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New York University, Institute for Systems Biology, University of Washington, Genedata, NHLBI, GeneGo, Genomatica, DSM, Spotfire, Taratec, GE Healthcare, Xention, Aureus Pharma, OSC, GRI

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Human Proteome Folding Project Enters Phase 2

The Human Proteome Folding Project — a collaborative effort between New York University, the Institute for Systems Biology, and the University of Washington — entered its second phase as of June 23.

The project, which initially kicked off in November 2004, runs on IBM's World Community Grid — an effort to harness spare compute cycles on millions of computers worldwide.

The goal of the project's first phase was to understand protein function by predicting the protein structures in more than 150 genomes. The second phase, called HPF2, will focus on increasing the resolution of the predictions for a "select subset" of human proteins, according to the project website.

To do so, the project participants intend to refine the Rosetta protein-prediction software in order to account for greater atomic detail.

HPF2 will focus on human-secreted proteins and key secreted pathogenic proteins, including Plasmodium, the organism that causes malaria. The project participants said that "higher resolution structure predictions for the proteins that malaria secretes will serve as bioinformatics infrastructure for researchers who are working hard around the world to understand the complex interaction between human hosts and malaria parasites."


Genedata Partners with EC-Backed Infections and Cancer Consortium

Genedata this week said that it is partnering with the Infections and Cancer (INCA) consortium, a European Commission-backed research program to discover the role of chronic infection in the development of cancer.

Genedata will provide research informatics to support the consortium's research. Financial details were not disclosed.

"INCA will help researchers develop new prevention measures and treatments against cancers such as leukemia, stomach cancer, and cervical cancer," Thomas Schulz, INCA's principal coordinator, said in a statement. The consortium will focus on five viruses and the Helicobacter pylori bacterium.

The four-year program kicked off in January and will receive €12.6 million ($15.9 million) of EC funding as part of Europe's Sixth Framework Life-Science-Health program. The consortium includes 30 research organizations from 13 European countries.


NHLBI Expands License to GeneGo's MetaCore

The National Heart, Lung and Blood Institute has extended and expanded its multi-year MetaCore license from GeneGo to include other groups and departments, GeneGo said this week.

The license will now cover NHLBI's core microarray group, the Center for Information Technology, and the Critical Care Medicine Department of the NIH Clinical Center. MetaCore will also be used in NHLBI's new systems biology group, GeneGo said.

NHLBI is using the MetaCore data mining software "to rationalize the extensive changes in gene expression due to experimental conditions or disease processes, and DNA sequence variations," GeneGo said.

Financial terms of the license were not disclosed.


Genomatica Signs Multi-Year Collaboration, Licensing Agreement with DSM

Genomatica said this week that it has signed a multi-year collaboration and licensing agreement with DSM.

Under the terms of the agreement, Genomatica will provide DSM, a Dutch chemical and biotechnology firm, with its metabolic modeling and simulation technologies.

The pact builds on an earlier agreement between the two companies [BioInform 04-25-05], and includes research and development support, technology license fees, and milestone payments.

Financial details were not disclosed.

Christophe Schilling, president and chief scientific officer at Genomatica, said in a statement that the company will provide integrated metabolic engineering solutions to DSM "for developing next-generation microbial bio-factories to produce valuable industrial products from sustainable feedstocks."

DSM sells ingredients based on fermentation and enzyme technology to the chemical, pharmaceutical, and food industries.


Spotfire Partners with Taratec on Drug Safety Analytics …

Taratec and Spotfire said this week that they have integrated their respective software tools in order to help pharmaceutical companies better analyze drug safety data.

Under the terms of the agreement, regulatory consultancy Taratec has embedded its pharmacovigilance and signal detection methodologies into guided analysis based on Spotfire's DecisionSite software.

Taratec provides regulatory compliance services to pharmaceutical, biotechnology, and medical device companies. The company has adapted DecisionSite "specifically for detection of potential signals or trends within drug safety data," the companies said.

The combined system can be used independently or in conjunction with any data-mining application, the companies said.


… and with GE Healthcare on High-Content Analysis

Spotfire and GE Healthcare said this week that they have integrated their software products to address high-content screening.

Spotfire's DecisionSite analytics software has been integrated with GE Healthcare's IN Cell Investigator software, which accompanies the IN Cell Analyzer 1000 and 3000 high-content imaging platforms.

GE Healthcare will include a customized version of DecisionSite with IN Cell Investigator "to support the standard quality control and data analysis workflows in cell-based screening," the companies said in a statement.


Xention Licenses Aureus Pharma's Ion Channel Database

Xention has licensed the AurSCOPE Ion Channel Knowledge database from Aureus Pharma to use in research, Aureus Pharma said this week.

AurSCOPE Ion Channel contains biological information for all known ion channels and their ligands, Aureus said.

Xention is a drug discovery and development company that focuses on ion channels.

Financial details were not disclosed.


OSC, GRI Seek Beta Testers for GRIDP Bioinformatics Platform

The Ohio Supercomputer Center and University of Cincinnati's Genome Research Institute said this week that they are recruiting research biologists to help test the Genome Research Institute Discovery Platform, or GRIDP, a new computational biology tool the organizations developed for researchers without access to advanced computer programming training.

GRIDP is a web service that lets scientists replace command-line programming with a point-and-click XML interface.

Matt Wortman, director of computational biology and information technology at GRI, said in a statement that he wants to recruit 15 to 20 beta testers to help with the final GRIDP development. Beta testers will have exclusive access to OSC's compute cluster, as well as new software that manages databases and moves data between processors.

Filed under

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.