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NHLBI Bio-ontology, Entrez Gene, Informatics Training, Ingenuity, Blueprint Initiative, BIND, Nonlinear Dynamics, Gattaca Xserve Cluster


NHLBI Seeks Information for Bio-ontology Inventory

The National Heart, Lung, and Blood Institute has issued a request for information on ontologies and ontological resources relevant to heart, lung, blood, and sleep research.

The RFI, available here, is looking for comments on "existing bio-ontological resources, platforms for bio-ontology development, and ontology-coupled data resources" that are relevant to NHLBI's research goals.

Responses should be submitted to NHLBI through this form by June 3.

NCBI to Stop Updating LL-Tmpl File as of June 1

As part of its ongoing transition from LocusLink to Entrez Gene, the National Center for Biotechnology Information last week said that it will stop updating the LL_tmpl file used for bulk downloads of functional annotation data as of June 1.

NCBI had continued updating the file after it discontinued the web interface to LocusLink on March 1 "to give users an opportunity to convert to extracting data from Gene either via E-Utilities, gene2xml, or the tab-delimited reports in the Data subdirectory," NCBI said in a listserv bulletin last week.

NCBI is accepting questions or comments regarding the switch to Gene at

Stanford, University of Western Cape Collaborate
On Informatics Training Program in South Africa

Stanford University has formed a collaboration with the University of Western Cape in South Africa to create a program to provide biomedical informatics training to South African researchers, Stanford said last week.

Researchers at Stanford and the University of Western Cape have received an $800,000 grant from the National Institutes of Health's Fogarty International Center for a program seeking to train graduate African scientists in areas such as HIV informatics, tuberculosis drug discovery, and bioinformatics.

The program will bring together HIV biologists, epidemiologists, and bioinformaticists from Stanford, the University of Western Cape, the University of Cape Town, and the National Institutes of Communicable Diseases. These researchers will help establish research programs including ones in HIV databasing, pharmacogenomics, and development of new languages for describing medical discoveries.

NCI Takes License to Ingenuity Pathway Analysis

Ingenuity said last week that the National Cancer Institute Center for Cancer Research has licensed access to its Ingenuity Pathways Analysis software.

Under the terms of the agreement, all researchers at the NCI will have access to the software.

In a statement, Ingenuity CEO Jake Leschly said that extending Ingenuity's reach into the academic and government research community is a "critical goal" for 2005.

"We are grateful for the support and guidance that we received from the NCI and other NIH institutes in developing a licensing arrangement that can serve as the model for providing access to Ingenuity Pathways Analysis for all leading research institutions," Leschly said.

BIND Doubles Three-Year Submission Target

The Blueprint Initiative said last week that it has more than doubled its projected three-year target for submissions to the Biomolecular Interaction Network Database (BIND), surpassing 170,000 records.

In April 2002, Blueprint set out to enter 80,000 interactions into BIND. As of April 8,the database contained more than 173,000 interactions.

Aureus Incorporates ChemAxon Software into AurQuest Interface

Aureus Pharma and ChemAxon have entered into an agreement under which ChemAxon's Java-based chemistry software components have been incorporated within AurQuest, Aureus Pharma's interface for its AurScope line of databases.

AurQuest will include new chemoinformatics functionality via ChemAxon's Marvin chemical structure sketching applet and the JChem application for searching and retrieving structures, Aureus said.

Nonlinear Developing Biomarker Product Line; First Software to Launch in Q3

Nonlinear Dynamics said last week that it has undertaken "a large-scale development program" to launch "multiple biomarker products" based on its suite of mass spectrometry and capillary electrophoresis analysis tools.

The first release from the development program will be a medium-throughput analysis tool based on its Phoretix software. Set for launch in the third quarter, Phoretix Biomarker will enable "entry-level" trace data analysis and visualization, the company said.

Nonlinear did not provide a timeline for future products planned for the biomarker suite.

University of Pittsburgh Installs 'Gattaca' Xserve Cluster

The University of Pittsburgh's Graduate School of Public Health has installed a 125-node Apple Xserve G5 cluster to support statistical genetics analysis, the university said last week.

More than 30 investigators and scientific teams will use the cluster, dubbed "Gattaca" after the 1997 sci-fi film, to support more than 120 research projects.

The University said it plans to extend the cluster's workload to analyze data from microarrays and SNP studies.


Filed under

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.