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

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)

Abstract

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. Availability: http://mammoth.biomodelsgroup.ru.

Original languageEnglish
Article number1740010
Number of pages16
JournalJournal of Bioinformatics and Computational Biology
Volume16
Issue number1
DOIs
Publication statusPublished - 1 Feb 2018

Keywords

  • de novo nucleotide synthesis
  • gene expression
  • gene network
  • generalized Hill functions
  • Mathematical models
  • respiration
  • METABOLISM
  • NETWORK MOTIFS
  • BIOLOGY
  • ALGORITHMS
  • Models, Theoretical
  • Escherichia coli/genetics
  • Gene Regulatory Networks
  • Metabolic Networks and Pathways
  • Software
  • Databases, Factual

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