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December 14, 2011 (20111214_ICR_WS_Mtg_Notes.doc)
John Speakman, Chief Program Officer, Center for Biomedical Informatics and Information Technology, National Cancer Institute, provided a caBIG® Program Update
Dr. Douglas Hinerfeld (caBIG talk-Hinerfield 508.pptx), Associate Director, Molecular Phenotyping Sciences from the Jackson Laboratory, talked about Next Generation Sequencing pipelines at The Jackson Laboratory.
November 8, 2011 (20111109_ICR_WS_Mtg_Notes.doc)
Dr. David Wheeler (dw-cabig-tele-9nov11508.pptx), Director of cancer genomics and Assistant Director of the Baylor College of Medicine's Human Genome Sequencing Center, spoke about approaches and challenges with next generation sequence data analysis pipelines.
Dr. Aris Floratos, Executive Director of the Columbia University Center for Computational Biology and Bioinformatics talked about the Columbia In Silico Center of Research Excellence (ISRCE) and their work on the algorithms they have developed for mapping molecular and regulatory interactions for several human malignancies (slides on request email@example.com).
October 26, 2011 (20101026_ICR_WS_Mtg_Notes.doc)
Jennifer Fostel (OBI_CEBS.pdf) presented the Ontology for Biomedical Investigations (OBI). The OBI project is developing an integrated ontology for the description of life-science and clinical investigations. OBI is built using BFO principles and provides terms for annotation of biomedical investigations, regardless of the particular field of study.
Stuart Jefferys (caBig-export.pdf) of UNC discussed SeqWare, open source software to process and summarize sample sequence data for large projects.
October 12, 2011 (20111012_ICR_WS_Mtg_Notes.doc)
- Sherri Decoronado (no slides) spoke about the NCI Provocative Questions. This is a list of important but non-obvious questions that will stimulate the NCI’s research communities to use laboratory, clinical, and population sciences in especially effective and imaginative ways.
- Zhong Li (ICR_WS_Meeting_2011_10_12 MATKC wiki.pptx) highlighted the new Molecular Analysis Tools Knowledge Center wiki which provides centralized, authoritative repository of knowledge, information, and web-based support to facilitate the deployment and ongoing development of caBIG® tools, standards, and infrastructure in the molecular analysis domain. Tools supported are caArray, caIntegrator, GenePattern and geWorkbench.
- Rashmi Srinivasa (caArray4ICR_WS_Meeting_2011_10_12.pptx) provided an update on caArray, the array data management system.
- Michael Reich (slides on request firstname.lastname@example.org) presented GenomeSpace, a community space for creating and sharing genomic analysis tools (It is seeded with with six popular genomics tools (Cytoscape , Galaxy , GenePattern , Genomica , Integrative Genomics Viewer (IGV) , and the UCSC Browser ).
September 28, 2011 (20110928_ICR_WS_Mtg_Notes.doc)
Dr. Ray Fergerson (2011 NCBO Organization and Outreach_508.pptx) is from the Stanford Center for Biomedical Informatics Research and is the NCBO Project Director. He is one of the developers of the Protégé OWL plugin. He spoke about the NCBO organization, outreach and factors for success.
Mukesh Sharma (no slides) from Washington University at St. Louis is the IRWG Liaison to the HL7 Clinical Genomics Work Group (HL7 CG WG). He reported in on the HL7 CG WG F2F meeting held in the context of the HL7 meeting in San Diego.
September 14, 2011 (20110914_ICR_WS_Mtg_Notes.doc)
Carlo Torniai (Torniai_eagle-i_508.pptx), an ontologist from Oregon Health and Science University, spoke on the eagle-I consortium and their research resource discovery network for biomedical scientists.
Scott Cain (caBIG GMOD talk_508.ppt), from The Ontario Institute for Cancer Research, presented the GMOD ( Generic Model Organism Database) project. GMOD is a collection of interoperable open source software tools for creating and managing genome-scale biological databases, including individual or web-accessible database creation, visualizing, annotation.
Baris Suzek (091411_CrowdSourcing_presentation_ICRWS_508.ppt) from Georgetown University reported on the recent meeting “Crowdsourcing: The Art and Science of Open Innovation”
August 24, 2011, 2-4 PM Eastern (20110824_ICR_WS_Mtg_Notes.doc)
Amnon Shabo (slides on request email@example.com) spoke about the HL7 Clinical Gemonics Work Group - From Healthcare to Research.
July 27, 2011, 2-4 PM Eastern (20110713_ICR_WS_Mtg_Notes.doc)
Mike Hucka (slides on request firstname.lastname@example.org) from Caltech spoke about SBML (Systems Biology Markup Language) as an open community standard initiative. SBML is a representation format, based on XML, for communicating and storing computational models of biological processes. Mike reviewed past, present and future directions for the community and provided lessons learned – what went right (involved actual stakeholders, addressed real needs -not perceived ones, transparent and inclusive process, etc.) and where there were challenges (testing, complexity creep, not formalizing processes sufficiently).
