February 5, 2009 | NIH Launches Three Informatics Pilots to Aid Translational Research
The National Institutes of Health (NIH) has awarded three contracts for pilot projects to improve informatics support for researchers conducting small-to medium-sized clinical studies. The two-year contracts, which will total up to an estimated $4 million, represent collaborations among individuals at three or more institutions that receive NIH Clinical and Translational Science Awards (CTSA).
Administered by the National Center for Research Resources (NCRR), one of the CTSA program goals is to advance collaborations in clinical and translational research by interdisciplinary teams of investigators. These collaborations help enable the translation of rapidly evolving information developed in basic biomedical research into treatments and strategies to improve human health. The pilot projects will be led by Case Western Reserve University, Cleveland, Ohio; University of Washington, Seattle; and Vanderbilt University, Nashville, Tenn. Full project descriptions provided by each lead institution, as well as a list of project partner institutions, are available at www.ncrr.nih.gov/ctsa/informatics. Read release.
An Open Access Database of GWA Results
Researchers Andrew Johnson and Christopher O’Donnell report collecting, “results from 118 GWAS articles into a database of 56,411 significant SNP-phenotype associations and accompanying information, making this database freely available here. In doing so, we met and describe here a number of challenges to creating an open access database of GWAS results. Through preliminary analyses and characterization of available GWAS, we demonstrate the potential to gain new insights by querying a database across GWAS.” Their report appears in BMC Biomedical Genetics. Read report.
Rewrite the Textbooks: Transcription is Bidirectional
Genes that contain instructions for making proteins make up less than 2% of the human genome. Yet, for unknown reasons, most of our genome is transcribed into RNA. The same is true for many other organisms that are easier to study than humans. Researchers in the groups of Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and Wolfgang Huber at the EMBL Bioformatics Institute in Hinxton, UK, have unravelled how yeast generates its transcripts and have come a step closer to understanding their function. The study, published online in Nature, redefines the concept of promoters [the start sites of transcription] contradicting the established notion that they support transcription in one direction only. Read release.
Ingenuity and Sigma-Aldrich Team Up on Portal
The two companies launched Your Favorite Gene powered by Ingenuity, a Web-based biological search portal for exploring dynamic gene-based content (http://www.sigma-aldrich.com/yfg). Based on Ingenuity's extensive library of research findings, Your Favorite Gene powered by Ingenuity positions Sigma-Aldrich's life science products within a content-rich environment of relevant biological and chemical information. The Web site also provides researchers with the capability to model and evaluate prospective experiments in the context of previously published scientific literature. The new portal is built upon Sigma-Aldrich's leading Your Favorite Gene search engine, and incorporates Ingenuity's Knowledge Base. Read release.
IBM Pushes Cloud Computing Initiative
IBM announced it is working with six universities to leverage IBM Blue Cloud solutions to speed up projects and research initiatives that were once constrained by time, limited or unavailable resources, or overloaded IT systems. The Qatar Cloud Computing Initiative, driven by three universities, will open its cloud infrastructure to local businesses and industries to test applications and complete various projects, including seismic modeling, computational biology, and the exploration for oil and gas. Read article.
Entelos Inks GSK Deal
GlaxoSmithKline signed an agreement to use Entelos’ Hematopoeisis PhysioLab platform, a computer model that can simulate the complex biology of anemic patients and large “virtual patient populations” to predict responses to drugs. Entelos says the Hematopoeisis PhysioLab has been used successfully by other pharma partners to assess the safety and efficacy of biologics, find the best doses for specific patient types, and optimize complicated, adaptive clinical trial designs. This is “the third in a series of projects we have conducted across multiple therapeutic areas for GSK,” according to James Karis, CEO of Entelos
Separately, Entelos announces the Imperium Master Fund acquired a total of 3,990,537 shares of Entelos’ common stock in December 2008. Imperium now holds 6.1% of the issued and outstanding common stock in Entelos and is, as such, a significant shareholder for the purposes of the AIM Rules for Companies. Read Entelos press releases.
Genedata and Roche Extend Proteomics Collaboration
Genedata, a provider of in-silico solutions for pharmaceutical R&D, announced a three-year license extension with Roche for the Refiner MS module of the Genedata Expressionist biomarker discovery system. Refiner MS solves key requirements of large-scale proteomics and metabolomics facilities that need to efficiently process, analyze and store mass spectrometry (MS) data. Read release.
