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Applied Biosystems, NIGMS, Spotfire, Incogen, NCGA, Inforsense, Partek, Ocimum, The MathWorks


Applied Biosystems Reorganizes: iScience Deemed ‘Cross-Functional’ Division

Applied Biosystems is undergoing a company-wide restructuring effort to reorganize its operations around four new business divisions. As part of the restructuring effort, ABI will cut 145 jobs, or about 3.5 percent of its 4,400-person workforce, the company disclosed in a July 13 US Securities and Exchange Commission filing.

A majority of the layoffs are in R&D, with additional jobs being cut in areas such as sales, manufacturing, and product management, the company said. ABI also said that its Foster City, Calif. headquarters location would be most affected. The layoffs commenced with the July 1 start of ABI’s fiscal year 2005.

The company’s activities will now fall under four new business divisions: molecular biology; proteomics and small molecules; applied markets; and service. Each of these divisions will have a dedicated president, product development and advanced manufacturing resources, and product line and marketing management, ABI said.

In addition, the company is creating several cross-divisional functions “intended to support execution of current business strategy.” One of these is the company’s iScience solutions team, which will have “responsibility to drive the group’s integrated science product suites for the developing market generally known as systems biology,” the company said in the SEC filing.

ABI’s information business, formerly known as its Knowledge Business, falls within the iScience effort [BioInform 03-15-04]

NIGMS Earmarks $3M for Protein Structure Modeling Projects

The National Institute for General Medical Science has committed $3 million in funding for the 2006 fiscal year for three to four projects to develop new comparative modeling methods for protein structure prediction.

NIGMS issued a request for applications last week for the program, called “High-Accuracy Protein Structure Modeling.” The grants fall under NIGMS’s Protein Structure Initiative, launched in 2000 with the goal of determining 8,000 experimental structures of protein family representatives by 2010. The purpose of this RFA, according to the agency, “is to foster rapid advances in high-accuracy protein structure modeling ... with the aim of producing models comparable in quality to experimentally determined structures for most proteins.”

With improved methods of comparative modeling, “it may be feasible to produce a million high-resolution protein structure from the 8,000 that will be directly determined experimentally,” NIGMS said in the RFA.

Letters of intent are due Jan. 14, 2005, and applications are due Feb. 14, 2005.

Further details are available at

Spotfire Launches Instrumentation Partner Program

Spotfire last week launched a new Instrumentation Partner Program to encourage manufacturers of research instrumentation systems to integrate the company’s DecisionSite software with their products.

Spotfire said it will provide program participants with a tool to enable customers to directly load data generated by the instruments into DecisionSite. Spotfire will also offer a corresponding tool to DecisionSite users that will merge experimental information with raw instrument data.

In addition, IPP participants can offer end-users a 90-day evaluation license of the Spotfire software with their instrument systems. Upon completion of the evaluation, DecisionSite may be licensed directly from Spotfire.

Spotfire announced the first of its IPP partners, Applied Biosystems, earlier this month [BioInform 07-05-04]. The company said that Cellomics is also a participant.

Incogen Licenses VIBE to NIAID

The National Institute of Allergy and Infectious Disease has purchased a multi-client license for Incogen’s VIBE (Visual Integrated Bioinformatics Environment) workflow management program, the company said last week.

NIAID’s research technologies branch will use the software. The branch provides technology, scientific expertise, and technical support to all NIAID researchers.

Incogen licensed VIBE to the US Naval Research Laboratory in March [BioInform 03-29-04].

NCGA Deposits Industry Maize Sequence in Public Database for Non-Profit Use

The National Corn Growers Association said last week that Ceres, Monsanto, and Pioneer Hi-Bred International have deposited their maize genome sequence data into a public database for use by non-profit researchers.

The database,, is hosted at the Donald Danforth Plant Science Center in St. Louis. Access to the data is limited to researchers in non-profit institutions willing to jump through a few hoops: In order to obtain access to the database, researchers must download and print a user agreement in PDF form. Each person within a laboratory who wants to access the data must complete two sections of the agreement and mail two signed originals to the NCGA. Upon receiving the documents, NCGA will verify that the submitting institution is eligible to access the database and then contact the Danforth center, where an account will be established for the primary investigator in the lab.

The organization anticipates that the data from the industry consortium will enable the corn genome to be completely sequenced by 2007 •- “potentially years ahead of when it would have been completed without this initiative,” NCGA said.

Toronto Microarray Facility to Use Inforsense Analysis Software

InforSense said last week that it has signed a software licensing agreement with the Center for Applied Genomics Microarray Facility at the Hospital for Sick Children in Toronto, Canada.

The facility has purchased a multi-user, multi-year license for the company’s Knowledge Discovery Environment informatics system to analyze data from the Affymetrix GeneChip platform, Inforsense said.

Financial terms of the agreement were not provided.

Partek Licenses Software to Yale

Researchers in Yale’s Chemistry Department will use Partek’s Partek Pro statistical software for pattern recognition of interactions between proteins and synthetic receptors, the company said last week.

Financial terms of the agreement were not provided.

Arius Licenses Ocimum’s LIMS

Ocimum Biosolutions said last week that Arius Research • a Toronto-based biotech focusing on monoclonal antibodies • has licensed its Biotracker LIMS platform to support its cancer research activities.

United Bioinformatica, Ocimum’s Canadian distributor, will work with Ocimum to implement the system.

Financial terms of the agreement were not provided.

Infinity Pharmaceuticals to Use Matlab for Data Analysis

The MathWorks said last week that Infinity Pharmaceuticals has licensed its Matlab numerical programming environment, Statistics Toolbox, and Curve Fitting Toolbox for analyzing data in its drug discovery processes.

Dennis Underwood, vice president of discovery informatics and computational science at Infinity, estimated that the integration of the company’s in-house tools and existing Java code into Matlab reduced development time significantly, resulting in an annual savings of $100,000.

Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.