GlaxoSmithKline Releases Cancer Cell Genomic Data via caBIG
GlaxoSmithKline said this week that it is releasing genomic profiling data for over 300 cancer cell lines via the National Cancer Institute's Cancer Biomedical Informatics Grid.
The data is from cell lines derived from a wide variety of tumors, including breast, prostate, lung, and ovarian cancers. It includes SNP profiling data for the cell lines generated using the Affymetrix GeneChip 500K Mapping Set and transcript profiling data generated using Affy’s U133 Plus 2.0 arrays.
“Cataloging this type of information in a network like caBIG leads to a ready-made body of biologic information that can be mined by all cancer researchers to further everyone's understanding of cancer,” said Richard Wooster, director of translational medicine oncology R&D at GSK, in a statement.
“In turn, we hope this data will further drive the identification of predictive biomarkers and lead to shorter, more directed clinical trials allowing us to bring drugs more quickly to patients who need them,” he said.
“We're excited about what this cancer cell data might provide to other researchers and we also hope it will be a catalyst for other organizations to follow the GSK example,” said Robert Clarke, professor of oncology and physiology and biophysics at the Lombardi Comprehensive Cancer Center, part of Georgetown University Medical Center and Georgetown University Hospital.
The data is freely available via caBIG’s caArray module here.
caBIG launches Enterprise Support Network’s First Service Programs
The National Cancer Institute is launching the first of a series of service programs for its Cancer Biomedical Informatics Grid Enterprise Support Network, or ESN, which supports and extends caBIG tools and infrastructure.
Through the ESN, external organizations — both academic and commercial — deliver knowledge management and support services in their particular areas of expertise.
The first programs awarded are five domain-specific Knowledge Centers, which are NCI-supported entities that form “the nucleus of an expanding research and clinical community around the specific domains in which they have expertise,” NCI said.
A Knowledge Center is a repository of knowledge and information about tools and technologies and will offer users technical and end-user documentation and up-to-date installation packages for caBIG tools. The centers will also administer open source development of caBIG tools, collect and monitor defect reports, feature requests, and end-user requirements, and also develop training programs.
The caBIG Knowledge Centers awarded are:
caGrid: Ohio State University and the Ohio State Comprehensive Cancer Center, with the University of Chicago and the Argonne National Lab. This center will develop caGrid, the software infrastructure set to connect cancer institutions across the country allowing them to securely share data.
Clinical Trials Management Systems: Duke University Comprehensive Cancer Center, with Robert H. Lurie Comprehensive Cancer Center at Northwestern University, Cancer and Leukemia Group B – Information Systems (GALGB-IS), and SemanticBits. This project will focus on developing caBIG’s clinical trials management system.
Molecular Analysis Tools: Columbia University’s Herbert Irving Comprehensive Cancer Center with the Broad Institute of MIT and Harvard. This project will develop geWorkbench, an open-source software platform for genomic data integration, and GenePattern, a software package for analyzing microarray data.
Tissue/Biospecimen Banking and Technology ToolsP: Siteman Cancer Center, Washington University at St. Louis. This center will develop caTissue, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation.
Vocabulary: Mayo Clinic with SemanticBits. This project will develop online resources to deliver vocabulary resources that will help others build their own interoperable tools and systems.
NCI said that it will shortly award an additional Knowledge Center for Data Sharing and Intellectual Capital to work on policy development in the areas of patient privacy protections and intellectual property interests.
Over the next few months, NCI will also announce specific support service providers selected for their “demonstrated ability to provide accurate and up-to-date support services for caBIG tools, standards, and infrastructure,” NCI said.
More information about the caBIG Enterprise Support Network can be found here.
SGI Forms Cross-Industry Program Linking Users to Accelerator Technology
SGI this week launched the SGI Accelerator Enabling Program, a collaborative initiative aimed to link high-performance computing users to accelerated technologies to “dramatically” boost the performance of their scientific applications.
Initial partners in the program include NVIDIA, XtremeData, PACT XPP Technologies, and ClearSpeed Technology. SGI said these firms will collaborate with software vendors and customers with the aim of determining “the optimal accelerator choice for specific scientific disciplines.”
Among these accelerator technologies are specialized processors, graphics engines, and other devices that increase the speed and performance of critical functions within an application and do so at a lower cost than a traditional scale-out, the company said.
The SGI Accelerator Enabling Program is targeted at bioinformatics, computational chemistry, weather and climate modeling, astrophysics, and other scientific applications, SGI said.
Fabrus Selects Core Informatics’ Core LIMS for Antibody Discovery
Core Informatics said this week that biotech startup Fabrus has chosen its Core LIMS after evaluating products from more than 30 LIMS vendors.
According to a statement from Core Informatics, Fabrus concluded “the flexibility of the Core LIMS and the customization services offered by Core Informatics provided the best fit” for its needs. Fabrus also appreciated the ease with which the tool could be integrated with its existing lab instrumentation, Core said.