You've Got Email -- A Human Genome
A new report published in the open-access journal Bioinformatics describes a method of compressing a whole human genome sequence into a file sufficiently small to serve as a standard email attachment. The work was published by Scott Christley, Yiming Lu, Chen Li and Xiaohui Xie at the University of California, Irvine. Read Bio-IT World article.
Genomatix Joins Illumina-Connect Program
Genomatix Software joined the Illumina-Connect program working to develop new tools and applications for Illumina-generated data. Read release.
TCAG deploys Genologics LIMS
The Centre for Applied Genomics at The Hospital for Sick Children is deploying Genologics’ lab and data management solution across multiple facilities of its genome centre. The GenoLogics solution will be deployed for TCAG’s Microarray Analysis and Gene Expression Facility, DNA Sequencing and Synthesis Facility, Cytogenomics and Genome Resources Facility and Genetic and Statistical Analysis Facility.
“We required a single LIMS that was flexible enough to automate data capture and workflows for each service provided, while still being able to integrate billing, reporting and sample tracking across the entire operation“, said Steve Scherer, Director of The Centre for Applied Genomics. “The solution from GenoLogics was the only one with proven capabilities to integrate data across the multiple platforms we use, while also meeting our need to effectively and efficiently serve customers around the world.” Read release.
LabVantage Ehances Links to SAP ERP
LabVantage reported enhancing the certified integration of LabVantage Sapphire LIMS with SAP’s ERP application. SAP NetWeaver technology platform powers the SAP Business Suite family of applications and solutions such as LabVantage Sapphire. SAP NetWeaver unifies integration technologies into a single platform and is pre-integrated with business applications, enabling change and reducing the need for custom integration. The SAP Integration and Certification Center (SAP ICC) has certified that the exchange infrastructure content "Package for LabVantage Sapphire Enterprise Connector R5" for the product LabVantage Sapphire R5 integrates with SAP NetWeaver PI 7.0 via the SAP integration scenario SAP NetWeaver – Exchange Infrastructure Content 3.0 (NW-XI-CNT). Read release.
AccelerEyes Launches GPU Engine for MATLAB
HPCWire report the nascent GPGPU computing world received another boost today with the commercial release of Jacket 1.0, a GPU engine for MATLAB. Jacket was developed by AccelerEyes, a two-year-old Atlanta-based startup that was founded by Georgia Tech grad John Melonakos, who also runs the company. AccelerEyes aims to tap into the enormous user base of engineers and scientists currently using MATLAB, but who would like to take advantage of the latest GPU hardware to accelerate computing and visualization. Read article.
Merck Poaches Star Cancer Specialist from Harvard
“Obama isn’t the only one stealing talent from Harvard. Merck has bagged D. Gary Gilliland, a prominent Harvard cancer scientist, to head the company’s research into new cancer drugs,” according to a report in the Wall Street Journal. WSJ calls Gillilan, “A star among cancer specialists,Gilliland (pictured) is pioneering research into the genetic underpinnings of leukemia and into therapies targeting those molecular roots. His hiring may raise the competitive juices of other big drugmakers that, like Merck, have stepped up their own pushes into cancer treatments.” Read article.
UCLA Tool Predicts How a Chemotherapy Drug Will Work on Individual Tumor
For many cancer patients, chemotherapy can be worse than cancer itself. UCLA scientists have tested a non-invasive approach that may allow doctors to evaluate a tumor's response to a drug before prescribing therapy, according to a report in PNAS.
"For the first time, we can watch a chemotherapy drug working inside the living body in real time," explained Dr. Caius Radu, a researcher at the Crump Institute for Molecular Imaging and assistant professor of molecular and medical pharmacology at the David Geffen School of Medicine at UCLA. "We plan to test this method in healthy volunteers within the year to determine whether we can replicate our current results in humans."
In an earlier study, Radu and his colleagues created a small probe by slightly altering the molecular structure of gemcitabine, one of the most commonly used chemotherapy drugs. They labeled the probe with a special tag that enabled them to watch its movement throughout the body during imaging. Read article.
This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. Click here for a free subscription.