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DecisionSite, VIBE 3.1, GenBank 147.0, Taverna 1.1, BIND, BioPrism, W.ND-Blast, PDBbind, BlueFuse, OEChempatible C++, Prism


Spotfire has added an open Computation Services framework to its DecisionSite analytics application that allows users to work with statistical tools written in SAS, Insightful S-PLUS, and R within the application. The company said that the framework will allow it and its partners to integrate the software with workflow applications from SciTegic and Inforsense, MatLab, and Excel.

Incogen has released version 3.1 of VIBE (Visual Integrated Bioinformatics Environment). The release includes Solaris 10 Sparc support, simplified setup and configuration, and improved usability. In addition, a beta version of VIBE-Ed, a version of the software geared toward educating bioinformatics personnel, is available for educational institutions.

GenBank 147.0 is now available from the National Center for Biotechnology Information at The release contains 48,235,738,567,base pairs and 44,202,133 entries. Uncompressed, the 144.0 flat files require about 168 GB for the sequence files only. The ASN.1 version requires around 145 GB. GenBank 147.0 includes a new division for sequences obtained via environmental sampling methods. The new division segregates 128,571 sequences for which the source organism is unknown, or can only be inferred by sequence comparison. The new sequence files are gbenv1.seq and gbenv2.seq.

Taverna 1.1 is now available from The new version of the open source workflow package includes API Consumer (an extension that allows the inclusion of third-party Java APIs), enhanced access to Soaplab metadata, and polling-based invocation for long running tasks.

The Blueprint Initiative has added the SOAP (simple object access protocol) web service to BIND (Biomolecular Interaction Network Database). According to the non-profit initiative, researchers can use BIND-SOAP to access the BIND Search Service using a remote API. Further information on BIND-SOAP is available at

NEC has released BioPrism, a proteomic analysis system that simultaneously displays multiple analytical data and information stored in public databases. The system is priced between $28,000 for a "compact model" and $46,700 for the "professional model." NEC said it expects to sell 100 units over the next three years.

The US Department of Agriculture has released W.ND-Blast, a free Windows .NET distributed Blast application, at The software allows researchers to distribute Blast queries to any number of Windows-based machines across local area networks.

The University of Michigan Medical School in Ann Arbor has released PDBbind version 2003 at The database is a collection of binding affinity data for the protein-ligand complexes in the Protein Data Bank. The latest version has binding affinity data for more than 1,700 protein-ligand complexes released by PDB before January 1, 2004.

BlueGnome has released a new version of its BlueFuse microarray analysis software that includes features for automated array CGH mapping. The software can analyze 20 or more arrays and return a list of regions of copy number change for each experiment in the batch, the company said.

OpenEye Scientific Software has released version 1.0 of the Case Toolkit, an extensible programming library that includes the object-oriented, OEChempatible C++ toolkit; numerous optimization algorithms; generalized gradient and non-gradient optimizers for well-defined functions; numerous coordinate frames; algorithms for protein active site minimization and other template shape minimizations; and constrained coordinates.

Silicon Graphics has released the Prism deskside visualization system, which includes up to 24 GB of memory and two full-bandwidth graphics pipelines and starts at under $8,500. The company said that the platform allows researchers to interactively study large data sets all at once, rather than working with segmented data sets.

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The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.