Software links

File format parsing

SBML

LibSBML (C/C++/Matlab, but callable from Java)
SBML.jar (Java) as part of JigCell from Virginia Tech

Systems Biology Workbench

Home

SBW at Sourceforge
SBW at the Keck Graduate Institute (newer SBW than Sourceforge)

Tools

Jarnac, Keck Graduate Institute
JDesigner , Keck Graduate Institute
SBW Inspector, Keck Graduate Institute
SBW Matlab Interface, Keck Graduate Institute
SBW Optimizers, Keck Graduate Institute
WinSCAMP, Keck Graduate Institute

Other tools

Pathway Tools, from SRI.