RT Journal Article
SR Electronic
T1 MAMMOTh: a new database for curated MAthematical Models of bioMOlecular sysTems
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 053652
DO 10.1101/053652
A1 Fedor Kazantsev
A1 Ilya Akberdin
A1 Sergey Lashin
A1 Natalia Ree
A1 Vladimir Timonov
A1 Alexander Ratushny
A1 Tamara Khlebodarova
A1 Vitaly Likhoshvai
YR 2016
UL http://biorxiv.org/content/early/2016/05/16/053652.abstract
AB 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 manually 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.Database URL: http://mammoth.biomodelsgroup.ru