E-Cell Project is an international research project aiming to model and reconstruct biological phenomena in silico, and developing necessary theoretical supports, technologies and software platforms to allow precise whole cell simulation.

NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. It evolved from a long collaboration between Michael Hines and John W. Moore at the Department of Neurobiology, Duke University. Their express goal was to create a tool designed specifically for solving the equations that describe nerve cells.

Linked from:
The SfN Neuroscience Database Gateway

GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.

Linked from:
The SfN Neuroscience Database Gateway

OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry(METI), Japan. The objective of the project is to bridge microstructural (or molecular) characteristics of soft materials with their material characteristics by simulation and modeling.