While large pharmaceutical firms aren't known for being generous with their data, a small group of pharma scientists is looking to change that perception with a call for pre-competitive bioinformatics projects and enhanced data sharing in the industry.
In an opinion piece published in the September issue of Nature Reviews Drug Discovery, computational biologists from AstraZeneca, GlaxoSmithKline, and Pfizer argue that "high-quality, open and accessible data are the foundation of pre-competitive research, and strong public-private partnerships have considerable potential to enhance public data resources, which would benefit everyone engaged in drug discovery."
They add that many companies are already beginning to embrace this idea, and that for some firms, "the focus has moved from the vigorous pursuit of intellectual property towards exploration of pre-competitive cross-industry collaborations and engagement with the public domain."
The paper comes in the wake of several initiatives that aim to encourage pharma scientists to open up a bit, including the non-profit Sage Bionetworks, founded by former Merck scientists, which plans to build a pre-competitive platform for annotated models of human disease; the cross-industry collaborative initiative Pistoia Alliance, which is developing standards for non-competitive aspects of the drug-discovery workflow; and the European public-private Innovative Medicines Initiative, a collaborative effort in which several pharmas are pooling resources in hopes of lowering the overall costs of drug development.
The borders around this emerging pre-competitive informatics space have yet to be defined, the authors of the Nature Reviews paper wrote, but noted that a first step is creating public-private partnerships that can expand on existing public resources to create "a series of foundational informatics resources."
In addition, pharma firms need to explore new types of IT infrastructure and tool development."
— Vivien Marx
Symyx Technologies established a new software research and development center in Bangalore, India. The company plans to hire 30 to 35 staffers for the center.
Clinical Trials & Surveys Corporation, a privately held clinical trials management firm, is set to make raw and processed genomic data available to clinical researchers as part of its StudyCTMS database. Under the program, C-TASC will accept gene data from investigators in either raw or processed format for upload.
Scientists at Virginia Tech will use a three-year, $1.4 million grant from the National Science Foundation to expand GenoCAD — a user-friendly software package that enables scientists to design genetic constructs using a genetic "parts list."
Amount the European Bioinformatics Institute received from the UK's Biotechnology and Biological Sciences Research Council
Text Mining Infrastructure for the Entire Biological Literature
Grantee: Gully Burns, University of Southern California
Began: Sep. 1, 2009; Ends: Aug. 31, 2012
This grant will fund the construction of SciKnowMine, a shared computational framework that "scales up processing large datasets across different communities through the automated mining of text, images, and other amenable media at the scale of the entire literature." The system will support the actions of bio-curators through a generic set of Web services that can be specialized.
Replica Exchange STMD for CHARMM: a Potentially Large Advance in Biophysical Computing
Grantee: Thomas Keyes, Boston University
Began: Sep. 1, 2009; Ends: Aug. 31, 2011
This award supports continued development of the CHARMM biosimulation application. The project aims to add the capability to use replica exchange statistical temperature molecular dynamics. The STMD algorithm and its extension to replica exchange "have substantially outperformed competing enhanced sampling algorithms in all tests," the abstract says.