July 13, 2011, 2-4 PM Eastern (20110713_ICR_WS_Mtg_Notes.doc)
Cecilia Neomi Arighi (PROICR_Arighi_2011.pdf) from U of Delaware presented on Protein Ontology. (PRO) provides the ontological representation of proteins and protein complexes and shows the relationships between them. It encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). There is a website with extensive browse and search capabilities and includes additional annotations using other ontologies like Pfam and GO.
Sal Mungal (2011-07-13_CardiovascularDAM_v01.05.pptx) of Duke University talked about his work on promoting interoperability through the creation of a cardiovascular domain analysis model. This will be a component of their initiative to streamline all data collection and analysis through integration of data, annotations and analytical tools. The cardiovascular DAM uses at
June 22, 2011, 2-4 PM Eastern (20110622_ICR_WS_Mtg_notes-1.doc)
- Gary Bader (2100Jun22_caBIG_ICRcc.pptx) gave a presentation on BioPAX, a standard language that enables integration, exchange, visualization and analysis of biological pathway data. BioPAX underlies the integration of public database content in Pathwaycommons.org, which has a comprehensive directory of interaction and pathway databases as well as search, download and visualization tools (from Cytoscape). Dr. Bader also gave a demo of GeneMANIA, a tool to predict gene function, gene sets, pathway members, complexes etc. It draws data from Pathway Commons and uses a Cytoscape webservice for visualization. Pathway Commons and GeneMANIA (and Cytoscape) are built entirely on open source software.
- Sarah Davis (slides on request email@example.com) spoke about the I-SPY 2 TRIAL. It is a breast cancer adaptive clinical trial which uses a different (neoadjuvant) approach allowing them to: determine new therapeutic efficacy on a much shorter time scale; use findings to assign patients to appropriate treatment arms of the trial. The need to integrate molecular and imaging data from consortium participants required a new bioinformatics infrastructure known as TRANSCEND which makes use of several caBIG tools.
June 8, 2011, 2-4 PM Eastern (20110608_ICR_WS_Mtg_Notes.doc)
John Speakman (Speakman_CTMS_Program_Status_Futures_20110608 Final_508.ppt), NCI CBIIT CPO kicked-off the workspace call with a caBIG Program Update. Mike Smoot (caBIG_Cytoscape_talk_6-8-2011.pdf), UCSD, is lead developer for Cytoscape. He provided an overview of the Cytoscape software platform for visualizing molecular interactions and pathways and integrating these with annotations and data. His talk also focused on the active Cytoscape community.
Sunny Jansen (Sunny_jansen_NBIA_mouseGBM_update_ICR_508.ppt) is a researcher at the Mouse Cancer Genetics Program on the Ft. Detrick campus in Maryland. She is doing a mouse GBM study using caBIG tools such as NBIA and caIntegrator with imaging, pre-clinical and genomic data. Ravi Madduri (RaviSlidesGalaxyConference508.pptx) from Argonne National Lab will provide an update on his work with Galaxy. He was recently in the Netherlands at the Galaxy users meeting and presented his work on high throughput data and identity management in Galaxy.
May 25, 2011, 2-4 PM Eastern (20110525_ICR_WS_Mtg_Notes.doc)
Mark Bray (2011_05_18_CaBIGdraft.ppt in the archive) from the Broad Institute gave a presentation on CellProfiler. It is a tool which integrates various algorithms. It is capable of extracting measurements for every individual cell in an image-based screen, ranging from standard assays (e.g., cell count, size, per-cell protein levels) as well as more complex morphological assays (e.g., cell/organelle shape or subcellular patterns of DNA or protein staining).
Judith Blake (caBIGwebinarMay2011.pptx) from the Jackson Laboratory discussed the Gene Ontology (GO). GO provides a standardized representation of gene and gene product attributes and is comprised of a controlled vocabulary, gene product annotation data and tools to access and process the data (GO Browser and OBO ontology editor). GO is maintained by the GO Consortium which is comprised of organism and protein databases and the biological research community.
May 11, 2011, 2-4 PM Eastern (20110511_ICR_WS_Mtg_Notes.doc)
- Rashmi Srinivasa (ICR_WS_Meeting_2011_05_11.pptx) hosted a caArray Users Meeting. She discussed features of the upcoming 2.4.1 release and the plans for the following release.
- Grace Stafford (CBIIT-April-2011-1.pptx) provided an update on The Jackson Laboratory caBIG Deployment Implementation. This included the impact of next generation sequencing technologies on the computational core tool needs and requirements emerging from new projects.
- Ravi Madduri (no slides) provided a demonstration of caBIG workflows run using the Galaxy platform.
April 27, 2011, 2-4 PM Eastern (20110413_ICR_WS_Mtg_Notes (2))
The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively.
