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BioWorks 3.2, Cytoscape 2.1, eArray, siRNA Design Tool, OmniViz Pathway Enterprise, Molecular Systems Biology, LabPAS 2.1, AlphaPart11Ease


Thermo Electron has released BioWorks 3.2, the latest version of its proteomics software suite, which supports the company's entire range of Finnigan ion trap mass spectrometers. BioWorks 3.2 now uses probability-based scoring to complement traditional Sequest scores, the company said. The software also includes a new unified search results file format and improvements in the Xpress stable isotope quantitation algorithm.

Cytoscape 2.1 is available at New features include performance improvements, an on-line help system, a cPath plug-in for downloading protein interactions, improved network filtering, and support for very large networks (grater than 100,000 nodes and edges). The new version also includes "significantly expanded" API technical documentation.

Agilent Technologies last week launched eArray (, a new web portal that includes chip design, probe sequence, and annotation information for all of its microarrays. The portal allows users to store and access probes and annotation, and also enables online custom microarray design. It is integrated with Agilent's ordering system.

MWG Biotech has released a new siRNA Design Tool through its website ( The tool allows researchers to preview the secondary structure formation of the siRNA/mRNA site before they order custom siRNA duplexes. MWG Biotech said that the new service is better than other design algorithms, which focus on siRNA duplex features. "Now, rather than just focusing on the GC content of the siRNA, more attention is given to the secondary structure of the mRNA target site," the company said in a statement.

OmniViz has released a new WebViewer for its OmniViz Pathway Enterprise (OPE) package. OPE is a database that provides a common framework for searching, viewing, and analyzing pathways from public and commercial sources, such as GenMAPP and PathArt, and those drawn directly using the OPE client. The new WebViewer enables OPE's content to be distributed to a broader user base within organizations, OmniViz said.

The European Molecular Biology Organization and the Nature Publishing Group have launched a new open-access journal, Molecular Systems Biology, which will publish papers "describing the properties and behavior of complex biological systems in terms of molecular components and their interactions," according to a statement. According to the publishers, the journal will use "innovative technology to allow formal, unambiguous descriptions of biological systems and the sharing of related data sets." This feature will allow readers to use data for their own experiments and simulations. The journal will accommodate authors submitting data sets in SBML (Systems Biology Mark-Up Language) and CellML, and will also publish figures with scalable vector graphics, a language for describing two-dimensional graphics and graphical applications in XML.

Green Mountain Logic has released LabPAS 2.1, a LIMS that includes process-automation functionality and a configurable toolset. LabPAS includes advanced sample tracking, automated worklist assignment, instrument interfacing, inventory management, and a free reporting tool, the company said. The new version also includes a Sample Genealogy screen, which allows labs to pool samples in multiple iterations while being able track the complete sample genealogy.

Alpha Innotech has released AlphaPart11Ease, a gel-imaging software package that is compliant with the US Food and Drug Administration's 21 CFR Part 11 regulation covering electronic signatures. The package enables digital image acquisition and analysis within 21 CFR Part 11 compliant environments, the company said. Features include read/write-protected audit trails, image validation, electronic signatures, and security features. AlphaPart11Ease starts at $5,995.

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The Scan

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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.