Affymetrix has released a beta version of the Affymetrix GeneChip Command Console, the next generation of its instrument-control software, which will replace the company’s current GeneChip Operating Software. AGCC will support all cartridge-based GeneChip arrays with a file-based system designed for easy data sharing, a streamlined workflow, and ease of use, Affy said. AGCC is scheduled to launch commercially in early 2007, and will include features for sample and array registration, data management, fluidics and scanning instrument control, and automatic and manual image gridding. AGCC will also produce Probe Cell intensity data (.CEL file generation). Affymetrix said it will continue to support GCOS into 2008. The beta release of AGCC is available here.
The National Center for Biotechnology Information has released GenBank 155.0 here. The release contains 65,369,091,950 base pairs and 61,132,599 entries. Uncompressed, the 155.0 flat files require about 230 GB for the sequence files only. The ASN.1 version requires around 199 GB.
Rescentris has released CERF (Collaborative Electronic Research Framework) Chemistry Edition, which offers access to ChemAxon's Marvin chemical drawing and editing software and JChem Base chemical structure management software.
Meanwhile, ChemAxon has released version 4.1 of Marvin. The release includes new structure-based calculations, “extensive” publication features, and support for Microsoft’s .NET, ChemAxon said. A free demo of Marvin is available here.
Release 0.5 of the Cell Cycle Ontology is available here. The new version includes more terms from BIND and other sources and an enhanced upper-level ontology. The ontology currently has 44,312 terms and 29 relationships. It is available in OBO, OWL, XML, and DOT formats.
RIKEN’s Genomic Sciences Center has released OmicBrowse 1.0.1, a browser for several different types of –omic data, here. The release includes new functions for the OmicBrowse server and OmicBrowseManager.
Media Cybernetics has released 3D Surface Inspector, an inspection module for its Image-Pro Plus software that enables users to visualize and measure industrial or biological images in three dimensions. The software allows users to rotate images and view surfaces from any angle. Images can be enhanced for further details using texture mapping, wire frame, or pseudo coloring. 3D Surface Inspector also includes several measurement tools for extracting quantitative data from 3D images.
Sweden's University of Lund has released BASE (BioArray Software Environment) 2.0, a free database for microarray data, here.
BDT, a graphic interface for the AutoGrid/AutoDock docking software package, is available here. BDT helps automate tasks such as the virtual screening of a library of ligands against a set of possible receptors and blind-docking experiments with the whole receptor surface.