From 2007.igem.org

Biological Simulators

1. CellDesigner: http://www.celldesigner.org/

2. Copasi (Complex Pathway Simulator): http://www.copasi.org/tiki-index.php

3. XPP/XPPAUT: http://www.math.pitt.edu/~bard/xpp/xpp.html

4. BioModels Database: http://www.ebi.ac.uk/biomodels/

EDA (Electronic Design Automation) Utilities

1. gEDA (GPL'd Suite of EDA Tools): http://www.geda.seul.org/index.html

2. Icarus Verilog: http://www.icarus.com/eda/verilog/