Dynamic network modeling and model analysis

Building network diagram for modelled process in SBML format with CellDesigner

Description
SBML, Systems Biology Markup Language, a free and open interchange format for computer models of biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using SBML, a standard for representing models of biochemical and gene-regulatory networks. By using the open source software CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.

Service provider
Molecular Cell Physiology, Vrije University

Location
Amsterdam, The Netherlands

Contacts
Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin 

Network diagram conversion into a first dynamic model in COPASI

Description
COPASI, Biochemical System Simulator, is another open source software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ordinary differential equations (ODEs) or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.

Service provider
Molecular Cell Physiology, Vrije University

Location
Amsterdam, The Netherlands

Contacts
Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin 

Fitting the dynamic model to experimental data

Service provider
Molecular Cell Physiology, Vrije University

Location
Amsterdam, The Netherlands

Contacts
Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin 

Model analysis

Description
Model analysis, e.g. sensitivity analysis, looking for network targets, metabolic control analysis.

Service provider
Molecular Cell Physiology, Vrije University

Location
Amsterdam, The Netherlands

Contacts
Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin 

Model refinement and tuning with available datasets

Service provider
Molecular Cell Physiology, Vrije University

Location
Amsterdam, The Netherlands

Contacts
Scientific contact: Hans V. Westerhoff 
Technical contact: Alexey Kolodkin