OpenScience / Software



DomainFinder

Posted on February 23, 2001 by Dan Gezelter

a free interactive program for the determination and characterization of dynamical domains in proteins. Find DomainFinder at: http://dirac.cnrs-orleans.fr/DomainFinder/

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Posted in Biophysical | Leave a comment

MMTK

Posted on February 23, 2001 by Dan Gezelter

The Molecular Modelling Toolkit (MMTK) is a Python-based Open Source program library for molecular simulation applications. Find MMTK at: http://dirac.cnrs-orleans.fr/MMTK/

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Posted in Theoretical and Computational | Leave a comment

The Brenner Potential

Posted on February 23, 2001 by Dan Gezelter

C code for Brenner Potential Molecular Dynamics Find The Brenner Potential at: http://www.rahul.net/pcm/brenner/

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Posted in Molecular Dynamics | Leave a comment

Edwin H. Connell: Elements of Abstract and Linear Algebra

Posted on February 23, 2001 by Dan Gezelter

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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Posted in Linear Algebra | Leave a comment

SciPy

Posted on February 23, 2001 by Dan Gezelter

SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering. In particular, these are some of the core packages: NumPy, SciPy library, Matplotlib, IPython, Sympy, and pandas Find SciPy at: http://www.scipy.org/index.html

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Fungimol

Posted on February 23, 2001 by Dan Gezelter

Fungimol is an extensible system for designing atomic-scale objects. The intent is to eventually extend it to be a useful system for doing molecular nanotechnology design work. At the moment it’s a PDB file viewer and Buckminsterfullerine editor. Find Fungimol … Continue reading →

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Posted in Theoretical and Computational | Leave a comment

FFTW

Posted on February 23, 2001 by Dan Gezelter

A fast, free C FFT library; includes real-complex, multidimensional, and parallel transforms. Benchmarked against many other FFTs. Find FFTW at: http://www.fftw.org/

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Posted in Numerical Libraries | Leave a comment

plotutils

Posted on February 23, 2001 by Dan Gezelter

The GNU plotutils package contains software for both programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector grap … Continue reading →

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Posted in 2D Plotting | Leave a comment

The Gri graphing language

Posted on February 23, 2001 by Dan Gezelter

Gri is an extensible plotting language for producing scientific graphs, such as x-y plots, contour plots, and image plots. It was written by a scientist and therefore has the sorts of things a scientist needs. It is much like LaTeX, … Continue reading →

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Posted in Visualization | Leave a comment

Open Visualization Data Explorer

Posted on February 23, 2001 by Dan Gezelter

IBM’s famous volume renderer that does much much more. Find Open Visualization Data Explorer at: http://www.opendx.org/

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Posted in 3D Plotting, Tools, Visualization | Leave a comment