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Annotation Express, Biology Workbench, BioJava 1.4, Mathematica 5.2, PhenotypeGenetics 2.0, STEM, DirectDesign, Agilent 2100 Bioanalyzer, EMBOSS 3.0.0, Mervyn Thomas, Steve Noblitt


Downloads & Upgrades

Inpharmatica has launched Annotation Express, a modular protein-annotation system. Four modules are available: Domain Professor, which contains pre-calculated detailed protein domain annotation; InGOt, a Gene Ontology resource; BluChip for linking Affymetrix probes through to biological process and high-level functional annotation; and Bio-Clip, which offers summary annotations of the above modules for genome-scale protein data sets.

Biobase has launched new versions of the Proteome line of databases that it acquired from Incyte in January [BioInform 1-24-05]. The new release includes additional disease data, links to Biobase's Transfac and Transpath databases, and the Proteome Workspace — a browser that allows users to manipulate network maps of physical and regulatory interactions between proteins.

The Systems Biology Workbench is available for Mac OS X 10.3 and 10.4 at The release includes a new simulator for the Mac and a new simDriver interface.

BioJava 1.4 is available at According to the BioJava development team, BioJava 1.4 took two years to develop and "offers considerably more functionality and stability over the previous official release (biojava 1.3)."

Wolfram Research has released Mathematica 5.2, a 64-bit multicore release of its mathematical software platform. Mathematica 5.2 also supports automatically threaded numerical linear algebra on all platforms.

PhenotypeGenetics 2.0, a plug-in for the CytoScape platform that constructs genetic-interaction networks from large sets of phenotype measurements, is available from the Galitski Lab at the Institute for Systems Biology at

The Center for Automated Learning at Carnegie Mellon University has released STEM (Short Time-series Expression Miner), a Java program for clustering, comparing, and visualizing short time-series gene expression data that is fully integrated with the Gene Ontology, at

Operon Biotechnologies has made the sequence data for probes in its Array-Ready Oligo Sets freely available at

Eidogen-Sertanty has launched DirectDesign, a de novo drug design service based on the company's discovery informatics software and database products. According to Eidogen-Sertanty, the service enables target-focused design of synthetically accessible, novel ligands.

Agilent Technologies has released new software for the Agilent 2100 Bioanalyzer lab-on-chip electrophoresis and flow cytometry analysis tool. The software includes a unique RNA integrity number algorithm for RNA quality control, as well as tools for compliance with the Food and Drug Administration's 21 CFR Part 11 regulation.

EMBOSS 3.0.0 is available at The release includes several new database-indexing programs — dbxflat, dbxfasta, and dbxgcg — which allow indexing of files larger than 2 GB; a new format-conversion application called codcopy; MYEMBOSS — a new EMBASSY package for developing your own code; and other features.


People in the News

Australian antibody array developer Medsaic has appointed Mervyn Thomas as senior biostatistician. Thomas is the founder of bioinformatics consultancy Emphron Informatics. He formerly ran the bioinformatics research program for the division of mathematics and information sciences at Australia's Commonwealth Scientific and Industrial Research Organization. Thomas will continue as CEO of Emphron Informatics, and will work at Medsaic as part of a strategic alliance between the two firms.

Nonlinear Dynamics has promoted Steve Noblitt to the position of US sales manager within the company's US subsidiary, Nonlinear USA Inc. Noblitt has served as Nonlinear's Midwest sales manager for four years. Prior to that, he worked for Molecular Dynamics and Amersham Pharmacia Biotech (now GE Healthcare) as a field applications specialist.

Filed under

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.