MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems [article]

Fedor Kazantsev, Ilya Akberdin, Sergey Lashin, Natalia Ree, Vladimir Timonov, Alexander Ratushny, Tamara Khlebodarova, Vitaly Likhoshvai
2016 bioRxiv   pre-print
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 whole 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 MAMMOTh (MAthematical Models of bioMOlecular sysTems) database that allows integrating
more » ... ly curated mathematical models of biomolecular systems, which are fit to the experimental data. The 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 database supports export of single model or their combinations in SBML or Mathematica standards. The database currently contains more than 100 mathematical 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 such biological processes as: de novo nucleotide biosynthesis, aerobic/anaerobic respiration, and nitrate/nitrite utilization in E. coli. All current models are functionally interconnected and sufficiently complement public model resources.
doi:10.1101/053652 fatcat:33jw3gcyiff4dfuaoiolcru72u