OpenScience / Software



iBabel cheminformatics and molecule viewer

Posted on July 5, 2006 by Dan Gezelter

This is an Applescript Studio application that provides a front-end for a variety of Cheminformatics tools. To date these include file conversion (between a vast range of chemical file formats), SMARTS-based substructure searching, similarity searching, list manipulation, overlaying using OpenBabel, … Continue reading →

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Posted in Molecule Viewers and Editors | Leave a comment

g3data

Posted on June 19, 2006 by Dan Gezelter

g3data is used for extracting data from graphs. In publications graphs often are included, but the actual data is missing. g3data makes the extracting process much easier. Find g3data at: http://www.frantz.fi/software/g3data.php

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Free-software licenses

Posted on May 31, 2006 by Dan Gezelter

Everyone should go read Brooks Moses on Free-software licenses: requirements vs. requests. His post has made me re-think the license we use for our group simulation code. I’ve never like GPL because it essentially guarantees that friends in the corporate … Continue reading →

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Posted in Science, Software | 2 Comments

The CCP1GUI

Posted on May 26, 2006 by Dan Gezelter

The CCP1GUI project aims to develop a free, extensible Graphical User Interface to various computational chemistry codes developed by the worldwide academic community, with an emphasis on ab initio Quantum Chemistry codes. Find The CCP1GUI at: http://www.cse.scitech.ac.uk/ccg/software/ccp1gui/

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Posted in Molecule Viewers and Editors | Leave a comment

Fast interpolation code?

Posted on April 10, 2006 by Dan Gezelter

Here’s a question for everyone who does numerical computation. Has anyone released an open-source 1-d interpolation algorithm with assembly code for the various kinds of processor SIMD extensions (i.e. SSE2, 3DNow, AltiVec)? Most (if not all) scientific codes make repeated … Continue reading →

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Posted in Science, Software | 7 Comments

OpenBugs

Posted on April 1, 2006 by Dan Gezelter

Open source software for Bayesian analysis using MCMC: a continuation of the WinBUGS project. Find OpenBugs at: http://www.mathstat.helsinki.fi/openbugs/

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Posted in Statistics | Leave a comment

SunlightLB

Posted on March 29, 2006 by Dan Gezelter

SunlightLB is an open-source 3D lattice Boltzmann code. It implements a standard lattice Boltzmann algorithm for three dimensional simulations, using a D3Q19 lattice with a twin relaxation time scheme. Objects, possibly moving, are included by a link bounce-back method. This … Continue reading →

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Posted in Fluid Dynamics | Leave a comment

Adium X

Posted on March 20, 2006 by Dan Gezelter

A brief break from the ongoing discussion to point out Adium X, which is an open source IM tool for Mac OS X. The cool thing about it is that if you happen to have the OS X Equation Service … Continue reading →

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Posted in Fun, Science, Software | Leave a comment

Making Money from OpenSource Science Software. III. Sell Services

Posted on March 14, 2006 by Dan Gezelter

This is the third post in a series exploring how scientific software companies might be able to make money while still keeping their code open. The previous articles are: How to make money from Open Source scientific software Sell Hardware … Continue reading →

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Posted in Policy, Science, Software | Tagged , , | 8 Comments

Making Money from OpenSource Science Software. II. Sell Hardware

Posted on March 13, 2006 by Dan Gezelter

This is the second post in a series in which I’m trying to figure out a general strategy for developers of open source scientific software to make a living without closing the source to their codes. The canonical examples of … Continue reading →

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Posted in Policy, Science, Software | Tagged , , | 3 Comments