ModelBricks-modules for reproducible modeling improving model annotation and provenance

NPJ Syst Biol Appl. 2019 Oct 8;5:37. doi: 10.1038/s41540-019-0114-3. eCollection 2019.

Abstract

Most computational models in biology are built and intended for "single-use"; the lack of appropriate annotation creates models where the assumptions are unknown, and model elements are not uniquely identified. Simply recreating a simulation result from a publication can be daunting; expanding models to new and more complex situations is a herculean task. 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 discuss a concept for building annotated, reusable models, by starting with small well-annotated modules we call ModelBricks. Curated ModelBricks, accessible through an open database, could be used to construct new models that will inherit ModelBricks annotations and thus be easier to understand and reuse. Key features of ModelBricks include reliance on a commonly used standard language (SBML), rule-based specification describing species as a collection of uniquely identifiable molecules, association with model specific numerical parameters, and more common annotations. Physical bricks can vary substantively; likewise, to be useful the structure of ModelBricks must be highly flexible-it should encapsulate mechanisms from single reactions to multiple reactions in a complex process. Ultimately, a modeler would be able to construct large models by using multiple ModelBricks, preserving annotations and provenance of model elements, resulting in a highly annotated model. We envision the library of ModelBricks to rapidly grow from community contributions. Persistent citable references will incentivize model creators to contribute new ModelBricks.

Keywords: Complexity; Computer modelling; Modularity; Software.

Publication types

  • Research Support, N.I.H., Extramural
  • Review

MeSH terms

  • Computational Biology / methods*
  • Computational Biology / standards*
  • Computer Simulation
  • Databases, Factual
  • Models, Biological
  • Software
  • Systems Biology / methods*
  • Systems Biology / standards