Welcome to the VCell web

Coding and docs

• The VCell project Sourceforge page
• The VCML specification: VcmlSpec
• Link to Virtual Cell SBML Converter
• Virtual Cell/MIRIAM annotations : Annotation discussions

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

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.
    • Hierarchical Modeling (former Model Composition) - L3 extension proposal
    • Structured Include of SBML Fragments (includes xi:include) - L3 core enhancement proposal
• Another workshop on rule-based features is being planned for late 2007 at EBI
  • Details can be found here

BioModels database integration

Spatial extension

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

BioNetGen and rules

• The BioNetGen@VCell page
• BioNetGenCustomization

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

• Systems Biology Pathway Exchange (SBPAX) - A New Glue to Integrate SBML/VCML-type Models with BioPAX-type Pathways
• Systems Biology Linker (Sybil) - An SBPAX-capable platform for the Virtual Cell for SBML/VCML/BioPAX 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