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Welcome to the VCell web

SBML Level 3 Extensions

Spatial Extension

A page dedicated to the efforts to create an L3 extension for spatial modeling.

Other SBML Extensions

Focused SBML Workshops
  • A workshop on model composition/modularity was held at UCHC on Sept 9-10, 2007 with participation via video link from EBI Hinxton and MPI Magdeburg
    • Details can be found here
    • The overall conclusion of the workshop was that 2 separate proposals will be developed. One will focus on the language elements required for the actual "model composition" (but brings also additional, initially unforeseen, functionality - such as encoding parameter sets and multiple related simulations). The other will focus on the mechanics of simply assembling SBML from bits and pieces (linking in multiple files and/or fragments thereof). It is expected that the first proposal will be a bonafide L3 extension, wehereas the second will be (part of) L3 core enhancement(s). Links to the proposals are providede below, followed by the original materials/details/agenda, etc. of the workshop.
  • Another workshop on rule-based features is being planned for late 2007 at EBI
    • Details can be found here

Coding and docs

Troubleshooting, FAQs and Wishes

SBML and related projects

Link to the SBML Level 3 page on http://sbml.org/

SBML feature support matrix

A table of SBML language features and tools that support them (or not): SBMLFeatureToolMatrix

BioModels database integration

BioNetGen and rules

Sybil - Integrating SBML/VCML-type Models with BioPAX-type Patheways, using SBPAX as a glue

VisIt/VCell integration

Other tools

Virtual Microscopy - microscopy data, modeling and simulation tools.

Virtual FRAP Tool - data driven spatial modeling tool for FRAP experiments

GFit - model-based analysis of experimental data

  • brings together computational models, data, and analysis tools

MicroFilaments Detector - detects and categorizes structures within a cell in microscopy images

VCell WikiUtilities

SED-ML (Simulation Experiment Description Mark-up Language)

CGSB (Cell and Genome Sciences Building)

Topic revision: r46 - 2012-03-22 - 14:23:31 - IonMoraru
 
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