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PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.

NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.

An Economy Simulation with many Possibilities trying to be near to reality. Using XML, Python an OpenGL to make it useable on many OS. And also beeing an simulation taht can be so realistic that ist could be used for research (maybe).

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.

Multiplayer framework for flight simulators. Based on M&S HLA 1.3 standards. Provides a 3D air traffic visualization tool and HLA plug-ins for FlightGear, Microsoft Flight Simulator X and X-Plane.

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.

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.

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... For more information on dependencies and usage, please read the Documentation. Users are welcome...

OOP simulation package of mechanical pulp and paper mill

The SIMP/STEP platform provides a fast, efficient, portable abstract framework for interactive and scripted cellular automata and lattice gas computing in the Python environment. SIMP provides a high-level 'programmable matter' laboratory built on

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.

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

pydaqtools provides a common interface to data-acquisition hardware for Python. Control analog/digital output or acquire analog/digital input for immediate analysis with Python for scientific, educational or engineering applications.

Charybdis is a Python-driven set of applications for solving partial differential equations on irregular domains.

Sempy is a Python package for the solution of partial differential equations using the spectral element method.

Dielectrophoresis for microfluidic applications, especially those biological, implemented in python

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.

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.

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.

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.

The Massive G Engine is a simple yet feature-rich extensible 3D simulation engine for Robotics Research and gaming.

Plouf is a set of algorithms that solve partial differential equations on sets of connected points. Emphasis is on fluid mechanics and plasma flows.

A python/C++ framework for Bayesian phylogenetic analysis.

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.