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.
Additional information is also found on the Molecular Analysis Knowledge Center site.
Open Development and Community Projects Speaker Series
ICR WS Teleconference Speakers
The Integrative Cancer Research (ICR) Workspace is hosting a series of speakers on various open development and community driven projects. While the applications may be of greatest interest to ICR, the conversations about success factors for these types of projects is of general interest to the caBIG community. Meeting minutes are posted below.
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/
- June 22
- BioPAX and GeneMANIA; Gary Bader, U. of Toronto
- I SPY/ Transcend; Sarah Davis, UCSF
- July 13
- Protein Ontology; Cecilia Neomi Arighi, U. of Delaware
- Data standards and the Cardiovascular DAM at Duke University; Sal Mungal, Duke University
- July 27
- SBML: Systems Biology Markup Language – Mike Hucka, California Institute of Technology
- Aug 24
- HL7 Clinical Genomics Working Group: Amnon Shabo, Head of the Healthcare and Life Sciences Standards Program, IBM
- Sept 14
- eagle-I consortium and their research resource discovery network for biomedical scientists: Carlo Torniai, Oregon Health and Science University
- GMOD ( Generic Model Organism Database) project: Scott Cain, The Ontario Institute for Cancer Research
- Sept 28
- NCBO Organization and Outreach; Ray Fergerson - NCBO Project Director, Stanford University
- Oct 12
- GenomeSpace – Michael Reich, Broad Institute
- Oct 26
- OBI (The Ontology for Biomedical Investigations), an international project developing an integrated ontology for the description of life-science and clinical investigations. - Jennifer Fostel, NIEHS
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.
*Nanotechnology Expert Dr. Stacey Harper Awarded $1.9 Million NIEHS Grant *
This new, five-year grant will provide extended research support to allow Dr. Harper of Oregon State University to continue to develop one of the nation’s leading programs to test the safety of compounds created through nanotechnology. While Dr. Harper has many credits to her name and too many accomplishments to list here, we want to congratulate her on this latest achievement , and we look forward to continuing to work with Dr. Harper through the caBIG^®^ Nanotechnology Working Group. Please join us in congratulating Dr. Harper on this truly outstanding achievement and wish her continued success in her research endeavors.
The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations
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.
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.
Amnon Shabo (slides on request email@example.com) spoke about the HL7 Clinical Gemonics Work Group - From Healthcare to Research.
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).
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.
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.
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).
The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively.
The ICR participants presented on their assigned projects.
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.
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
caArray Users Meeting featured upcoming plugin architecture for support the addition of new parsers and data storage mechanisms.
Jenny Kelley, NCI Population Sciences, updated the community on caLIMS v2 new features. She also provided a thorough demonstration of the tool.
The ICR Workspace is hearing reports on activities for the last period.
Looking for older notes? Access ICR Meeting Notes Archive