This page provides links to software tools available from the BNMC for the campus community. This software listed here was developed in conjunction with, or acquired by, the BNMC from collaborative projects for use on campus. To see information about general software that is not from us or one of our close collaborators off-campus, please see our resources page.
Image Analysis
CLSM Tools - nuclear segmentation and lineage analysis (CIT/JPL)
Costanza - Confocal Stack Analyzer Application, plugin for ImageJ (CIT/Lund)
SASSIGN - MatLab library for tracking based on softassign matching algorithm (UCI/CIT/JPL)
SegTrack - MatLab libray for segmentation and Tracking (UCI/CIT/JPL)
Simulation Software
Cellerator (CIT)
xCellerator/xlr8r (CIT)
Cellzilla2D (CIT)
ERLeap (UCI/CIT)
Organism- ODE based simulation in C++ (Lund/CIT)
Plenum - Interpreter for Stochastic/Dynamical Grammars (UCI/CIT)
PPM (ETH) - Parallel Particle Mesh Library - meshing and simulation library of continuous and discrete systems using particle-mesh methods.
Sigmoid/Sigmoid Model Explorer (UCI/CIT/JPL)
SSA- Stochastic Simulation (Gillespie Algorithm) in Mathematica (CIT)
Analysis Tools
LDSA - Lam-Delosme Simulated Annealing in Mathematica (UCI)
mPower - Mathematica wrappers for QHULL computational geometry package. (CIT)
Modeling Databases
Biomodels Database (CIT/EBI/Others)
Plenum Model Database (UCI)
Model Exchange
Cambium (CIT/UCI)
CelleratorML (CIT)
Systems Biology Markup Language (CIT/Others)
