TUTCRIS - Tampereen teknillinen yliopisto


Towards Human Cell Simulation



OtsikkoHigh-Performance Modelling and Simulation for Big Data Applications
AlaotsikkoSelected Results of the COST Action IC1406 cHiPSet
ToimittajatJoanna Kolodziej, Horacio Gonzalez-Velez
KustantajaSpringer Verlag
ISBN (elektroninen)978-3-030-16272-6
ISBN (painettu)978-3-030-16271-9
DOI - pysyväislinkit
TilaJulkaistu - 25 maaliskuuta 2019
OKM-julkaisutyyppiA3 Kirjan tai muun kokoomateoksen osa


NimiLecture Notes in Computer Science
ISSN (painettu)0302-9743
ISSN (elektroninen)1611-3349


The faithful reproduction and accurate prediction of the phenotypes and emergent behaviors of complex cellular systems are among the most challenging goals in Systems Biology. Although mathematical models that describe the interactions among all biochemical processes in a cell are theoretically feasible, their simulation is generally hard because of a variety of reasons. For instance, many quantitative data (e.g., kinetic rates) are usually not available, a problem that hinders the execution of simulation algorithms as long as some parameter estimation methods are used. Though, even with a candidate parameterization, the simulation of mechanistic models could be challenging due to the extreme computational effort required. In this context, model reduction techniques and High-Performance Computing infrastructures could be leveraged to mitigate these issues. In addition, as cellular processes are characterized by multiple scales of temporal and spatial organization, novel hybrid simulators able to harmonize different modeling approaches (e.g., logic-based, constraint-based, continuous deterministic, discrete stochastic, spatial) should be designed. This chapter describes a putative unified approach to tackle these challenging tasks, hopefully paving the way to the definition of large-scale comprehensive models that aim at the comprehension of the cell behavior by means of computational tools.


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