ASALI is an open-source code for chemical engineers
An eXtended Finite Element Method (XFEM) Software.
Modular System for Shelves and Coasts
PySCeS is the Python Simulator of Cellular Systems
Real-time interactive 3D graphics API for scientific simulations
Biomolecular electrostatics software
Molecular Dynamics Cell Construction
Advanced numerical instruments: adaptive meshing, FE methods, solvers
Open source codes related to dissipative particle dynamics