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GenBank, Blast, PathwayLab, Ensembl 33, ISYS, PRIDE, ImageMaster, Human Protein Atlas, and more

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GenBank release 149.0 is now available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/. The release contains 51,674,486,881 base pairs and 46,947,388 entries. Uncompressed, the 149.0 flat files require about 179 GB for the sequence files only. The ASN.1 version requires around 156 GB.


NCBI has also released Blast 2.2.12 at http://ncbi.nih.gov/BLAST/download.shtml. The release includes several bug fixes, as well as a number of improvements to megablast, rpsblast, bl2seq, formatdb, and fastacmd. The release also includes new compositional score adjustment algorithms in blastpgp [Bioinformatics 21:902-911, 2005]. A new automatic downloader for Blast preformatted databases is also available at http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl.


Wolfram Research has begun shipping PathwayLab, a systems biology software system developed by InNetics that runs on Wolfram's Mathematica platform. With the software, a model of a pathway can be created using a drag-and-drop GUI. The model, a system of coupled nonlinear differential equations, can then be directly simulated, and the simulation result can be further analyzed, including visualization of the output, the company said. A trial version of PathwayLab is available at http://www.wolfram.com/products/applications/pathwaylab. The commercial price for an annual license to PathwayLab is $3,950, and the academic price is $1,450. The company is offering a 35-percent discount when PathwayLab and Mathematica are purchased together.


Ensembl 33 is available at http://www.ensembl.org. The release includes new human cDNAs, an updated Ensembl-Vega database for human, the ability to fetch mouse BAC clones, and additional features.


The National Center for Genome Resources has released an open source version of its ISYS (Integrated System) bioinformatics integration platform at http://sourceforge.net/projects/isys2/. ISYS uses DynamicDiscovery, a Java-based service brokering technology, to integrate software components and data sets. It offers an API so that users can to adapt their own programs and databases for integration with ISYS. ISYS has been available as a downloadable executable since 2001, but the release of the open source version is expected to expand access to the system, NCGR said.


The European Bioinformatics Institute and Flanders Interuniversity Institute for Biotechnology have launched the PRoteomics IDEntifications database (PRIDE) at http://www.ebi.ac.uk/pride. PRIDE includes the results of the Human Proteome Organization's Plasma Proteome Project and a human platelet proteome set published by Ghent University. The results of other proteomics initiatives, such as the Human Proteome Organization's Liver Proteome Project, will be available as they are published, EBI said.


CLC Bio, a bioinformatics company based in Aarhus, Denmark, has released CLC Free Workbench 1.0, a free package that includes several basic bioinformatics tools for Windows, MacOS X, and Linux platforms. The software is available at http://www.clcbio.com. The company said that it will release CLC Protein Workbench in November, followed by CLC Gene Workbench in March 2006. A number of more "sophisticated" bioinformatics programs will follow later in 2006, the company said.


GE Healthcare has released two new 2D gel analysis tools: ImageMaster 2D Platinum Version 6.0 and ImageMaster 2D Platinum Version 6.0 DIGE. Designed in collaboration with The Swiss Institute of Bioinformatics and GeneBio, the software tools capture data from an acquisition device such as a scanner or camera and then locate spots, assign molecular weights, and calculate the volume of each spot.


The Swedish Human Proteome Resource (HPR) program, funded by the Knut and Alice Wallenberg Foundation, has released its Human Protein Atlas at http://www.proteinatlas.org/index.php. The atlas contains histological images from sections of human tissue, indicating the expression and localization of proteins. The atlas currently includes 718 antibodies and 413,568 images.


The Norwegian Microarray Consortium has released GeneTools, a collection of web-based bioinformatics tools, at http://www.genetools.no/. GeneTools includes the NMC Annotation Database V2.0 and eGOn (explore Gene Ontology).


Genedata has released a version of its Expressionist gene expression analysis software for mass spectrometry analysis. The platform supports analysis of gel-free proteomics and metabolomics technologies, including "hyphenated" MS technologies, the company said.


Geneva Bioinformatics has released an updated version of its Phenyx protein-identification platform. The release incorporates the Phenyx Web Interface (PWI), a new web-based client used to interact with the Phenyx calculation engine. Other new features include a Protein Details View, displaying an extensive interpretation of a specific protein; Excel and XML reports of complete jobs; and a configurable management console that allows users to define their own amino acid modifications and enzymatic cleavage rules and to generate a variety of specific reports.


GenoLogics Life Sciences Software has released OmixLIMS, lab information management software for proteomics, genomics, transcriptomics, and metabolomics research.


Rescentris has released CERF Notebook 2.4 Xserve Edition. CERF (Collaborative Electronic Research Framework) is a server-based electronic lab notebook and research document-management system for the Apple Xserve platform running Mac OS X.


Molecular DNA has launched SQLPDB, a Microsoft SQL 2000 relational database that contains more than 29,000 PDB .ENT files. Researchers can use SQLPDB when developing custom software applications that query access to the molecular definition files that are published at the Protein Data Bank, the company said. The software is priced at $1,795 for commercial users and $595 for academic users, and is available at http://www.moleculardna.com/purchasePage.htm.


The US Department of Energy's Joint Genome Institute has released an enhanced version of its Integrated Microbial Genomes (IMG) data-management system. The new release, IMG 1.2, includes 270 additional public genomes and nine new JGI genomes, bringing the total number of genomes in IMG to 618 (318 bacterial, 25 archaeal, 15 eukaryotic, 260 bacterial phage). Of these, 40 are finished and 80 are draft genomes sequenced by DOE JGI. IMG is available at http://img.jgi.doe.gov/. The next update is scheduled for Dec. 1.


Stone Bond Technologies has released Microarray Quick Start, a microarray LIMS product designed for microarray core research facilities that automates microarray workflows and streamlines laboratory administration. The company said that the system can be implemented "in a matter of days," and can manage core operations procedures, lab requests, patient and grant billings, materials tracking, and load balancing.


Oak Ridge National Laboratory has released Vigyaan 1.0 at http://www.vigyaancd.org/. Vigyaan is a Linux CD containing a suite of applications for bioinformatics, computational biology, and computational chemistry. The latest version is based on Knoppix v3.7.


Strand Life Sciences (formerly Strand Genomics) has launched admetis, an in silico predictive ADMET tool. The software is for modeling and predicting drug-relevant properties of molecules in silico. Users can build custom models from scratch using their own data or use pre-built models, truPK and truTox, for predicting bioavailability, protein binding, volume distribution, elimination half life, rate of absorption, and hERG binding.

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