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Synthetic Biology Software Suite (SynBioSS) is composed of a wiki for biochemical kinetic constants, a graphical interface for simulating synthetic biological pathways, and a simulator that runs on either a desktop or supercomputer.
General purpose discrete event simulation (DES) framework for the Python programming language. Khronos gathers ideas from other simulation software and tries to provide a simple and poweful toolset for simulation of discrete systems.
Combines Blender's graphical interface and rendering capabilities with MBDyn's multi-body dynamics, aerodynamics, and aeroelastics simulation and analysis, for rapid modeling and realistic rendering of physics based multi-body simulations.
Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator
MIPGEN is a python program that will calculate Molecular Interaction Potential grids
over a given molecule, that could be either a protein or a small organic compound (drug).
The output will be a series of grids with DX format (*.dx) that the user will be able
to visualize using any Molecular visualization program like VMD, PyMol, Chimera...
This project is a complete cross-platform (Windows, Linux) framework for Evolutionary Computation in pure python. See the project site at http://pyevolve.sourceforge.net or the blog at http://pyevolve.sourceforge.net/wordpress
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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.
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.
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.
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.
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.
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.
MC Traffic es un software que modela el tráfico de la Ciudad de México. Escrito principalmente en Python y Pygame, MC Traffic permite usar imágenes descargadas de Google Maps para hacer simulaciones controladas.