January 12, 2010
For more information, please view the version release notes that are posted on the NPO project website, http://www.nano-ontology.org/documentation/version-release-notes/2010-10-31 .
The ICR Workspace is hearing reports on activities for the last period.
Ken Smith from the Molecular Analysis Tools Knowledge Center presented an update on geWorkbench, which is a platform for integrated genomics. A demo involving data from an ovarian cancer study highlighted features from the last two releases including BLAST tools, gene annotation, GO viewer, pathway visualization tools and more.
Ulli Wagner presented the website eMICE: electronic Models Information, Communication, and Education. It is a communication tool for the NCI Mouse Models of Human Cancers Consortium (MMHCC). Currently the program has a strong focus on education and the website was constructed to reach the broad spectrum of general audience to researcher. Mukesh Sharma reported in on the recent HL7 Meeting. He gave a review of Clinical Genomics working group activities in the three different tracks. He reported in on the discussion of the generic assay model which was developed as part of a caBIG ICR Information Representation Working Group collaboration with HLy Clinical Genomics Working Group.
Rashmi Srinivasa polled the workspace on interest in generic assay management. She provided an update on caArray which included features anticipating handling next generation sequencing data such as: the ability to handle fastq and BAM/SAM files, the ability to move and store large volumes of data. There were also security and technology stack related updated. Rashmi also presented Annotare which provides templates and tools to annotate MAGE-TAB experiments.
Karen Ketchum provided an overview of caIntegrator, a tool that provides the ability to develop web portal without software skills and allows you to import your data and query it. NCI hosts 5 studies in the caIntegrator platform. Newest features include enhancements to subject annotation interface, list management, upgraded connectivity to the NBIA, external links, expanded microarray platform support and copy number analysis capabilities. The call was closed out with ICR Working Group Reports (LS SMEs, Nano WG, IRWG).
Jenny Kelley presented the features and functionalities under development for caLIMS2. The purpose of the caLIMS2 project is to create a Laboratory Information Management System (LIMS) that is interoperable within established caBIG® standards and guidelines and will track a complete laboratory workflow that uses materials from a specimen management service (e.g. caTissue) to generate experimental results for one of the caBIG® data management services (e.g. caArray). Core LIMS functions include the management of personnel, equipment, lab supplies and reagents, samples, laboratory workflow and experimentally derived metadata and data. caLIMS2 will complete the caBIG® bench to bed model by bridging the gap between biospecimen repositories, data repositories and analysis tools. Stephen Goldstein provided the Workspace with a demo on JIRA which is the NCI CBIIT's new issue tracking and project management tool. External users can log into JIRA to create issues and feature requests for specific products. Product teams can use JIRA to manage their development cycles. Testing teams can use JIRA to manage their testing efforts. And the Program team can use JIRA to create reports around issue lifecycles and development progress.
Liz Hahn-Dantona of the EVS team demonstrated how to access and use the NCI term browser, NCI thesaurus and NCI Metathesaurus. She described content in various tabs and pointed out features of interest. In preparation for the caBIG® Annual Meeting, Dr. Robert Freimuth created a 508 compliant presentation. He offered many helpful hints and his lively demonstration showed just how easy it is to create compliant presentations using layouts and alt text. Rashmi Srinivasa gave an overview of caArray. The caArray users meeting is now held in the ICR WS calls. Current features and those being added in the next release features were highlighted, including support for next generation sequencing experiments files FASTQ and BAM.