March 9, 2012

Announcing CARLSBAD:

We are pleased to announce the upcoming release of CARLSBAD, a system for chemical pattern detection in biological networks, designed for drug- and probe-discovery research and related fields, and for use at no cost for academic and non-commercial research.  This initial release will coincide with the upcoming ACS meeting in San Diego (March 25-29).

What is CARLSBAD?

CARLSBAD = Confederated Annotated Research Libraries of Small-molecule BioActivity Data.   CARLSBAD is a database and knowledge inference system integrating multiple bioactivity datasets to provide chemical biology scientists with new ways to mine and explore available SAR (structure‑activity relationships) throughout chemical biology space. CARLSBAD integrates PubChem/MLP, ChEMBL, PDSP, IUPHAR-DB and WOMBAT in a unified schema. Advanced cheminformatics and pattern recognition algorithms combined with network analysis methodology enable inference of novel associations, via the powerful biological network visualization environment Cytoscape.  Currently, CARLSBAD contains 755,329 compounds, 3613 protein targets, and 1,449,924 activities.

Whence CARLSBAD?

CARLSBAD has been developed by the University of New Mexico Division of Biocomputing and funded by an NIH R21 award (PI Tudor Oprea).  The CARLSBAD team is:

  1. Jerome Abear
  2. Cristian Bologa
  3. Jarrett Hines-Kay
  4. Stephen Mathias
  5. Tudor Oprea
  6. Oleg Ursu
  7. Jeremy Yang
  8. Gergely Zahoransky-Kohalmi

Invitation to participate:

You are invited to participate in CARLSBAD as an early adopter and beta tester, by joining the CARLSBAD User Group.  CARLSBAD development continues and will be improved by expert feedback from users.   Your research may be advanced by CARLSBAD while your feedback can guide CARLSBAD development.

For more information:

For additional information, see the CARLSBAD Project home page at: http://carlsbad.health.unm.edu/.  The website includes:

  1. Documentation
  2. Example use cases (e.g. drug-repurposing)
  3. How to join CARLSBAD User Group
  4. Database inventory & methodology
  5. Links to online tools (for user group members).
  6. News
  7. Contact information

See CARLSBAD at ACS meeting:

The CARLSBAD system will be presented (by Gergely Zahoransky-Kohalmi) at the upcoming ACS National Meeting in San Diego, CINF session "Systems Chemical Biology", Tuesday, March 27th, San Diego Convention Center, Room 25C, at 2:30pm (organizers: Jan Kuras and Tudor Oprea).  We (Tudor Oprea, Jeremy Yang and Jarrett Hines-Kay) will also be available throughout that day to demo the system and answer questions.  Attendees who join the CARLSBAD User Group will be provided first access credentials for the online CARLSBAD system.  In the days following the meeting others who have registered online will be provided with access.

With Best Regards,

The CARLSBAD Team