Fabrus, the first occupant of Pfizer’s business incubator at the La Jolla Research and Development Center, will use the LIMS to manage the production, inventory, and screening of its antibody libraries.
Microsoft BioIT Alliance Adds KineMatik
KineMatik said this week that it has joined the Microsoft-led BioIT Alliance.
KineMatik markets eNovator, a software system that lets researchers manage their lab data through an electronic notebook and collect and share their data across groups.
The BioIT Alliance aims to enable the sharing of best practices in the biomedical area and to develop standards for data sharing.
U of Manchester Joins €170M European Biobank Venture
The University of Manchester said this week that it is joining the European Union’s €170 million ($266 million) plan to build infrastructure that links new and existing biobanks across Europe.
The university currently hosts the DNA Banking Network, a facility that manages samples from patients across the UK and associated data.
According to a statement from the university, the Centre for Integrated Genomic Medical Research, in the School of Translational Medicine is playing a key role in developing the Biobanking and Biomolecular Resources Research Infrastructure alongside scientists and funding agencies in other European member states.
The initial planning phase will last two years and cost €5 million. This phase of the project aims to address questions such as the degree to which physical buildings across Europe, a virtual infrastructure, or a combination of both, will best serve the project.
Tibco to Acquire Data Analysis Firm Insightful
Tibco Software is acquiring statistical software firm Insightful in a deal valued at approximately $25 million.
Insightful markets predictive analytics and reporting software for statistical data analysis and data mining in many industries, including the life sciences, government, and research institutions.
Under the terms of the agreement, Insightful stockholders will receive $1.87 in cash for each outstanding share of common stock they own.
This price is a premium of 29 percent over the average closing price of Insightful's common stock over the sixty-trading day period ending on June 18, 2008, the last trading day before the date of this announcement.
The transaction is expected to close in the third quarter of 2008 after which Insightful will become a wholly-owned subsidiary of Tibco.
Last year, Tibco bought Spotfire for $195 million in cash to expand it business-intelligence offering [BioInform 05-07-08].
US EPA Licenses Simulations Plus’s ADMET Predictor Software
The US Environmental Protection Agency has licensed Simulations Plus’s ADMET Predictor software tool, the company said this week.
The EPA licensed both the Toxicity and New Enslein Metabolism Modules to study the impact of refuse containing drugs and inactive ingredients.
Simulations Plus said that the deal marks its first purchase order from the EPA.
The company said that the agency will use its software to assess the environmental impact of drugs that are thrown away, which can end up in sewage treatment and landfill systems and therefore risk reaching fresh water streams, the oceans, or other environmental ecosystems.
Robert Fraczkiewicz, team leader for Simulations Plus’ ADMET Cheminformatics and product manager for ADMET Predictor, said in a statement that the EPA has generated the data for a number of the toxicity predictions using the company’s software.
So it is “especially appropriate that it has now come full circle in the form of high quality predictive models for them to use in their ongoing efforts to protect our environment.”
ADMET Predictor will allow the EPA to predict a number of potential toxicities for industry chemicals, agricultural chemicals, and drug molecules plus excipients, which are inactive drug additives.
Even if a chemical in question is not toxic, its metabolites might have toxic properties. According to the company, ADMET Predictor’s Enslein Metabolism Module helps scientists recognize which of the liver detoxification enzymes among the cytochrome P450 family will metabolize a given chemical and at what speed that process will occur.
Finnish Red Cross Licenses Ariadne Genomics' Software
Ariadne said this week that the Finnish Red Cross has licensed Pathway Studio Enterprise to do in-house pathway, biological process, and disease modeling.
According to a statement, the scientists will use the software to extract information from text, create custom cell type-, ICD10 disease-, and organism-specific databases, and carry out disease research and risk group identification.
Pathway Studio is delivered with ResNet, a database of more than a million molecular interactions and functional relationships extracted from literature, with references to the original sources. It includes tools to query the database, create molecular networks, and interpret gene expression and other experimental data. Pathway Studio includes MedScan, a text mining module to update ResNet and create custom databases.
Victoria, Australia to House $100M Life Science Supercomputer
The premier of Victoria, Australia, said this week that the region plans to build “the world's largest life sciences supercomputer” with $100 million in funding.
John Brumby said that his government would invest $50 million in a supercomputer complementing $50 million in funding from the university and other sources to kick off the Victorian Life Sciences Computation Initiative at the University of Melbourne’s Parkville Precinct.
The Parkville Precinct, on the northern edge of Melbourne’s business district, is a hub of health, research, and educational institutions including the University of Melbourne and Royal Melbourne Hospital and is currently undergoing expansion.
In a statement, Brumby said the supercomputer will enable accelerated research in areas such as cancer, cardiovascular and neurological disease, chronic inflammatory and bone diseases, and diabetes.
The University of Melbourne will release initial expressions of interest for the computing facility this year, with installations slated for 2009 and 2011.