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Compugen, DNAStar, GeneGo, BioCreative, Ingenuity, GenoLogics, Ariadne, EBI


Compugen's Q1 Revenue Slides as Loss Narrows

Compugen said this week that first-quarter revenue declined 58 percent as R&D spending decreased 22 percent and net losses shrank 19 percent.

Total receipts for the three months ended March 31 slipped to $200,000 from $481,000 in the year-ago period. Compugen said the decrease is "in line with [its] evolution to utilizing its scientific know-how and computational biology capabilities for the discovery of potential therapeutic and diagnostic products."

In a statement, Compugen said it has previously said that its "anticipated primary sources of future revenues" are milestone and revenue-sharing payments from licensing and other arrangements "covering the development and marketing of diagnostic and therapeutic products based on the [its] discoveries.

Compugen said it expects to begin to receive such payments from current partnerships by the end of this year or early next year.

R&D spending for the quarter fell to $2.7 million from $3.5 million.

Net losses narrowed to $3 million, or $.11 per share, from $3.7 million, or $.13 per share, year over year.

Compugen said it had around $33.8 million in cash, equivalents, and marketable securities as of March 31.

Wash U Takes Site License to DNAStar's Lasergene

DNAStar said this week that it has signed a site license agreement with Washington University in St. Louis that gives researchers at the university access to its Lasergene sequence-analysis software anywhere on its campus for a four-year period.

Financial terms of the agreement were not disclosed.

"With tight federal funding, we are seeing increased market demand for site license arrangements with major research institutions," said Tom Schwei, DNAStar's vice president and general manager, in a statement. "They find it very beneficial to adopt a standard software platform institute-wide. It is simpler for centralized IT managers to administer and coordinate and there is a significant volume pricing benefit."

GeneGo, XB TransMed Integrate Software Products

GeneGo and XB TransMed Solutions have integrated their software platforms, the companies said this week.

GeneGo's MetaCore pathway software and XB TransMed's translational medicine software, called XB-BioIntegration Suite, have been integrated so that mutual customers can capture, manage, and mine integrated clinical, preclinical, and molecular data, the companies said.

BioCreative Issues Call for Participation

Organizers of the BioCreative (Critical Assessment of Information Extraction systems in Biology) text-mining challenge have issued the first call for participation in BioCreative II, which will be held in October, with the workshop to be held in Spring 2007.

Training data will be released in June.

The evaluation will include three tracks. The first will focus on finding the mentions of genes and proteins in sentences drawn from Medline abstracts; the second will involve producing a list of Entrez Gene identifiers for all the human genes and proteins mentioned in a collection of Medline abstracts; and the third track will involve identifying protein-protein interactions from full text papers for curation into the IntAct and MINT databases.

Further information is available at

Daiichi Expands License to Ingenuity Pathways Analysis

Ingenuity Systems said this week that Daiichi Pharmaceutical has expanded its existing agreement for access to its Ingenuity Pathways Analysis software.

Daiichi has taken a corporate-wide license to IPA, which will enable it to broadly deploy the system across its discovery and development sites.

Financial terms of the agreement were not disclosed.

Fred Hutchinson Cancer Center to Use GenoLogics' Proteus Software

GenoLogics Life Sciences Software said this week that the Fred Hutchinson Cancer Research Center will use its Proteus proteomics data-management system to support its cancer biomarker discovery research in early detection of ovarian cancer.

GenoLogics said that it has integrated Proteus with the Hutch's Computational Proteomics Analysis System data repository. The software will be used in the Center's Computational Proteomics Laboratory, which develops approaches for protein and proteomics research.

Ariadne's PathwayStudio 4.0 Gains GeneChip-compatible Status

Ariadne Genomics said this week that it has joined the Affymetrix GeneChip-compatible Applications Program and that its PathwayStudio 4.0 pathway analysis software has earned GeneChip-compatible status.

"Pathway-level annotation and functional analysis is fast becoming a standard part of gene expression microarray data analysis," said Steve Lincoln, vice president of informatics at Affymetrix, in a statement. "The integration between the Affymetrix GeneChip platform and Ariadne's PathwayStudio allows our mutual customers to extract the greatest value from their microarray data."

EBI to Change Format of EMBL Nucleotide Database in June

The European Bioinformatics Institute is planning a format change for the EMBL Nucleotide Database that is scheduled to take place in June.

EBI said in a listserv notice this week that the "ID" line will have a different structure and the "SV" line will be removed beginning with release 87 of the database.

A test dataset that includes the new ID lines called new_id_line.test.gz is available with the March release of the EMBL database at

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