Open Source Python Simulation Software

Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.

A toolkit in C++ and python to process both experimental and simulation data of colloidal particles. Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)

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.

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