Edwin H. Connell: Elements of Abstract and Linear Algebra

A free online textbook on abstract algebra with emphasis on linear algebra.
Find Edwin H. Connell: Elements of Abstract and Linear Algebra at: http://www.math.miami.edu/~ec/book/

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PARI-GP

PARI-GP is a software package for computer-aided number theory.
Find PARI-GP at: http://www.parigp-home.de/

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Avida

Avida is an auto-adaptive genetic system designed primarily for use as a platform in Digital or Artificial Life research. In lay terms, Avida is a digital world in which self-replicating computer programs mutate and evolve. Avida allows the user to study questions and perform experiments in evolutionary dynamics and theoretical biology that are intractable in real biological systems.

Find Avida at: http://devolab.cse.msu.edu/software/avida/

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Swarm

Swarm is a kernel and library for the multi-agent simulation of complex systems. The basic architecture of Swarm is a collection of concurrently interacting agents: within this architecture, a large variety of agent based models can be implemented.
Find Swarm at: http://savannah.nongnu.org/projects/swarm

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XDrawChem

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems.
Find XDrawChem at: http://xdrawchem.sourceforge.net/

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SNA Package

S Routines for Social Network Analysis the R Statistical Computing Environment
Find SNA Package at: http://erzuli.ss.uci.edu/R.stuff/

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Garlic

Garlic is a free molecular visualization program written for unix and unix clones.
Find Garlic at: http://www.zucic.org/garlic/

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VASP Data Viewer

A free, open source 3D viewer for molecular charge distributions.
Find VASP Data Viewer at: http://vaspview.sourceforge.net/

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xyz2rgb

xyz2rgb makes pretty pictures and movies of molecules. It expects input in the form of an XYZ file, one of the file formats frequently used by computational chemists. As output, it produces one or more line-interlaced RGB files.
Find xyz2rgb at: http://www.ccl.net/cca/software/SOURCES/to_do_2/xyz2rgb/xyz2rgb.html

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GAlib

GAlib contains a set of C++ genetic algorithm objects.
Find GAlib at: http://lancet.mit.edu/ga/

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