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ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
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Java based multi-agent platform built on an organizational model (agent, group, role). MadKit provides general agent facilities (lifecycle management, message passing, distribution, ...), and allows high heterogeneity in agents.
Emulica provides manufacturing control engineers and researchers with generic modeling components to build industry-scale virtual (emulated) shop floor systems, and thus test control approaches.
PCSIM is a tool for distributed simulation of heterogeneous networks composed of different model neurons and synapses. The development of PCSIM was supported by the FACETS EU project.
LaserFoam performs simulations of laser pulses using an adaptive split step Fourier method to solve the generalized nonlinear Schrödinger equation. It provides a graphical environment to run and visualize the results.
pyFoam is a Python front-end to the OpenFOAM (Open Source CFD Toolbox). It introduces interactivity into OpenFOAM, simplifies connection with third-party functionality and streamlines design of custom user solvers
This is a set of Python classes that can be used to simulate dynamic multi-body systems. It used to be a project for studies. Now it is not being worked on anymore, but it is completely GPLized.
Ouroborus is an artificial life framework for mobile agents on a background of cellular automata. It can be used to teach and research topics such as population genetics, ecology and evolution. The demo includes a curses view and live Csound audio.
FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
A Software project to assimilate solar magnetograms into suitable physics based models of the solar wind expansion. To predict the solar wind conditions at the Earth and at outer planets. Or any space-craft location in the solar system.
Guanxi is a robust analysis and simulation application for Social Network Analysts. Guanxi allows researchers in the field to create, import, and export an endless array of networks, analyze their structure, and run custom dynamics over them.
vtkModeling-beta.zip: it is an extension of Visualization ToolKit 5.0. Basically it's a collection of deformation algorithms, like laplacian surface editing, moving least square, mass spring system, etc.
IFoam is an OpenFOAM derived framework. It uses Python programming language for definition of its API. Itegrates visual components for limited post-processing. Provides access to some GUI components for more efficient set up the simulation cases.
Translates OpenFOAM (Open Source CFD Toolbox, see http://sourceforge.net/projects/foam) data into MED format (see http://www.code-aster.org/outils/med). The initial goal to develop this utility was to be able integrate OpenFOAM functionality with SALOME
The Location Containment Object Model(LCOM) is a simulation framework written in Python. LCOM provides a rule-based solution to handling partial object containment, object migration, message passing, and simulation observation.
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures.
Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html