <perl> <libdir> myProg.pl -F <input.filename> -o <output.file>  Click “Modules & Pipelines” - >”New Module”  Easily possible in MDACC GP , but not Broad due to access rights  Decide if you want it to be public or private  Ref: http://www.broadinstitute.org/cancer/software/genepattern/tutorial/ gp_web_client.html#creating_tasks

  8. How do I create customized GP pipelines? Input File(s) Module 1 Module 2 Output File(s) … GP Pipeline  See demo

  9. How do I share my software/data with others?  See demo

  10. How do I make my research reproducible using GP?  Jill Mesirov , “Accessible Reproducible Research,” Science, 22 January 2010: Vol. 327. no. 5964, pp. 415 – 416 Reproducible Research System (RRS) Reproducible Research Reproducible Research Publisher (RRP) Enviroment (RRE) e.g. MS Word GP plugin, e.g. GenePattern, R SWEAVE

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