Ocimum Biosolutions has launched iRNAWiz, an siRNA design tool. Users can use the software to define search templates, set regions of interest based on a variety of criteria, and post design analysis of successful siRNAs.
GepSoft has released APS (Automatic Problem Solver) 3.0, a modeling package based on the company’s GEP (Gene Expression Programming) technique. A free demo of the software is available at http://www.gepsoft.com/gepsoft/.
Vigyaan, an electronic workbench for computational biology and computational chemistry, is available from Oak Ridge National Laboratory at http://www.vigyaancd.org/. The package includes ClustalX, NCBI Blast, Open Babel, EMBOSS, Gromacs, Ghemical, PyMol, Garlic, XDrawChem, GNU R, Gnuplot, Octave, Xmgr, Xfig, The GIMP, ImageMagick, GNU C/C++/Fortran compilers, and ps2pdf. The package is available under the GNU GPL.
Ensembl 20 is available at http://www.ensembl.org/. The release includes significant changes to the API and schema. Details of these changes are available at http:// www.ensembl.org/Docs/wiki/html/EnsemblDocs/EnsemblCore.html. There are no new assemblies in the release, but all species databases have been updated to the new schema.
The BioJava project has released an upgrade of the Dazzle DAS (distributed annotation system) server at http://www.biojava.org/download/dazzle/. The new release includes improvements to the plug-in API, updates to work with BioJava 1.4, and other minor improvements.
Rensselaer Polytechnic Institute has released a QSAR modeling package called DDASSL (Automated Design and Discovery of Novel Pharmaceuticals using Semi-Supervised Learning in Large Molecular Databases). The package includes several modules — Analyze for data mining, RECON for the reconstruction of molecular charge densities and charge density-based electronic properties of molecules, and MetaNeutral for back-propagation — and is available at http://www.rpi.edu/locker/82/001182/.
DeLano Scientific has released PyMol 0.95 at http://pymol.sourceforge.net/. New features of the molecular modeling software include improved usability, an appearance wizard, and two new surface types (dot and tri-mesh).