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Microsoft Research, Active Motif, SoftGenetics, Progeniq, Syngene, BioJava 1.5, Applied Biosystems, Insightful, BioFocus DPI, Illumina, and DNAStar

Microsoft Research has released the source code for four computational biology software packages here. The software was developed for AIDS vaccine research and is freely available, the company said, noting in a statement that it “hopes to spur other scientists and researchers to take up the tools and even build on them, thereby speeding the way toward a vaccine.”
The packages include PhyloD, a statistical tool for identifying HIV mutations that defeat the function of HLA proteins; Epitope Predictor, which computes the probability that a given k-mer is a T-cell epitope restricted to a given HLA allele; HLA Completion, which takes MHC-I alleles from a set of patients and completes an incomplete (two-digit) information to four digits; and HLA Assignment, which takes lab data from a series of patients and determines probabilistically which HLA genes are responsible for the reaction.

Active Motif has released a new knowledge application programming interface for Bioalma’s AKS2 text-mining system. The Java-based programming library allows software developers to have more direct and structured access to the AKS2 information, said Active Motif, Bioalma’s marketing partner.
The interface can present and analyze the AKS2 information in a very versatile and flexible fashion, facilitating integration with other biomedical software. KAPI allows developers to implement a script that performs both a sequence similarity search with Blast and a disease search using AKS2, based on the Blast hits, according to Bioalma CEO Juan Carlos del Castillo.

SoftGenetics has released an enhanced version of its JelMarker Image Reader software, which incorporates SoftGenetics’ physical comparison DNA variant technology. In addition to automatically identifying gel image
lanes and bands, the mutation-detection module of the software converts the image into a synthetic electropherogram that is then compared to a wild type reference.
JelMarker is compatible with fluorescence, chemiluminescence, and autoradiography gel image files, especially those generated by the LI-COR 4300 DNA Analyzer and the KODAK Image Station 4000R; and can import up to two TIFF, BIP, GEL, JPEG, BMP or TXT files for comparison analysis.

Progeniq, a provider of reconfigurable computing applications, has launched the Universal version of its BioBoost accelerated HMMer application for Apple’s Mac OS X Universal operating system. BioBoost provides hardware-accelerated processing based on field-programmable gate array technology for computationally intensive applications. The Universal version of BioBoost allows applications to run natively on both PowerPC- and Intel-based Macs.

Syngene has released an updated version of its Dymension software for automated 2D protein-gel analysis. The software now includes common spot outlines, a new algorithm for automatically detecting the presence or absence of proteins in large data sets, and other features relevant to automating 2D protein gel analysis.
Syngene said the new algorithm produces common spot outlines by warping all the gel images in an experiment together to create an averaged gel image and then performing detection on this image. These spot outlines are overlaid onto each gel in the experiment’s series.

BioJava 1.5, with numerous bug fixes and enhancements, is available for download here. The release includes new parsers for common file formats such as GenBank and Fasta; a new BioSQL persistence layer that uses Hibernate to interact with sequence databases; and a set of classes for creating genetic algorithms. The combined unit is part of the new org.biojavax package, which includes BioJava extensions that “would not fit easily into the existing package structure,” according to the BioJava development team.

Applied Biosystems has released Variant Reporter, a new software application that the company claims speeds analysis of genetic variation data. The software reduces manual review time by automating the detection of genetic variants and streamlining the data-analysis process, ABI said. The company said that it expects the software to reduce by up to half the time needed to study genetic variation data in medical sequencing projects.

Insightful, which offers predictive analytics and reporting solutions, has launched the Comprehensive S-PLUS Archive Network for sharing free S-PLUS packages for open source and commercial statistical programmers. The company said that more than 25 packages are currently available on the CSAN site, including submissions from AstraZeneca, Rockefeller University, and the International Agency for Research on Cancer in Lyon, France.

BioFocus DPI, a Galapagos company, has launched the Kinase SARfari knowledgebase, a repository and research workbench designed to help scientists focus on the protein kinase family of drug targets. The tool combines chemical and biological data from internal proprietary and public sources in a single system. It comes pre-populated with a variety of features such as protein kinase clinical candidates, FDA-approved drugs, more than 14,000 protein-kinase compounds, more than 57,000 structure-activity relationship screening and ADMET data points from BioFocus DPI’s StarLITe database, and five binding site definitions based on analysis of known ligand-binding footprints with pre-calculated binding site physicochemical distances.

Illumina has unveiled iControlDB, a genotyping control repository developed for researchers performing case-control whole-genome-association studies. iControlDB is designed to be a more efficient system for investigators to obtain control samples, affording them the freedom to focus primarily on genotyping disease samples. Combined with the National Center for Biotechnology Information’s dbGaP database, iControlDB includes nearly 10,000 control samples donated by researchers using Illumina’s SNP-genotyping technology.


DNAStar has introduced ArrayStar v2.0, the company’sfirst product for gene expression analysis. ArrayStar offers visualization and statistical analysis tools to track changes in gene-expression levels. Previously, DNAStar created software such as sequence analysis suite Lasergene and GenVision, a data-visualization software application.

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