Columbia University and The Broad Institute of MIT and Harvard caBIG® Molecular Analysis Tools Knowledge Center

Main Points What are caBIG, ESN, and Knowledge Centers Q: Should I explore it further afterwards What tools does the Molecular Analysis Tools Knowledge Center (MATKC) support Q: What do these tools do Q: Is there anything I can use What does the MATKC do to help you use the tools

caBIG Software Development Software tooling and infrastructure development is one critical aspect of caBIG Tools Organized by Scientific Domains Clinical Trials Management Systems Integrative Cancer Research In Vivo Imaging Tissue Banks and Pathology Tools Cross-Cutting Tools Architecture/caGrid Data Sharing and Intellectual Capital Documentation and Training Vocabularies and Common Data Elements The ESN was developed to support users of caBIG tools listed above Knowledge Centers Support Service Providers

Supported Tools geWorkbench ( desktop apphttp:// Component-based integrative analysis platform with 60+ components. Integration of large number of data domains (sequence, expression, literature, network, structure). GenePattern ( web apphttp:// Modular analysis platform for genomic data with ~120 components. Powerful scientific workflow framework, web-based. caArray ( web apphttp://caarray.nci.nih.gov/ Web and programmatically accessible array data management system. MIAME compliant. caIntegrator ( web apphttp://caintegrator-info.nci.nih.gov/ Novel informatics platform supporting translational informatics. Integration and aggregation of clinical, genomic, analysis data.

Integration of MATKC Tools Import Data Use Modules Gene Expression Analysis Sequence Analysis Structure Analysis SNP/CNV Analysis Proteomic Analysis SNP/CNV Analysis Sequence Analysis Gene Expression Analysis Gene Expression Data Network Analysis SNP/CNV Data Clinical Data Image Data Import Data

MATKC Mission Build Community Support end users Collect user feedbacks Cultivate community involvement Manage Knowledge Organize and enhance existing documentation Develop new searchable knowledgebase Develop Software Collect defects reports and feature request Fix defects and implement feature requests (on geWorkbench and GenePattern) Promote Tool Adoption Provide hands-holding training/tutoring sessions Develop training materials Give demos/exhibits/workshops

MATKC Team Columbia University Dr. Andrea Califano, MATKC co-Director Dr. Zhong Li, MATKC Operating Manager Dr. Aris Floratos, geWorkbench Lead Dr. Fan Lin, Documentation Mr. Michael Honig, System Administration Mr. Kiran Keshav, Technical Lead Dr. Ken Smith, Domain Expert Dr. Udo Tobben, QA/QC Dr.. Zhou Ji, Software Development The Broad Institute of MIT and Harvard Dr. Jill Mesirov, MATKC co-Director Mr. Michael Reich, GenePattern Lead Ms. Barbara Hill, QA Ms. Heidi Kuehn, Documentation Mr. Peter Carr, Software Development

MATKC Support Mechanisms The MATKC Forum Best way to share your issues and get fast response Very easy to make a post after getting a free account Help the community along the way The MATKC Wiki Up-to-date information on supported tools The rapidly growing knowledgebase answers a great majority of user questions You can make it better by adding new content or revise existing content Direct and Web Conference Can be arranged when necessary and when resource is available Workshops/Demos Pre-arranged

MATKC Forum

MATKC Forum Post Examples

Build Community: Forum Became the primary source of support to the community Sustained community participation/utilization Positive feedbacks from forum users

Build Community: Forum Forum NameNumber of TopicsNumber of Posts General Discussion1228 geWorkbench Users45110 geWorkbench Developers1435 caIntegrator Users1466 caIntegrator Developers11 caArray Users caArray Developers37141 GenePattern Users51190 GenePattern Developers42245 caIntegrator2 Users33 caIntegrator2 Developers11

MATKC End User Support: Wiki

Manage Knowledge: Knowledgebase Rich content FAQs as well as in-depth articles Recorded demos as well as ppt-based tutorials Relevant content Addressing questions raised in MATKC forums or from direct user interactions Easy to follow Narratives are taken from user’s prospective Concise and rich in graphics Steadily growing From 50 by June 2009 to 115 in Feb 2010 Get the users involved Give users the opportunity to add comments or suggestions while maintain the integrity of a government-owned web presence

MATKC Knowledgebase FAQs as well as in-depth articles Addressing questions raised in MATKC forums or from direct user interactions

Tying Knowledge Together

Manage Knowledge: Knowledgebase

Build Community: Open-Source Community Development Motivation: Significant community demand caBIG objective Activities caArray backend data import extension by Dr. Matt Eldridge at Cambridge Research Institute of Cancer Research UK Cultivate relationship Develop with the caArray team a code contribution/testing process Help testing the extension Facilitate the up-coming release caArray backend data upload extension by Dr. Umit Topaloglu’s team at University of Arkansas Medical Center Cultivate relationship Help address issues on integrating Matt’s code with UAMS’ code Facilitate the up-coming release caArray Nimblegen parser by Jim McCusker at Yale University Participated in program discussions GenePattern: contribution of suite of 29 flow cytometry modules by British Columbia Cancer Research Center GenePattern: source code requested by ~20 organizations for development of general and site-specific features, integration with internal resources, evaluation, and education

Develop Software Software Releases in Year 2 One major release for caArray One major release for caGWAS One major and one minor releases for caIntegrator2 Two major releases for geWorkbench One major and one minor releases for GenePattern Software Integration geWorkbench-caArray Integration GenePattern-caArray Integration GenePattern-caIntegrator2 Integration geWorkbench-caBIO Integration geWorkbench-GenePattern Interoperability

Tool Adoption: Promotion Interactions with caBIG Deployment Leads Meeting Exhibit and Presentations Exhibit and Demo at caBIG 2009 Annual Meeting Presentation at ISMB 2009 Presentation and workshop at MGED 2009 Workshops and Demos Hosted a Netherlands group site visit at Columbia Univ. GenePattern workshops at Harvard Medical School and Broad Institute (4) geWorkbench-caArray integration at caArray User Meeting caArray Demo to U. Chicago geWorkbench demo to Millennium Pharmaceuticals geWorkbench demo at ICR WS GenePattern demo at Broad Institute /phone-based Outreach

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