Towards human cell simulation

Salvatore Vitabile, Zuzana Komínková Oplatková, Roman Senkerik, Aleš Zamuda, Natalija Stojanovic, Marco S. Nobile, Adam Viktorin, Tomas Kadavy, Simone Spolaor, Natalija Stojanovic, Marco Gribaudo, Esko Turunen, Mauro Iacono, Giancarlo Mauri, Sabri Pllana

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4 Citazioni (Scopus)

Abstract

The faithful reproduction and accurate prediction of the phe-notypes 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.
Lingua originaleEnglish
Titolo della pubblicazione ospiteLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pagine221-249
Numero di pagine29
Stato di pubblicazionePublished - 2019

Serie di pubblicazioni

NomeLECTURE NOTES IN ARTIFICIAL INTELLIGENCE

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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    Vitabile, S., Oplatková, Z. K., Senkerik, R., Zamuda, A., Stojanovic, N., Nobile, M. S., Viktorin, A., Kadavy, T., Spolaor, S., Stojanovic, N., Gribaudo, M., Turunen, E., Iacono, M., Mauri, G., & Pllana, S. (2019). Towards human cell simulation. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (pagg. 221-249). (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE).