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The Integrative Cancer Research Workspace is producing modular and interoperable tools and interfaces that provide for integration between biomedical informatics applications and data. This will ultimately enable translational and integrative research by providing for the integration of clinical and basic research data. The Workspace is developing a software-engineered, well-documented and validated biomedical informatics toolset for use throughout the research community.

Workspace Logistics

General Workspace Meetings

  • 2nd & 4th Wednesdays of each month
  • 2:00 PM - 4:00 PM EST
  • Telecon:  Number 800-593-0616, passcode 2927756 #
  • Adobe connect http://cbiit.acrobat.com/icrws/

Additional information is also found on the Molecular Analysis Knowledge Center site.

Subscribe to the ICR listserv.

Upcoming Speakers

ICR WS Teleconference Speakers

Thank you very much for the many suggestions we received for ICR Workspace teleconference speakers.  Based on your feedback, here are the speakers and topics for our upcoming meetings:

  • Philippe Rocca-Serra, Oxford University, will provide a demo of ISA Tools.
  • April 25: TBD
  • May 9: Richard McCombie will talk about the Cold Spring Harbor Laboratory Genome Center
  • May 23: Sorena Nadaf will speak about USSF's application of NGS technology including data management, interoperability and secondary use of data.

You are welcome to join us on the 2nd and 4th Wednesdays of each month from 2:00 – 4:00 pm ET.

Teleconference information:  800-593-0616 passcode: 2927756
Adobe Connect: http://cbiit.acrobat.com/icrws/


Recent News

caBIG® Life Sciences Domain Analysis Model (LS DAM) v2.2.2 is Released



We are pleased to announce the release of the caBIG® Life Sciences Domain Analysis Model (LS DAM) v2.2.2. The LS DAM provides a shared view of semantics for the Life Sciences domain, which includes hypothesis-driven basic and pre-clinical research as well as discovery science.
The changes to the LS DAM in this release are described in the Release Summary and include

Changes to the Experiment Core for clearer alignment with the ISA-TAB standard and to address feedback from HL7 Clinical Genomics Work Group collaborators
Deletion of several classes determined not to be in scope of the model
Addition of an LS DAM Users Guide
Report and models from an LS DAM Ontological Representation Pilot project

For a complete list of modifications and additions to the LS DAM v 2.2.2, please see the Release Summary and Change List .  For an exemplar on how the Experiment Core of the LS DAM could be instantiated to support a sample scenario, please see the Experiment Implementation Guide.

The LS DAM v2.2.2 model is available in two formats:

An Enterprise Architect file may be downloaded LS DAM v 2.2.2 EA file
A web based view of the model is also available using Internet Explorer LS DAM v2.2.2 HTML

New Article: Informatics and Standards for Nanomedicine Technology



A recent focus article in “Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology,” explores nanotechnology and its impact on medicine and biomedical research, as well as the need for informatics standards in Nanomedicine.  To read more about how Nanotechnology has the potential to make medicine more personalized, predictive, and preemptive, click here.



Teleconference Materials

The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations

Date

Executive Summary

March 28, 2012

Rakesh Nagarajan (Washington University in St. Louis) gave a presentation on operations of the Wash U Genome Center. Kenneth Smith (Columbia University, NY) gave an update on new features in geWorkbench.

March 14, 2012

Guy Coates of the Wellcome Trust Sanger Institute will talk about the iRODS genomic data management system.

February 22, 2012

Dr. Deanna Church, NCBI project lead for the Genome Reference Consortium (GRC) and projects such as Map Viewer, Ideogram Service, Coordinate Remapping Service and CloneDB, spoke about The Human Reference Assembly and Resources for Navigating Genomic Information.
Dr. Nagarajan is the Director of the Cancer Center Bioinformatics Core and he described the MAGE-TAB export functionality that will be available in caTissue v2.0
Integration of caTissue and caArray using MAGE-TAB.

February 8, 2012

Susanna-Sansone and Philippe Rocca-Serra gave a presentation on the ISA Framework. They talked about ISA  as a successful community driven initiative (organizational model, success factors, lessons learned, funding, decision making and how prioritization decisions). They will also talk about the specification, tools, and newly launched commons. You can learn more about what they are doing in the Feb's Nature Genetics issue (http://www.nature.com/ng/journal/v44/n2/index.html); with the "It's not about the data" editorial and the ISA Commons' commentary "Toward interoperable bioscience data". Also nano-Tab/ISA-TAB-Nano is on the isacommons.org website.
Juli Klemm, ICR WS Federal Lead, talked about the newly launched caBIG® Community Code Resource Directory.