Jason Hipp (SIVQ-LCM+ICR-v7final-may13jh.pptx) of University of Michigan gave a presentation on the use of Laser Capture Microdissection in --omics research.
April 13, 2011, 2-4 PM Eastern (20110413_ICR_WS_Mtg_Notes (2).doc)
The ICR participants presented on their assigned projects.
Jim McCusker (LessonsLearned_caIntegrator_Yale.ppt), caIntegrator Community Contribution of Code, discussed his implementation experience and future recommendations.
Dennis Thomas (DGT-caBIG_ICR_WS-04-13-2011-Final.pptx), Extending the Use of the NanoParticle Ontology, addressed challenges for using NPO with nano-TAB and caNanoLab NPO for data annotation, semantic integration of data, unambiguous interpretation and data sharing.
Mukesh Sharma (CG_Update_To_ICR_WS_04132011a.ppt), HL7 Clinical Genomics WG, discussed “Considering changing mission and charter to reflect changing technology” and “Mission to include bridging semantics between clinical and research domains.”
Nathan Baker (ICR+Nanotechnology+Working+Group.ppt) reviewed the updates and future goals of the Nanotechnology Working Group.
Bob Freimuth (IRWG_110413_508.ppt), Information Representation Working Group, reviewed the activities and future recommendations for the period.
March 23, 2011, 2-4 PM Eastern (20110323_ICR_WS_Mtg_Notes.doc)
Alex Kanous (ICR+DSIC+032311.ppt) from the DSIC Knowledge Center provided a presentation on the electronic Data Use Agreement tool. The tool may be used for generating DUAs for outgoing data based on a catalog of standardized, modular contract clauses, each of which corresponds to one of the E-DSSF’s sensitivity ratings.
Joshua Phillips and Ravi Madduri (/icr_presentation_20110323.pdf) discussed the prototyping activities on workflows for caGrid 2.0. They described use cases and requirements for workflows, defining metadata needed for discovery, composition, and execution of workflows and their consideration of how best to use W3C technologies (e.g. RDF, SPARQL, SA-WSDL, inference). They also provided a demo of a workflow engine prototype based on SADI and Taverna.
Ken Quinn (RPCI_CDN_CDL.ppt) spoke about the Roswell Park deployment of caGrid technology and use of caB2B to do federated queries across disparate, decentralized heterogeneous databases and clinical systems to support non-interventional clinical research. He described the process and challenges including: gathering senior leadership support, understanding the myriad research databases, gaining technical expertise, lack of common vocabularies and the excellent collaboration and support provided by the caB2B knowledge center.
February 23, 2011, 2-4 PM Eastern (ICR_WS_Mtg_Notes.doc)
Anton Nekrutenko (Galaxy.pdf) and Daniel Blankenberg and of The Pennsylvania State University gave a presentation on Galaxy, an open-source next generation sequence (NGS) analysis software system. It addresses the need to empower the scientists without access to extensive infrastructure to do the analysis. Galaxy is a free web service, and has a plethora of analysis tools and has workflow generation capabilities
Stacey Harper (nanoTAB_briefing_508.ppt) gave a briefing on nano-TAB, a general purpose framework that provides a standard means to communicate nanomaterial data and metadata. The needs the data exchange format addresses and an overview of the file structure were discussed.
February 14, 2011, 2-4 PM Eastern (20110208_ICR_WS_Mtg_Notes.doc)
caArray Users Meeting (ICR_WS_Meeting_2011_02_09.pptx on SVN) featured upcoming plugin architecture for support the addition of new parsers and data storage mechanisms.
January 26, 2011, 2-4 PM Eastern (20110126_ICR_WS_Mtg_Notes.doc)
Jenny Kelley (caLIMSv2Update_ICR_26Jan11_final.pptx), NCI Population Sciences, updated the community on caLIMS v2 new features. She also provided a thorough demonstration of the tool.
The details on the upcoming release of caB2B in March were presented by Baris Suzek (01262011_caB2B_presentation.pdf) of Georgetown University. The tool will assist Bioinformaticians and Researchers discover and collect data on the Grid.
Nano WG (2011-01-26 ICR WS Nano WG update.ppt) and LS SME WG (ICR LS WG update 26Jan11.ppt) each presented an overview and current goals to the community.
January 12, 2011, 2-4 PM Eastern (20110112_ICR_WS_Mtg_Notes.doc)
The ICR Workspace is hearing reports on activities for the last period.
• Bob Freimuth (IRWG_110112_508.pptx on GForge) discussed IRWG work on the LS DAM Updates and additions to the model will appear in the next release. Work on the portion of the model shared with HL7 Clinical Genomics Working Group is extending the generic assay core to include concepts for gene variation.
• Dennis Thomas (DGT-caBIG_ICR_WS-01-12-2011-Final.pptx on GForge) reported on the processes to integrate the NanoParticle Ontology into the NCI Metathesaurus. This expands NPO accessibility and brings more semantics into the NCImt.