- Analytical Services Best Practices (ASBP)
- ICR Interoperability (ICRi)
- [Workflow (WFWG)]
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
Recent News
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.
Teleconference Materials
The meeting Date is hyperlinked to the notes and hyperlinks in the Executive Summary are for specific presentations
Date |
Executive Summary |
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[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. |
[August 24, 2011, 2-4 PM Eastern|^20110824_ICR_WS_Mtg_Notes.doc] |
Amnon Shabo 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 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). Mike’s presentation is available on request efreund@3rdmill.com |
[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. |
[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. |
[June 22, 2011, 2-4 PM Eastern |^20110622_ICR_WS_Mtg_Notes-1.doc] |
[Gary Bader|ICR:ICR Wiki Home Page^2011Jun22_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. |
[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 |
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Mark Bray |
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Rashmi Srinivasa |
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The ICR workspace heard reports on the recent BioIT and AACR meetings from Mark Adams (BAH) and Jens Poschet (Sapient) respectively. Jason Hipp |
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The ICR participants presented on their assigned projects. Jim McCusker |
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Alex Kanous |
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Anton Nekrutenko |
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caArray Users Meeting |
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Jenny Kelley |
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The ICR Workspace is hearing reports on activities for the last period. |
Looking for older notes? Access ICR Meeting Notes Archive
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