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Sophic, Biomax, University of Texas at Austin, Geospiza, Illumina, Golden Helix, Imperial College London, University of Edinburgh, the University of Alabama at Birmingham, the University Hospital of Schleswig-Holstein in Kiel, Germany, the Hospital for Si

Sophic and Biomax to Create Cancer Gene Database
Sophic, a life sciences software company and services integrator, said this week that it has begun an NCI-funded project to complete the Cancer Gene Index, a database of 6,610 cancer-related genes found in Medline abstracts along with manually annotated gene-disease and gene-compound relationships.
Sophic said the project will take 12 months and has a budget of $1.3 million.
Sophic said it began developing the curated cancer database four years ago through a collaboration with the NCI and the German company Biomax Informatics. The collaboration has already resulted in a compendium of 4,658 annotated cancer genes that are now available through the NCI’s website, the company said.
"This knowledge base is the foundation for reliable, accurate cancer research for all types of cancer diseases, clinical trials, biomarkers and much more,” Sophic’s CEO Pat Blake said in a statement.
Biomax CEO Kleus Heumann said the collaborators are using a “factory assembly line" approach to develop the database “that allows the automated text mining results to be fed to the scientific team who curate and annotate the information in an efficient, quality-controlled, work-flow process.”

Geospiza Becomes Illumina Connect Partner
Geospiza said this week that has joined the Illumina Connect program and that its FinchLab software can now be used with Illumina’s Genome Analyzer for data integration and analysis.
By joining the Illumina Connect program, a partnership program for third-party bioinformatics providers that Illumina launched last year, Geospiza has shown that its FinchLab Next Gen Edition workflow software can work with Illumina analyzers to track samples, review data, and characterize datasets.

Golden Helix Expands CNV Analysis Collaborator Group
Genetic-association software company Golden Helix is expanding its collaboration program for copy number variation analysis research to include five new academic partners, bringing the total number of partners to 11, the company said this week.
Golden Helix said it will provide data processing, quality control analysis, and consulting services in exchange for the purchase of its software and feedback on its products and services.
The new collaborators working with the company are: Imperial College London, the University of Edinburgh, the University of Alabama at Birmingham, the University Hospital of Schleswig-Holstein in Kiel, Germany, and the Hospital for Sick Children in Toronto.
The company launched the collaboration program in January [BioInform 01-18-08].
Initial partners included researchers from the University of California Los Angeles, the Zucker Hillside Hospital, Montreal Heart Institute, Emory University, Case Western Reserve University, and the University at Lubeck, Germany.
“Collaborating with these leading institutions will be invaluable for helping develop and improve the analytic methods needed to advance this field,” Golden Helix CEO Christophe Lambert said in a statement.
These collaborations will cover a number of diseases and sample characteristics and data generated from Illumina and Affymetrix genotyping platforms, said Golden Helix.

GeneGo Licenses Software to VTT of Finland
GeneGo said this week that the VTT Technical Research Centre of Finland, which is developing high-throughput methods for cancer research, drug discovery, and diagnostics, has licensed its software suite.
VTT’s Medical Biotechnology Knowledge Centre is funded by the European Commission and the Academy of Finland.
Under the agreement, for which no financial details were released, VTT will use GeneGo’s MetaCore and MetaDrug software in compound screening, RNA interference experiments, cell biology, and bioinformatics projects to identify pathways and networks for cancer research projects.
These projects include studying the mechanisms behind cancer development and progression and anti-cancer compound activity.

Progeniq Expands to California
Progeniq has opened its first office location outside of Singapore in Redwood City, Calif., the company said this week.
Progeniq sells a line of accelerated computing systems, including BioBoost, an FPGA-based system that accelerates bioinformatics applications like Smith-Waterman, ClustalW, and HMMer.
“Establishing our US operations as the first of our overseas offices reflects our strong commitment to provide our global clients and partners with timely support in an efficient manner,” said Progeniq’s CEO Darran Nathan in a statement.
Nathan added that the company has been “on a rapid expansion ramp-up” in the last few months.

UNC Receives EPA Grant for Computational Toxicology Research
The United States Environmental Protection Agency has awarded the University of North Carolina at Chapel Hill School of Public Health a $3.4 million grant to strengthen the school's research effort in computational toxicology and bioinformatics.
The four-year grant will be used to create the Carolina Center for Computational Toxicology, which aims to develop new methods and computational tools and foster interdisciplinary collaborative projects within UNC and with other environmental health science researchers.
Ivan Rusyn, principal investigator of the project and associate professor of environmental sciences and engineering in UNC’s School of Public Health, said in a statement that the new center will “strengthen our capacity for understanding and predicting the inter-individual differences in risk from environmental exposures."
Rusyn noted that more than 30,000 chemical compounds are being currently manufactured in industrially developed countries. While many of these compounds have been tested for the “regulatory agencies to reach unequivocal conclusions regarding potential risks,” rapid, efficient, and cheap screening methods are needed.
Rusyn said computational toxicology offers “unique opportunities” to accelerate safety screening and to handle the vast amounts of data that overwhelm established analytical methods.
"The mathematical tools that have been used traditionally by the regulators to decide which chemicals are safe are useful, but they can not be scaled up to meet current challenges in toxicology," Rusyn said.

Tibco’s Q2 Revenues Rise 15 Percent, but Profits Drop
Tibco this week reported a 15 percent increase in revenues for its second fiscal quarter, accompanied by a 62 percent drop in net income.
For the quarter ended June 1, Tibco’s revenues rose to $150 million from $130.5 million in the year ago period.
The company did not break out revenues for its Spotfire division, which it acquired last May [BioInform 05-04-07]. Officials said during a conference call that the life science vertical comprised 6 percent of total sales during the quarter, or $9 million.
Net income for the quarter fell to $3.5 million from $9.2 million in the comparable period of 2007.
R&D spending rose to $26.8 million from $22 million in the second quarter of 2007.
As of June 1, the company had cash and cash equivalents of $244.9 million.
Tibco said in a statement that it expanded its business with several companies during the quarter, including Boehringer Ingelheim and Sanofi-Aventis.

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