Simbody

This project is a SimTK Core toolset providing general multibody dynamics capability. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. This toolset was developed specifically for the SimTK Core by Michael Sherman, but descends directly from noble parentage: (1) the public domain NIH Internal Variable Dynamics Module (IVM) facility for molecular dynamics developed and kindly provided by Charles Schwieters, and (2) the TAO dynamics engine for robotics and biomechanics simulation and control, contributed to the open source SimTK effort by Arachi Corporation.
Find Simbody at: https://simtk.org/home/simbody

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KNIME

KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.
Find KNIME at: http://www.knime.org/

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Weka

Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.
Find Weka at: http://www.cs.waikato.ac.nz/ml/weka/

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EigenMath

Very compact, but useful CAS coded entirely in C.
Find EigenMath at: http://eigenmath.net

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Zeobuilder

Zeobuilder is a user-friendly GUI toolkit for the construction of advanced
molecular models. The program contains several advanced tools to build, align,
manipulate and analyze molecular structures. Most of its novel functionality is
based on a hierarchical data-structure of reference frames to represent a
molecular structure.
Find Zeobuilder at: https://github.com/molmod/zeobuilder

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FriCAS

FriCAS is an advanced computer algebra system. Its capabilities range from calculus (integration and differentiation) to abstract algebra. It can plot functions and has integrated help system.
Find FriCAS at: http://fricas.sf.net

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Mathomatic

Mathomatic is a general purpose CAS (Computer Algebra System) and calculator software that can symbolically solve, simplify, combine, and compare algebraic equations, perform complex number and polynomial arithmetic, etc. It does some calculus and handles all elementary algebra, except logarithms.
Find Mathomatic at: http://mathomatic.org

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Gerris

Gerris is for solving problems involving incompressible flow (time-dependent incompressible variable-density Euler, Stokes or Navier-Stokes equations). It uses an adaptive mesh refinement to allow for flows around complex geometries.
Find Gerris at: http://gfs.sourceforge.net

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OpenLB

The OpenLB project provides a C++ package for the implementation of lattice Boltzmann simulations that is general enough to address a vast range of problems in computational fluid dynamics. The package is mainly intended as a programming support for researchers and engineers who simulate fluid flows by means of a lattice Boltzmann method.
Find OpenLB at: http://openlb.net

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NCAR Graphics

NCAR Graphics is a Fortran and C based software package for scientific visualization
Find NCAR Graphics at: http://ngwww.ucar.edu/

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