January 25, 2012

Presentations on working group reports concluded with reports from Mukesh Sharma and Jim McCusker. Mukesh Sharma participates in HL7 and is co-leading an effort on an OMICS DAM for the Clinical Genomics Work Group and he discussed their progress. Jim McCusker participates in W3C in the Health Care and Life Sciences (HCLS) and Provenance Interest Groups. HCLS is building a Translational Medicine Ontology (TMO) and Knowledge Base and the Provenance group is interested in defining a language for exchanging provenance information among applications.

January 11, 2012

Dr. Dan Stanzione from the U of Texas at Austin’s Texas Advanced Computing Center, spoke about iPlant.  iPlant Collaborative is a community of plant and computer scientists and educators developing an infrastructure of computing resources, interoperable analysis software and data services in a collaborative environment. iPlant activities and mission are shaped by community driven questions and requirements and resources are provided to advance the science being done by community members.
There were working group reports from Information Representation Working Group (IRWG) and Nanotechnology Working Group (Nano WG). The IRWG report was given by Robert Freimuth of Mayo Clinic and it included updates on the pilot project to generate an ontological representation of a portion of the Life Sciences Domain Analysis Model (LS DAM) and the model changes in response to feedback. The Nano WG report by Nathan Baker of PNNL, included an update on the nano-TAB data exchange format, expansion of the NanoParticle Ontology, and various outreach activities.

December 14, 2011

John Speakman, Chief Program Officer, Center for Biomedical Informatics and Information Technology, National Cancer Institute, provided a caBIG^®^ Program Update
Dr. Douglas Hinerfeld, Associate Director, Molecular Phenotyping Sciences from the Jackson Laboratory, talked about Next Generation Sequencing pipelines at The Jackson Laboratory.

November 8, 2011

Dr. David Wheeler, 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 efreund@3rdmill.com).

October 26, 2011

Jennifer Fostel 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 of UNC discussed SeqWare, open source software to process and summarize sample sequence data for large projects.

October 12, 2011

  • 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 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 provided an update on caArray, the array data management system.
  • Michael Reich (slides on request efreund@3rdmill.com) 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

Dr. Ray Fergerson 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

Carlo Torniai, 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, 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 from Georgetown University reported on the recent meeting “Crowdsourcing: The Art and Science of Open Innovation”

August 24, 2011, 2-4 PM Eastern

Amnon Shabo (slides on request efreund@3rdmill.com) spoke about the HL7 Clinical Gemonics Work Group -  From Healthcare to Research.

July 27, 2011, 2-4 PM Eastern

Mike Hucka (slides on request efreund@3rdmill.com) 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

Cecilia Neomi Arighi 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 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

  • Gary Bader 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 efreund@3rdmill.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

John Speakman, NCI CBIIT CPO kicked-off the workspace call with a caBIG Program Update. Mike Smoot, 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 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. RaviSlidesGalaxyConference508.pptx
Ravi Madduri 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 highthroughput data and identity management in Galaxy.

May 25, 2011, 2-4 PM Eastern

Mark Bray 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 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

  • Rashmi Srinivasa hosted a caArray Users Meeting. She discussed features of the upcoming 2.4.1 release and the plans for the following release.
  • Grace Stafford 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

The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively.
Jason Hipp of University of Michigan gave a presentation on the use of Laser Capture Microdissection in --omics research.

April 13, 2011, 2-4 PM Eastern

The ICR participants presented on their assigned projects.
Jim McCusker, caIntegrator Community Contribution of Code, discussed his implementation experience and future recommendations.
Dennis Thomas , 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 , 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 reviewed the updates and future goals of the Nanotechnology Working Group.
Bob Freimuth , Information Representation Working Group, reviewed the activities and future recommendations for the period.

March 23, 2011, 2-4 PM Eastern

Alex Kanous 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 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 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

Anton Nekrutenko 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 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

caArray Users Meeting featured upcoming plugin architecture for support the addition of new parsers and data storage mechanisms.

January 26, 2011, 2-4 PM Eastern

Jenny Kelley, 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 of Georgetown University. The tool will assist Bioinformaticians and Researchers discover and collect data on the Grid.
Nano WG and LS SME WG each presented an overview and current goals to the community.

January 12, 2011, 2-4 PM Eastern

The ICR Workspace is hearing reports on activities for the last period.
Bob Freimuth 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 reported on the processes to integrate the NanoParticle Ontology into the NCI Metathesaurus. This expands NPO accessibility and brings more semantics into the NCImt.

Looking for older notes?  Access ICR Meeting Notes Archive  Jan 2008 - Nov 2010

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