The Computable Plant

[Image Analysis]

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

[Cambium Intermediate Process Language]

• TR (Download)
• Cellerator
• Plenum
• Organism

[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^*†

[Models]

• Activator Model (Jönsson et al, Bioinformatics 21:i232, 2005)
• One-Dimensional Auxin Model (Jönsson et al, PNAS 103(5):1633-8, 2006)
• For more models see Sigmoid

[Other Useful Software Links]

• 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

[Computing Frameworks]

• 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

[Computational Geometry]

• CGAL
• Qhull Library
• regtet/pwrvtx