Scientific Inference Systems Laboratory
The Computable Plant
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Software and Documentation

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

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

Cambium Intermediate Process Language

Other Useful Software Links: Computing Frameworks: Computational Geometry:

revised Mon Jun 1 13:20:03 2009