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GeneBio, SciTegic, Biomedical Software, LocusLink, Ingenuity, Gene Logic, Ocimum, Rosetta Biosoftware, Gene Codes, Jubilant, and more


GeneBio Teams with Current Science on New Proteomics Platform

Geneva Bioinformatics said last week that it has formed a joint venture with the Current Science Group — a consortium of biomedical publishers — to develop a new proteomics software platform.

The joint venture, called Current BioData, will develop, promote, and distribute ProXenter, a web-based platform focused on specific groups of proteins of “high interest” to the drug discovery industry.

GeneBio said that it has been developing ProXenter internally for three years. The system is built upon a protein relational database that contains information on each known protein in the group under scrutiny. This includes data extracted from UniProt and other databases, manual annotation, and pre-computed protein properties. ProXenter will also include browsing, visualization, and analysis tools, GeneBio said.

Andrew Smith, marketing manager at GeneBio, told BioInform that ProXenter “is complete but not yet commercially available.” Smith couldn’t provide a specific timeline for the launch of the system, noting that the Current Science team will handle “the bulk” of the sales and marketing.

SciTegic Signs Multi-Site License with Unilever

Accelrys subsidiary SciTegic said last week that it has sold a multi-year license of its Pipeline Pilot software to Unilever.

The company’s data-pipelining software platform will be deployed at four Unilever sites across Europe and the US, Scitegic said.

Unilever is using Pipeline Pilot for informatics analyses and molecular modeling of compounds for its home and personal care, foods and safety, and health and environmental R&D.

Pipeline Pilot has helped Unilever “reduce the time necessary to complete internal informatics activities by as much as 90 percent,” said Jerry Winter, head of informatics for Unilever, in a statement.

NIH Pledges Support for Maintenance of Biomedical Software

The National Institutes of Health has issued a program announcement entitled, “Continued Development and Maintenance of Software,” that aims “to assure the availability and continued usefulness of existing biomedical informatics/computational biology software.”

The program announcement is meant for existing software that serves a biological, clinical, or behavioral community of users, NIH said. Applications under the program can seek support to improve existing software packages in several different ways, including improved extensibility, better documentation, enhanced interoperability, and the incorporation of ontologies or controlled vocabularies.

NIH said that the size and duration of awards under the program will vary, “because the nature and scope of the proposed research will vary from application to application.”

The program replaces “Continued Development and Maintenance of Bioinformatics and Computational Biology Software,” which was issued in 2002 and has just expired. The new program will be in effect until Sept. 14, 2007.

Applications are due May 17 and Sept. 13 in 2005, 2006, and 2007.

Additional information is available at

LocusLink Retires on Schedule

As planned, the National Center for Biomedical Information retired the public LocusLink website on March 1.

Standard URLs to LocusLink will now be redirected to Entrez Gene, and the files at the LocusLink ftp site have been moved or copied to the Archive subdirectory.

The LL_tmpl file used for bulk downloads of functional annotation data was copied as LL_tmpl_050301.gz. It will continue to be refreshed “temporarily,” NCBI said.

Pfizer Expands Ingenuity License

Ingenuity said last week that Pfizer has expanded its license for the Ingenuity Pathways Analysis software.

The company did not disclose financial terms of the expanded license.

Gene Logic Adopts Executive Cash Incentive Plan

Gene Logic disclosed in SEC filings last week that its board of directors has adopted a cash incentive compensation plan under which the company’s executive officers will be eligible to earn incentive compensation based on 2005 company and individual performance.

Under the plan, CEO Mark Gessler’s target incentive compensation is 65 percent of his base salary, while other officers’ targets are between 20 percent and 50 percent of their base salaries. Gessler’s base salary for 2001-2003 was $400,000, according to the company’s most recent proxy statement, with a bonus of $197,381 in 2003, $208,872 in 2002, and $249,986 in 2001.

The board of directors also established an annual retainer of $50,000 for its chairman, J. Stark Thompson, and of $25,000 for the other directors.

Ocimum Biosolutions to Acquire MWG Microarray Assets

Bioinformatics firm Ocimum Biosolutions of Hyderabad, India, has signed a letter of intent to acquire core assets of MWG Biotech’s microarray business, the companies said last week.

Ocimum said it will take over “the microarray know-how, expertise, and assets” of MWG’s microarray business line, including inventory, stock, and more than 300 customers, but not any employees. The microarray business will be located in Hyderabad, with some services offered from Ocimum’s US office in Indianapolis, Ind.

Financial details of the acquisition were not disclosed.

Serono Licenses Rosetta Resolver

Rosetta Biosoftware said that Serono has licensed its Rosetta Resolver enterprise-wide gene expression analysis system.

Financial terms of the licensing agreement were not disclosed.

Gene Codes Wraps up WTC Project, Turns to Tsunami Victims

Gene Codes said last week that it has ended its collaboration with New York City’s Medical Examiner to apply its DNA analysis software to identify victims of the World Trade Center attacks of Sept. 11, 2001.

Gene Codes CEO Howard Cash said that the company’s Gene Codes Forensics subsidiary is now working with the Minister of the Interior of Thailand to apply the same software, called M-FISys (Mass-Fatality Identification System), to identify human remains from the recent tsunami in South Asia.

Cash said in a statement that the company has been working on the tsunami project since early January, and that the first DNA match “was made several weeks ago.”

Jubilant Licenses ChemBioBases to Pfizer

Jubilant Biosys has sold a global license for its ChemBioBase suite of gene-family-specific small-molecule inhibitor databases to Pfizer, the company said last week.

Financial terms of the agreement were not provided.

FMI Licenses Genedata’s Expressionist

Genedata said last week that the Friedrich Miescher Institute for Biomedical Research, a branch of the Novartis Research Foundation, has licensed its Expressionist gene expression analysis system.

FMI will use the software to support its research activities in epigenetics, growth control, and neurobiology.

SRI Tapped as Pathway Modeling Partner on $12.7M LBNL Grant

SRI International said last week that it will serve as a subcontractor on a $12.7 million grant awarded to Lawrence Berkeley National Laboratory by the National Cancer Institute to develop tools for predicting cancer therapy response.

SRI’s subcontract is worth $1 million. Under the terms of the contract, SRI will apply its Pathway Logic software to develop a model of cellular signaling networks related to human breast cancer.

SRI’s Biosciences Division and Computer Science Laboratory will co-develop the Pathway Logic model of cellular networks.

FDA Uses Pharsight Trial Simulation Software

Pharsight said last week that the US Food and Drug Administration has used its quantitative-based modeling and simulation program to help design an end-of-Phase IIa trial for an anti-HIV drug.

The relationship between Pharsight and the FDA is partly the result of the agency’s EOPIIa program, which is part of the Critical Path Initiative. The program enables the FDA to provide sponsors of clinical trials with input earlier in the drug-development cycle.

Pharsight said it believes that quantitative-based modeling and simulation during drug development can increase the productivity and efficiency of the process.

Thermo to Launch Commercial Version of ProSight PTM Proteomics Software in June

Thermo Electron will launch in June a commercial version of ProSight PTM, software developed by the University of Illinois, Urbana-Champaign, for identifying intact proteins and their post-translational modifications, according to ProteoMonitor, BioInform’s sister publication.

Thermo will be the exclusive distributor of the software, called ProSight PC, Amy Zumwalt, a proteomics marketing specialist at Thermo Electron, told ProteoMonitor.

A non-commercial version of the software is currently available at


Filed under

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.