Indicates Partially or fully funded by NSF Award 0330786

Indicates tools developed by or in collaboration with the Computable Plant project

[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]

[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]


[Other Useful Software Links]

[Computing Frameworks]

[Computational Geometry]