MAMMOTh: A new database for curated mathematical models of biomolecular systems.
Journal of bioinformatics and computational biology
Databases, Factual; Escherichia coli; Gene Regulatory Networks; Metabolic Networks and Pathways; Models, Theoretical; Software; Mathematical models; de novo nucleotide synthesis; gene expression; gene network; generalized Hill functions; respiration
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.
Institute for Systems Biology
Kazantsev, Fedor; Akberdin, Ilya; Lashin, Sergey; Ree, Natalia; Timonov, Vladimir; Ratushny, Alexander; Khlebodarova, Tamara; and Likhoshvai, Vitaly, "MAMMOTh: A new database for curated mathematical models of biomolecular systems." (2018). Articles, Abstracts, and Reports. 1449.