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 mesh generators. freeFEM3D, as well as its cousins (FreeFEM, FreeFEM+ and FreeFEM++), is a PDE solver driven by a user friendly language.
Find freeFEM3D at: http://www.freefem.org

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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 require interpolations of data on several meshes and their manipulation within one program. In this report we build on a fast quadtree-based interpolation algorithm, propose a language for the manipulation of data on multiple meshes (generated with bamg) and test by designing an extension of freefem. and of freefem+. FreeFem++ is written in a C++ idioms, this software run on all unix OS (with g++ 2.95.2 or more and X11R6), on Window95, 98, 2000, NT, and on MacOS 9 and X (carbon version).
Find freeFem++ at: http://www.freefem.org/

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Aquatic Optics Monte Carlo Model

Posted on August 29, 2003 by Dan Gezelter

The AOMC model is an Open Source Aquatic Optics Monte Carlo model. It simulates the propagation of light in an optically shallow, vertically heterogeneous aquatic medium. It is written in FORTRAN 90.
Find Aquatic Optics Monte Carlo Model at: http://aomc.fugadeideas.org/

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Synthon.net

Posted on August 23, 2003 by Dan Gezelter

An online resource of chemical information provided in a variety of digital formats for the practicing organic chemist.
Find Synthon.net at: http://www.synthon.net

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GAP – Groups, Algorithms and Programming

Posted on July 16, 2003 by Dan Gezelter

GAP is a free system for computational discrete algebra.
Find GAP – Groups, Algorithms and Programming at: http://www.gap-system.org/

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PyGeo: a Dynamic 3d geometry laboratory

Posted on July 14, 2003 by Dan Gezelter

PyGeo is a dynamic geometry laboratory and toolkit. PyGeo may be used to explore the most basic concepts of Euclidean geometry at an introductory level, including by elementary schools students and their teachers. But is particularly suitable for exploring more advanced geometric topics – such as projective geometry and the geometry of complex numbers The intent is to bring a rich visual experience to the study of both synthetic and analytic geometry.
Find PyGeo: a Dynamic 3d geometry laboratory at: http://pygeo.sourceforge.net/

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COIN-OR

Posted on June 17, 2003 by Dan Gezelter

The Computational Infrastructure for Operations Research (COIN-OR) project is an initiative to spur the development of open-source software for the operations research community. Projects include linear and nonlinear optimization solvers and a tabu search framework.
Find COIN-OR at: http://www.coin-or.org/

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GLPK

Posted on June 17, 2003 by Dan Gezelter

GLPK (GNU Linear Programming Kit) is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. GLPK supports the GNU MathProg language, which is a subset of the AMPL language.
Find GLPK at: http://www.gnu.org/software/glpk/glpk.html

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DoseLab

Posted on June 6, 2003 by Dan Gezelter

DoseLab is a set of software programs for quantitative comparison of measured and computed radiation dose distributions. It is written in the Matlab programming language and is easily extensible to more general applications in radiation physics.
Find DoseLab at: http://doselab.sourceforge.net/

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