MAMMOTh: A new database for curated mathematical models of biomolecular systems

J Bioinform Comput Biol. 2018 Feb;16(1):1740010. doi: 10.1142/S0219720017400108. Epub 2017 Nov 3.


Motivation: Living systems have a complex hierarchical organization that can be viewed as a set of dynamically interacting subsystems. Thus, to simulate the internal nature and dynamics of the entire biological system, we should use the iterative way for a model reconstruction, which is a consistent composition and combination of its elementary subsystems. In accordance with this bottom-up approach, we have developed the MAthematical Models of bioMOlecular sysTems (MAMMOTh) tool that consists of the database containing manually curated MAMMOTh fitted to the experimental data and a software tool that provides their further integration.

Results: The MAMMOTh database entries are organized as building blocks in a way that the model parts can be used in different combinations to describe systems with higher organizational level (metabolic pathways and/or transcription regulatory networks). The tool supports export of a single model or their combinations in SBML or Mathematica standards. The database currently contains 110 mathematical sub-models for Escherichia coli elementary subsystems (enzymatic reactions and gene expression regulatory processes) that can be combined in at least 5100 complex/sophisticated models concerning more complex biological processes as de novo nucleotide biosynthesis, aerobic/anaerobic respiration and nitrate/nitrite utilization in E. coli. All models are functionally interconnected and sufficiently complement public model resources.


Keywords: Mathematical models; de novo nucleotide synthesis; gene expression; gene network; generalized Hill functions; respiration.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Factual*
  • Escherichia coli / genetics
  • Gene Regulatory Networks*
  • Metabolic Networks and Pathways*
  • Models, Theoretical*
  • Software