Page History

[April 27, 2011, 2-4 PM Eastern

https://wiki.nci.nih.gov/download/attachments/3833902/20110427_ICR_WS_Mtg_Notes.doc

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. In addition, 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.