Partially or fully funded by NSF Award 0330786:

• xCellerator Modeling and Simulation
  • mPower Wrapper for qhull, regtet,pwrvtx
  • SSA Stochastic Simulation
  • Cellzilla Static multicellular modeling using Voronoi
• PhasePlot example of doing phase portrait
• segtrack segmenting and tracking matlab function library
• sassign tracking software based on softassign matching algorithm
• Tissue3D Mathematica package for compartmental modeling
• Plenum Interpreter for Stochastic/Dynamical Grammars
• SBML Level 3 Proposal: Dynamic Arrays

• List of Finite Element Packages
• Cellerator
• kMech
• MathSBML
• Sigmoid

• amira
• DINO realting 3D visualization for structural biology
• LSBR Laboratory of Structural Biology at NIH, includes: Bsoft, PIC, PFT/EM3DR, and other image processing tools
• FARSIGHT (Badri Roysam, RPI)
• GoFigure - Caltech Biological Imaging Center
• IDL
• Imaris (Bitplane AG)
• IMOD (Electron Microspy Image Analysis - University of Colorado
• OpenDX
• PRIISM/IVE from UCSF
• UCSB Center for Bioimage Informatics
• Virtual Embryo
• VTK (Kitware)

• SAGE Open Source Math Project (Mathematica/Matlab/Maple Alternative)
• Pyre Caltech Center for Advanced Computing Resources
• Peach Caltech Jensen Lab
• Systems Biology Workbench (SBW)
• Systems Biology Markup Language - SBML

• CGAL
• Qhull Library
• regtet/pwrvtx