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Rice University, MD Anderson, BioDiscovery, Ocimum Biosolutions, I3C, Oracle, Mouse Genome Resequencing, Biotique Systems, SciTegic, Ohio Supercomputer Center

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Rice, MD Anderson Launch Computational Cancer Center

Rice University and the University of Texas MD Anderson Cancer Center are collaborating to create the Gulf Coast Center for Computational Cancer Research.

Center scientists plan to develop new computational approaches for cancer research, such as systems to simulate clinical trials before they begin. The center also plans to build large gene and protein databases in order to identify mutations that cause different cancers, create tests for each possible variation, and design patient-specific treatments.

“We will apply high-level computing to virtually every aspect of cancer treatment, from cancer diagnosis and protein modeling of each patient, to drug discovery and clinical trial design,” said Donald Berry, professor of biostatistics and applied mathematics at MD Anderson.


BioDiscovery Sells GeneDirector to Two Irish Research Centers

BioDiscovery has sold its GeneDirector enterprise microarray analysis platform to two Irish research organizations: the Alimentary Pharmabiotic Center at University College Cork and Teagasc (the Irish Agricultural Research Center).

Financial terms were not disclosed for either licensing agreement.


NRCC Opts for Ocimum’s LIMS

Ocimum Biosolutions said last week that the National Research Council of Canada has purchased its Biotracker laboratory information management system for the NRCC DNA sequencing facility at Halifax, Nova Scotia.

Financial details of the deal were not disclosed.


I3C Recruites Two More Members

The Interoperable Informatics Infrastructure Consortium said on Jan. 12 that cheminformatics firm Synthematix, and Optive Research, a computational drug discovery company, have joined the consortium.

The companies join the I3C’s current members: Avaki, the Biotechnology Industry Organization, Chiron, Genaissance, Hewlett-Packard, IBM Life Sciences, Infinity Pharmaceuticals, the University of Manchester, Merck, Millennium, the Object Management Group, Platform Computing, the PDB, the Sanger Institute, Scimagix, TIGR, TurboWorx, the University of California at San Diego, and the Whitehead Institute Center for Genome Research.


Oracle Buys Clinical Trials Software Company

Oracle last week acquired the assets of SiteWorks Solutions, a privately held supplier of clinical trial management software products.

According to an Oracle statement, the acquisition gives the company “the most complete and integrated suite of clinical trial applications in the industry.”

Oracle said it plans to integrate SiteWorks’ SiteMinder and TrialMinder trial management applications with the Oracle Clinical suite.


NIEHS Issues RFP for Mouse Genome Resequencing, Database Project

The National Institute of Environmental Health Sciences is seeking contractors for resequencing the genomes of 15 commonly used laboratory mouse strains and building an associated database.

The objective of the project is to identify “which sequence determines the genetic basis of trait differences between the different inbred mouse strains. … Specifically, the contractor shall determine the identity of each base in each position along each mouse chromosome and develop and maintain an annotated record of the sequence data obtained for each of 15 different inbred mouse strains.”

The contract is expected to cover a three-year period with two one-year options. Proposals are due on March 18, 2004. Further details are available at http://grants1.nih.gov/ grants/guide/notice-files/NOT-ES-04-003.html.


Berlex Extends Biotique BLIS License

Biotique Systems said last week that Berlex Biosciences, the US affiliate of Schering, has taken a three-year license to the Biotique Local Integration System.

The agreement expands a previous agreement that began in July 2002, in which Berlex licensed BLIS for its research operations in Richmond, Calif. The expanded agreement provides worldwide access to Schering’s research operations.

“Based on our positive experience and the interest of our Schering colleagues in the system, our international collaboration team has chosen to secure a global license for BLIS,” said Hugh Salamon, who leads the computational biology department at Berlex.


Novartis Licenses SciTegic’s Pipeline Pilot

SciTegic said last week that Novartis Pharma AG has purchased a license to its Pipeline Pilot workflow management software for use by researchers in the Novartis Institutes for Biomedical Research.

“We hope to see an improved productivity on some aspects of drug discovery using the integrative capability of Pipeline Pilot,” said Rene Amstutz, vice president of discovery technologies for NIBR.

Financial terms of the licensing agreement were not disclosed.


OSC to Use IBM Storage for Genomics Data

The Ohio Supercomputer Center has selected IBM storage hardware and software to manage its growing repository of research data, including bioinformatics data, “which is generated through shared research applications provided by OSC,” according to an OSC statement.

The IBM storage infrastructure, which includes TotalStorage FAStT storage servers, a TotalStorage SAN file system, and TotalStorage SAN Volume Controller, will increase OSC’s data storage capacity five-fold over its previous system, and will provide more than 600 terabytes of physical storage capacity.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.