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The Free Finite Element Package is a library which contains numerical methods required when working with finite elements. The goal of FFEP is to provide basic functions for approximating the solution of elliptic and parabolic PDEs in 2D. Until 2016 FFEP was developed using C. Science 2016 the language was switched to GNU Octave with some C Mex-Functions. Mesh generation or import is not part of FFEP. We recommend the use of Gmsh.

This package provides high-level interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A...

NEVESIM is a software package for event-driven simulation of networks of spiking neurons with a fast simulation core in C++, and a scripting user interface in the Python programming language. It supports simulation of heterogeneous networks with different types of neurons and synapses, and can be easily extended by the user with new neuron and synapse types. To enable heterogeneous networks and extensibility, NEVESIM is designed to decouple the simulation logic of communicating events...

SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. Additionally the...

Over 75 C++ function for working with vectors, matrix and quaternions. Inside the package there is no cycles, if's, classes or structures. Ideal for designing 3D engines. Headlines of functions are intuitive. For each headline there is a one line comment in Russian. Matrix are presented in OpenGL form 0 4 8 12 1 5 9 13 2 6 10 14 3 7 11 15 Now we are working on adding 50+ more functions for processing the planes, splines, bezier curves and interpolation methods.

Spasmos is a Python package that allows scientists to simulate the dynamics of highly collisional plasmas using a number of numerical methods.

Neurofitter is a parameter tuning package for electrophysiological neuron models. For more information please take a look at http://neurofitter.sourceforge.net