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Monthly Archives: August 2004
New entries in Bioinformatics
Today we are starting to look at bioinformatics software, most of which is collected at a very nice site, bioinformatics.org. The new entries for today are: AnnHyb, Alkahest, ALiBio, and ABE, all of which are nascent bioinformatics suites. Take a … Continue reading
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AnnHyb
AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features includes format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination… Find AnnHyb at: http://bioinformatics.org/annhyb/
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The Alkahest Initiative
Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. The goal is to produce a comprehensive package for data management and bioinformatics research which is composed of separable but interoperable … Continue reading
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ALiBio: Algorithms Library for Bioinformatics
The goal of ALiBio is the give libraries and efficient fundamental algorithm to be used when developing applications in the bioinformatics field. Find ALiBio: Algorithms Library for Bioinformatics at: http://bioinformatics.org/ALiBio/
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ABE
ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve. Find ABE at: http://bioinformatics.org/abe/
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Forums and Comments
Thanks to a generous donation from Ed Richley for some undergraduate support we have been able to add two new features to the OpenScience site. We’re allowing users to comment on our news items as they are posted, and we … Continue reading
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Monday is Molecular Dynamics Day!
Today we’ve added two new entries to our Molecular Dynamics section. The Molecular Workbench looks like a great interactive teaching tool for exploring material and molecular properties. We’re also proud to include OOPSE which is the object-oriented parallel simulation engine. … Continue reading
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OOPSE
OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded … Continue reading
Posted in Molecular Dynamics
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