OpenScience / Software



Standard Objects for Astronomy

Posted on February 25, 2004 by Dan Gezelter

This website is a collection of links to resources and papers related to the selection of standard objects for astronomical calibration. Find Standard Objects for Astronomy at: http://sofa.astro.utoledo.edu/SOFA/

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Set Theory on ProvenMath

Posted on February 24, 2004 by Dan Gezelter

(1) precise (strictly formal) statement of the axioms for set theory; (2) proof of the equivalence between the Axiom of Choice and Zorn’s Lemma (3) cardinality theorems and other things Find Set Theory on ProvenMath at: http://www.apronus.com/provenmath/settheory.htm

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Open-SESSAME Framework

Posted on February 19, 2004 by Dan Gezelter

The Open-Source, Extensible Spacecraft Simulation And Modeling Environment (Open-SESSAME) is a collection of libraries, toolkits, and extension points that provide a framework for creating and analyzing spacecraft models of varying complexity. Find Open-SESSAME Framework at: http://spacecraft.sourceforge.net/main.html

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JAligner – Java implementation of biological sequence alignment algorithms

Posted on January 22, 2004 by Dan Gezelter

JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh’s improvement … Continue reading →

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Fityk

Posted on January 14, 2004 by Dan Gezelter

Fityk is a program for nonlinear fitting of analytical functions (especially peak-shaped) to data (usually experimental data). The most concise description: peak fitting software. There are also people using it to remove the baseline from data, or to display data … Continue reading →

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JSci – A science API for Java

Posted on November 13, 2003 by Dan Gezelter

JSci is a set of open source Java packages. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software. Features include: abstract math interfaces, linear … Continue reading →

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The Chemistry Development Kit (CDK)

Posted on November 12, 2003 by Dan Gezelter

e CDK classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them. They are a complete re-write of the CompChem classes that were … Continue reading →

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NeoBio – Bioinformatics algorithms in Java

Posted on October 7, 2003 by Dan Gezelter

NeoBio is a Java class library of Computational Biology Algorithms. The first version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman. Find NeoBio – Bioinformatics algorithms in Java at: http://neobio.sourceforge.net

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freeFEM3D

Posted on September 19, 2003 by Dan Gezelter

freeFEM3D is a 3D version of freeFEM. It is a 3D finite element PDE solver. It does not use standard FEM approximation but is based on fictitious domain method. The main reason for this is the absence of free 3D … Continue reading →

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freeFem++

Posted on September 19, 2003 by Dan Gezelter

FreeFem++ is an implementation of a language dedicated to the finite element method. It provides you a way to solve Partial Differential Equations (PDE) simply. Problems involving partial differential equations (pde) of several branches of physics such as fluid-structure interactions … Continue reading →

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