Downloads & Upgrades
The Institute for Systems Biology has released BioNetBuilder, a Cytoscape plug-in, at http://db.systemsbiology.net/cytoscape/bioNetBuilder/. The plug-in provides an interface to create biological networks integrated from several databases. Users can create networks for 1,136 different species, including most common model organisms and human.
Sigma-Aldrich has launched PathFinder, a free online collection of interactive biological signaling and metabolic pathways, at http://sigma-aldrich.com/pathfinder. The resource provides links to appropriate products from Sigma-Aldrich, including small molecules, antibodies, enzymes, QPCR components, and siRNAs for gene knockdown. PathFinder, co-developed with Protein Lounge, currently includes 20 pathways, but is expected to include more than 100 signal transduction pathways when completed later this year.
IDBS has launched BioBook, a data-management system that supports data capture, analysis, report creation, and publication in a 21 CFR Part 11 compliant environment. According to IDBS, the system can help reduce the use of paper lab notebooks and third-party data visualization and statistical analysis applications.
SeqFreed, a bioinformatics desktop application, is available at http://seqfreed.sourceforge.net/. SeqFreed provides access to sequence data and gene features and includes a customizable command line interface to run locally installed bioinformatics tools. It also serves as an EMBOSS GUI.
The National Center for Biotechnology Information has released the Blood Group Antigen Gene Mutation Database (BGMUT), which includes information about the genetics of blood group systems. NCBI is hosting the database as part of the dbRBC, a resource dedicated to the genetics of red blood cell antigens. It is available at http://www.ncbi.nlm.nih.gov/projects/mhc/xslcgi.fcgi?cmd=bgmut/home. NCBI has also released its annotation of Human Genome Build 36.1 via Map Viewer at http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606.
MeltDNA, a software package for predicting DNA duplex hybridization and melting thermodynamics, is available at http://meltdna.sourceforge.net. According to its developers, the software considers all factors that determine thermodynamic values and has wide applicability in primer selection in PCR, probe selection in microarrays, and DNA secondary structure stability prediction.
The University of Pennsylvania and the Children's Hospital of Philadelphia have released FABLE (Fast Automated Biomedical Literature Extraction) v1.0, a software system for identifying genes and proteins in Medline, at http://fable.chop.edu. The software performs document retrieval of Medline abstracts for queries of genes, transcripts, and proteins by automatically annotating text. The system is optimized for human genes.
Terra Soft Solutions has released Y-Bio v1.1, which has been incorporated into Penguin Computing's ClusterWare Life Sciences Suite. Y-Bio v1.1 includes five new packages: T-coffee, MrBayes, mpiBLAST, Modeltest, and Probcons. These add to the original application suite offered in v1.0: NCBI Blast, EMBOSS, Glimmer, ClustalW, HMMER, Wise, and FastA.
Media Cybernetics has released IQstudio 2.1. The latest version of the company's analytical imaging toolkit enables users to prototype new imaging applications or add components to existing applications. New imaging functionality includes the ability to filter with very large kernels, optimized filtering algorithms for both 2D images and 3D sets of images, hough transform analysis tools, and a licensing dialog. A 30-day trial version of IQstudio is available at http://www.mediacy.com.
Simulations Plus has released DDDPlus (Dose Disintegration and Dissolution Plus) 2.0, software for predicting how changes in drug formulation or changes in experimental setup are likely to affect dissolution rate.
People in the News
David Edwards has joined Stratagene as director of software solutions. In this role, he will manage the company's line of expression and pathways analysis software. Edwards most recently served as director of life sciences at Accelrys.
Pace University presented Howard Cash, president and founder of Gene Codes, with its award for Distinguished Leadership in the Sciences at its 10th annual Dyson Distinguished Achievement Awards in New York this week.
The Moores Cancer Center at the University of California, San Diego, has named Nicholas Schork, UCSD professor of psychiatry and biostatistics, to lead its center for bioinformatics a new initiative it has launched that includes UCSD's School of Medicine and the Skaggs School of Pharmacy and Pharmaceutical Sciences, the Division of Biological Sciences, the California Institute for Telecommunications and Information Technology, the San Diego Supercomputer Center, the Center for Human Genetics and Genomics, faculty from the departments of mathematics and bioengineering, and other campus departments and resources. Schork is also co-leader of the cancer center's Cancer Genetics Research Program.
Bill Brammer, director of small and mid-market solutions and partner business management at Microsoft, has joined the board of directors of VizX Labs. Brammer began his career as a design engineer at Texas Instruments, and later worked for Tektronix and DEC before joining Microsoft's sales organization in 1995. Brammer became director of Microsoft's HP Alliance in 2001.