{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T03:45:09Z","timestamp":1772163909380,"version":"3.50.1"},"reference-count":68,"publisher":"World Scientific Pub Co Pte Ltd","issue":"01","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2018,2]]},"abstract":"<jats:p>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.<\/jats:p>\n                  <jats:p>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.<\/jats:p>\n                  <jats:p>Availability: http:\/\/mammoth.biomodelsgroup.ru<\/jats:p>","DOI":"10.1142\/s0219720017400108","type":"journal-article","created":{"date-parts":[[2017,11,3]],"date-time":"2017-11-03T07:57:33Z","timestamp":1509695853000},"page":"1740010","source":"Crossref","is-referenced-by-count":12,"title":["MAMMOTh: A new database for curated mathematical models of biomolecular systems"],"prefix":"10.1142","volume":"16","author":[{"given":"Fedor","family":"Kazantsev","sequence":"first","affiliation":[{"name":"Institute of Cytology and Genetics SB RAS, Lavrentyev Avenue., 10, Novosibirsk 630090, Russia"},{"name":"Novosibirsk State University, Pirogova str. 2, Novosibirsk 630090, Russia"}]},{"given":"Ilya","family":"Akberdin","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics SB RAS, Lavrentyev Avenue., 10, Novosibirsk 630090, 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