OpenScience / Software



BioJava

Posted on February 24, 2001 by Dan Gezelter

Java tools for processing biological data Find BioJava at: http://www.biojava.org/

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Posted in Life Sciences | Leave a comment

Kemistry

Posted on February 23, 2001 by Dan Gezelter

KDE-inspired molecular weight calculator Find Kemistry at: http://kemistry.sourceforge.net/

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Posted in Chemistry | Leave a comment

Netlib

Posted on February 23, 2001 by Dan Gezelter

An incredibly useful set of libraries for numerical computation. Find Netlib at: http://www.netlib.org

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Posted in Mathematics | Leave a comment

Physis

Posted on February 23, 2001 by Dan Gezelter

Artificial life research platform to study the evolvability of different assembly-like computer languages. Find Physis at: http://sourceforge.net/projects/physis/

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Posted in Artificial Life | Leave a comment

MOSCITO

Posted on February 23, 2001 by Dan Gezelter

Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT … Continue reading →

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Posted in Molecular Dynamics | Leave a comment

CACTVS

Posted on February 23, 2001 by Dan Gezelter

CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. Find CACTVS at: http://www2.chemie.uni-erlangen.de/software/cactvs/index.html

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Posted in Theoretical and Computational | Leave a comment

EMBOSS

Posted on February 23, 2001 by Dan Gezelter

EMBOSS is “The European Molecular Biology Open Software Suite”. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety … Continue reading →

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Posted in Biochemistry | Leave a comment

ATLAS

Posted on February 23, 2001 by Dan Gezelter

Automatically Tuned Linear Algebra Software Find ATLAS at: http://www.netlib.org/atlas/index.html

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Posted in Numerical Libraries | Leave a comment

Moldy

Posted on February 23, 2001 by Dan Gezelter

MOLDY is a parallelised OpenMP short-ranged molecular dynamics program, first written at Harwell Laboratory in the 1980s. The program is rewritten in a modular fashion to allow for easy user modification, in particular the implementation of new interatomic potentials. Using … Continue reading →

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Posted in Molecular Dynamics | 1 Comment

Chemtool

Posted on February 23, 2001 by Dan Gezelter

Chemtool is a program for drawing organic molecules easily and store them as an Postscript, X-Bitmap, LaTeX and XFig file. Find Chemtool at: http://ruby.chemie.uni-freiburg.de/~martin/chemtool/

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Posted in Molecule Viewers and Editors | Leave a comment