CARLSBAD News

The Division of Biocomputing (P.I., Tudor Oprea) has been awarded a two-year NIH grant (R21 award 1R21GM095952-01) for development of a database system integrating multiple bioactivity datasets to provide biomedical scientists with new ways to mine and explore available SAR (structure-activity relationships) throughout chemical biology space. The new database, CARLSBAD (Confederated Annotated Research Libraries of Small molecule BioActivity Data) integrates PubChem, ChEMBL, PDSP, IUPHARDb and other datasets in a unified schema. Advanced cheminformatics and pattern recognition algorithms enable knowledge discovery by domain scientists in convenient, robust, and interoperable ways, including the powerful biological network visualization environment Cytoscape.

Date Milestone
Dec 2010 NIH R21 grant award notification.
Jan 2011 Work begins: database schema, data acquisition and integration, software method implementation.
Jan 2011  Many "data wrangling" issues to be resolved.  Each source database has its peculiarities and challenges.
Feb 2011 HierS scaffold code rewritten in Java with ChemAxon JChem.
Mar 2011 Initial db version includes IUPHARdb and Wombat.  PDSP is next.
Apr 2011 MCES and scaffold data loaded.
Apr 2011 Sub-net extraction code and web app developed ("SNAKE").  XGMML can be imported by Cytoscape.
May 2011 Evaluation of application for biomedical research can begin, along with progress withCytoscape expertise. 
Aug 2011 Presentation of CARLSBAD at q-bio computational biology conference in Santa Fe by Tudor Oprea, Jeremy Yang and Gergely Zahoransky-Kohalmi.
Sep 2011 PDSP data integrated and loaded.
Oct 2011 ChEMBL data integrated and loaded.
Nov 2011 PubChem MLP data integrated and loaded.
Jan 2012 CytoscapeWeb v1.0 released and integrated by SNAKE web app for rapid and convenient network analysis.
Feb 2012 Carlsbad database search web app developed for target/compound data exploration and inclusion in suite of tools. Documentation and community website efforts increased.
March 2012 CARLSBAD Project presented at the OpenEye CUP XIII Meeting in Santa Fe (poster session), March 5.
March 2012 CARLSBAD announcement (March 9) posted to CHMINF-L and selected others. The CARLSBAD Project Homepage goes live.
March 2012 CARLSBAD presented at "Systems Chemical Biology" CINF session at ACS National Meeting in San Diego, organized by Jan Kiras and Tudor Oprea, March 27, 2012.
April 2012 CARLSBAD User Group receives login credentials; beta system, as presented at the ACS meeting, goes live.
April 2012 CARLSBAD presented at UNM Drug Discovery Day (1 day research conference)
May 2012 CARLSBAD update released, including ChemBL v13, PubChem updates, IUPHAR corrections, composite activity values, and scaffold association weighting.
Aug 2012 CARLSBAD to be presented at The Sixth q-bio Conference, Santa Fe, NM.
Aug 2012 CARLSBAD to be presented at 34th Annual International IEEE EMBS Conference, (Engineering in Medicine and Biology Conference), San Diego, CA.


CARLSBAD Project, UNM Division of Biocomputing
Last revised: Feb 27, 2012