Welcome to the ModelBricks project


Many computational models in biology are built and intended for "single-use"; the modeling assumptions and descriptions of model elements must be found in the corresponding paper. Expanding models to new and more complex situations is non-trivial. As a result, new models are almost always created anew, repeating literature searches for kinetic parameters, initial conditions and modeling specifics. It is akin to building a brick house starting with a pile of clay. Here we present tghe ‚Äča database of ModelBricks - well-annotated, reusable component mechanisms that can be assembled into fully annotated mathematical models for cell biology. Here we present a database of ModelBricks - well-annotated, reusable component mechanisms that can be assembled into fully annotated mathematical models for cell biology.

Each ModelBrick contains

1. Sets of molecules (species) uniquely identified with universal identifiers, their initial concentrations and transport properties.

2. Reaction(s) (changes in state) identified by known biochemical mechanisms and defined by a flux reaction with parameters for forward and reverse rates (kf and kr). Flux terms can be simple mass action kinetics or complex functions.

3. An identified cellular Compartment(s) where the reaction occurs and the species reside.

4. A Publication ID or other identifier of the author and peer-review status for the original model from which a ModelBrick is derived




ModelBricks can be

1. Downloaded in mulltiple formats, such as SBML or VCML formats

2. Inserted into an existing SBML compatible model including all annotations and defined parameters.

3.Created from existing models and submitted for inclusion in the repository.