Open Source C Simulation Software

TinkerCell is a software for synthetic biology. The visual interface allows users to design networks using various biological "parts". Models can include modules and multiple cells. Users can program new functions using C or Python. www.tinkercell.

PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

SFS_CODE (Selection on Finite Sites under COmplex Demographic Events) performs forward population genetic simulations under a general Wright-Fisher model with arbitrary demographic, selective, and mutational effects.

A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8

Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes. Please check our new repository: https://github.com/CNS-OIST/STEPS

Neurospaces is a development center for tools in computational neuroscience. See http://www.neurospaces.org/

Hy3S uses advanced MPI parallelized hybrid stochastic simulation methods to quickly compute the dynamics of biochemical networks with thousands of species/reactions. Many features included (see Home Page). An easy-to-use GUI (Matlab req) is included.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

The EvoGrid is an effort to develop a distributed simulation system to simulate potential pre-biotic chemical environments.

Fast-DCM (Fast-DynamicCausalModelling) is an open-source addon for the SPM5 toolbox (http://www.fil.ion.ucl.ac.uk/spm/software/spm5/). It accelerates the estimation of Dynamic Causal Models.

NeMo is a high-performance spiking neural network simulator which simulates networks of Izhikevich neurons on CUDA-enabled GPUs. NeMo is a C++ class library, with additional interfaces for pure C, Python, and Matlab.

SpiNet is a neural simulation tool for large spiking networks with highly heterogeneous synapses. Neurons are modelled as I&F units with dual exponential synaptic conductances. Complex network models can be easily built using the included tool NetBuilder

This software has moved to http://www.poissonboltzmann.org/.

Arena is a computer simulation in which programs compete for CPU time and access to main memory. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density dependent natural selection are amenable to investigation.

The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.

CellMC is a multi-platform XSLT-based SBML compiler producing executable SSA models based on the optimised direct method.

GENESIS (GEneral NEural SImulation System) is a software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

This project provides the source code for the Mitochondiral Infectious Damage Adaptation (MIDA) model of aging. A probabilistic modeling approach is applied by solving the master equation in mitochondrial quality state space in the presence of fusion-fission events, decay of functional quality, mitophagy and mitochondrial biogenesis, as well as molecular damage originating from a random source or from infectious events during fusion and fission. The provided source code is written in C and performs the time integration of the master equation for the time-evolution of the probability to find mitochondria in states of quality q at time t. Output is generated in terms of data files and the graphical visualization of readout parameters is automatically performed using the Graphical Layout Engine (GLE; see: http://glx.sourceforge.net/). Please, send email to thilo.figge<at>hki-jena.de to request a copy of the source code.

This is a C library with a set of functions that allow the user to evolve biological networks. The user provides a fitness function in C, and the library will do the rest. A few simulation algorithms and examples are included.

RANGE: produce random genetic transcription networks in the NEMO language, which when compiled outputs models in Systems Biology Markup Language. Generate synthetic microarray data, or use NEMO alone to SBML-ize a network, or visualize it in cytoscape.

SunlightCBM is a suite of perl scripts for constraint-based modelling and flux-balance analysis in metabolic networks.

The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!

This project aims to develop various tools for artificial life and complex systems simulations: from the simulator itself to generic generation tools.