OpenScience / Software



ChemCraft

Posted on August 17, 2004 by Dan Gezelter

A new user-suggested entry today in Molecule Viewers and Editors. Grigoriy Zhurko pointed out ChemCraft, which is a windows-based viewer for looking at the orbitals calculated in GAMESS or Gaussian. The source code (in Delphi) is available.

Share
Posted in Software | 1 Comment

What’s your favorite plotting program?

Posted on August 13, 2004 by Dan Gezelter

Join us over in the Forums to discuss Plots and Graphs. What do you use for day-to-day plotting of your data? What do you use for presentation-quality plots? What are your other essential tools for doing science?

Share
Posted in Software | Leave a comment

New entries in Bioinformatics

Posted on August 10, 2004 by Dan Gezelter

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 →

Share
Posted in Software | Leave a comment

AnnHyb

Posted on August 10, 2004 by Dan Gezelter

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/

Share
Posted in Bioinformatics | Leave a comment

The Alkahest Initiative

Posted on August 10, 2004 by Dan Gezelter

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 →

Share
Posted in Bioinformatics | Leave a comment

ALiBio: Algorithms Library for Bioinformatics

Posted on August 10, 2004 by Dan Gezelter

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/

Share
Posted in Bioinformatics | Leave a comment

ABE

Posted on August 10, 2004 by Dan Gezelter

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/

Share
Posted in Bioinformatics | Leave a comment

Monday is Molecular Dynamics Day!

Posted on August 9, 2004 by Dan Gezelter

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 →

Share
Posted in Software | Leave a comment

OOPSE

Posted on August 9, 2004 by Dan Gezelter

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 →

Share
Posted in Molecular Dynamics | Leave a comment

The Molecular Workbench Software

Posted on July 14, 2004 by Dan Gezelter

The Molecular Workbench is a set of tools that can be used to compute and visualize the motion of ensembles of atoms and molecules. The motion of each entity is estimated using classical dynamics and applicable forces, including van der … Continue reading →

Share
Posted in Molecular Dynamics | Leave a comment