Image Analysis

• SegTrack^*† - segmenting and tracking matlab function library
• SASSIGN^*† - tracking software based on softassign matching algorithm
• Costanza^† - Confocal Stack Analyzer Application, plugin for ImageJ
• CLSM Tools^*† - nuclear segmentation and lineage analysis

Modeling, Simulation, and Analysis

• xCellerator^*† - ODE Based Modeling in Mathematica
• ERLeap^*† - Stochastic Simulation (Exact Reaction Leaping)
• SSA^*†- Stochastic Simulation (Gillespie Algorithm) in Mathematica
• LDSA - Lam-Delosme Simulated Annealing in Mathematica
• Organism^† - ODE based simulation in C++
• mPower^*† - Mathematica wrapper for computational geometry using qhull
• Cellzilla^*† - Static multicellular modeling using Voronoi in Mathematica
• PhasePlot^*† - Phase portraits in Mathematica
• PPM - Particle Particle Mesh Library - meshing and simulation library of continuous and discrete systems using particle-mesh methods.
• Tissue3D^*† - Mathematica package for compartmental modeling
• Cellerator† - an earlier version of xCellerator
• kMech† - Cellerator plugin for enzyme kineteics
• MathSBML† - SBML reader and simulator in Mathematica
• Sigmoid† - Model database and simulation package (uses Cellerator)

Stochastic Grammars and Model Description Tools

• Plenum^*† Interpreter for Stochastic/Dynamical Grammars
• Plenum Model Collection^*†
• SBML Level 3 Proposal: Dynamic Arrays^*†

^†Indicates tools developed by or in collaboration with the Computable Plant project.
^*Indicates Partially or fully funded by NSF Award 0330786.

• List of Finite Element Packages
• List of Image Analysis Software Applications
• CSELab Tools - Software tools from the Computational Science and Engineering Laboratory at ETH Zurich.

• 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

revised Mon Jun 1 13:20:03 2009