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CLC Bioinformatics Cell, Surflex-Sim, Ontologizer 2, Cell Electrophysiology Simulation Environment 1.4.6, VALID, Nautilus

CLC Bioinformatics Cell, Surflex-Sim, Ontologizer 2, Cell Electrophysiology Simulation Environment 1.4.6, VALID, Nautilus
CLC Bio has released the CLC Bioinformatics Cell, an SIMD-based bioinformatics accelerator that plugs into the USB port of any desktop or laptop PC. According to the company, the CLC Bioinformatics Cell can accelerate the Smith-Waterman and ClustalW algorithms up to 110 times faster than a fast desktop PC.

Tripos has released Surflex-Sim, a flexible molecular alignment algorithm that is integrated with its Sybyl molecular modeling environment. Surflex-Sim optimizes the pose of query molecules to evaluate their three-dimensional similarity to a known active compound. The method is useful for modeling therapeutically relevant biological targets based only on their known ligands, which enables the prediction of off-target effects, the company said. Surflex-Sim was developed by Ajay Jain, founder and chief scientist at BioPharmics and a professor at the University of California, San Francisco. Tripos also markets Jain's Surflex-Dock program.

Ontologizer 2, a tool for analyzing and visualizing biological data using the Gene Ontology, is available here. New features include a new procedure for statistical analysis of term overrepresentation.

Cell Electrophysiology Simulation Environment (CESE) 1.4.6, a framework for performing electrophysiological simulations, is available here. CESE is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations, according to its developers. CESE 1.4.6 includes improved results printing, the capability to export to scalable vector graphics format, and improved support for continuous simulations.

Concurrent with the launch of several new products for forensic DNA testing, Applied Biosystems said that it will release a new software package, called VALID, for automating forensic DNA validation studies, in early summer. ABI said that the software is designed to support, simplify, and standardize validation studies, while complying with government standards for forensic DNA lab operation.

Thermo Fisher Scientific has released version 8.0 of its Nautilus laboratory information management system. Nautilus LIMS 8.0 is built upon Microsoft .NET, and includes an improved user interface, cut-and-paste workflows, improved interaction with plate-handling systems, new data types, and a new data manager module.

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