Do you have an idea for a project?

Posted on September 21, 2004 by Dan Gezelter

Over in the OpenScience Forums, we have a discussion starting on New Project Ideas. Got an idea for a project? Need some collaborators? Come on over and brainstorm it here.

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Two new user-contributed links

Posted on September 21, 2004 by Dan Gezelter

Today we have added links to GAMGI in the Molecule Viewers and Editors section and MultiWell in the Chemical Kinetics section. Thanks to the two OpenScience users who pointed these out!

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GAMGI

Posted on September 21, 2004 by Dan Gezelter

The General Atomistic Modelling Graphic Interface. GAMGI aims to be useful for: 1) the scientific community working in Atomistic Modelling, that needs a graphic interface to build input data and to view and analyse output data, calculated with Ab-Initio and Molecular Mechanics programs; 2) the scientific community at large, studying Chemistry, Physics, Materials Science, Geology, etc., that needs a graphic interface to view and analyse atomic structural information and to prepare images for presentations in classes and seminars; 3) teaching chemistry and physics in secondary schools and universities, even inviting students to install and run GAMGI at home; 4) science promotion, in schools, exhibitions and science museums.
Find GAMGI at: http://gamgi.org/

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Jalview

Posted on August 20, 2004 by Dan Gezelter

Jalview is a multiple alignment editor written entirely in java.
Find Jalview at: http://www.ebi.ac.uk/~michele/jalview/

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Readseq

Posted on August 20, 2004 by Dan Gezelter

Read & reformat biosequences
Find Readseq at: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

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When more is more: Parallel Computing

Posted on August 19, 2004 by Dan Gezelter

We’ve added two new links to very useful tools for scientific programming. Both are in our Data Communication section. MPICH is the ubiquitous MPI implementation, which our own research groups have been using for years. LAM/MPI is a newer MPI implementation from Lumsdaine group. Both are incredibly useful if you write parallel code.

In the OpenScience Forums, we’ve started a new topic to discuss MPI implementations. Come on over and join the discussion!

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LAM/MPI Parallel Computing

Posted on August 19, 2004 by Dan Gezelter

LAM/MPI is a high-quality open-source implementation of the Message Passing Interface specification, including all of MPI-1.2 and much of MPI-2. Intended for production as well as research use, LAM/MPI includes a rich set of features for system administrators, parallel programmers, application users, and parallel computing researchers.
Find LAM/MPI Parallel Computing at: http://www.lam-mpi.org/

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Monte Carlo

Posted on August 18, 2004 by Dan Gezelter

There is a new user-suggested entry today in our Monte Carlo methods section. MCCCS Towhee is an advanced Monte Carlo simulation package which can do Gibbs ensemble MC simulations in liquid, solid, and porous phases. Do you have a favorite open source Monte Carlo program? If so, submit it here!

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MCCCS Towhee

Posted on August 18, 2004 by Dan Gezelter

Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or porous) phases.
Find MCCCS Towhee at: http://towhee.sourceforge.net/

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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.

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