WebCell

Category Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract WebCell (Modeling and Simulation of Cellular Networks Online) is an integrated simulation environment for managing quantitative and qualitative information on cellular networks, and for interactively exploring their steady-state and dynamic behaviors over the web.

A user-friendly web interface allows users to efficiently create, visualize, simulate and store their reaction network models, thereby facilitating kinetic modeling and simulation of biological systems of interest.

Supported analysis methods for such models include, but not limited to, structural pathway analysis, metabolic control analysis (MCA), conservation analysis and dynamic simulation.

A variety of model collections publicly available have been compiled to provide comprehensive implications for the cellular dynamics of the models.

WebCell features/capabilities include:

Model construction --

Provides a simple and comprehensive environment for the modeling of cellular networks through a well-designed web interface:

1) Describe the project summary info.

2) Define model components (e.g., molecular compounds or metabolites) and their relations (e.g., reactions or interactions).

3) Set relevant kinetic information (e.g., rate equations, user- or pre- defined kinetic type and relevant parameters, and initial concentrations).

4) Easily edit, modify and save model information about the project summary, components, relations and kinetics.

5) Dynamically generate tabularized view pages for model information on the summary info, compounds, reactions and kinetic equations.

6) Provide interactive access to detailed information on each reaction or compound using hyperlinks.

7) Automatically layout a model network for dynamic visualization.

Model exchange --

Enhance the modeling capabilities via:

1) SBML support (import/export) - Systems Biology Markup Language (SBML) is an eXtensible Markup Language (XML)-based modeling language for representing biochemical networks.

2) MATLAB export.

Model analysis --

Provide various analysis techniques:

1) Validate a kinetic model.

2) Time course simulation -

Once the valid kinetic model is constructed, one can explore the dynamic behavior of the cellular system by solving ordinary differential equations (ODEs) or differential algebraic equations (DAEs) with conserved moieties which can be identified through conservation analysis.

3) Conservation analysis -

Some models contain combinations of metabolite masses that are constant in time, due to stoichiometric constraints.

These conserved masses, also known as conserved moieties, are a time-invariant property of the system.

WebCell reveals all conserved moieties automatically from initial concentrations.

4) Structural pathway analysis - Null space analysis/Elementary mode analysis -

Pathway analysis investigates structural and functional properties of a given biological network by identifying independent pathways and futile cycles as well as optimal pathways with respect to product/biomass yield.

5) Metabolic control analysis (MCA) -

Metabolic Control Analysis (MCA) is a mathematical formalism for the steady-state control and sensitivity analysis of biological systems.

MCA attempts to describe the relative control of each component in the system (the independent variables or parameters) that are exerting on the pathway fluxes and metabolite concentrations (the dependent variables).

The sensitivity of network components to perturbations is quantified by evaluating flux control, concentration control, elasticity and response coefficients, thus identifying the inherent relationship between relative changes in the system variables (e.g., flux or metabolite concentration) and the perturbed parameter.

Model library --

Provides various kinetic models in metabolic, signaling and regulatory networks:

1) JWS Online - JWS Online is a Systems Biology tool for the simulation of kinetic models from a curated model database.

2) BioModels Database - BioModels Database is an annotated resource of quantitative models of biomedical interest.

Models are carefully curated to verify their correspondence to their source articles (see G6G Abstract Number 20295).

System Requirements

Web-based.

Manufacturer

WebCell is developed in collaboration with the Process Systems Laboratory (PSL) and the Metabolic and Biomolecular Engineering National Research Laboratory (MBEL).

Manufacturer Web Site WebCell

Price Contact manufacturer.

G6G Abstract Number 20457

G6G Manufacturer Number 104084