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.

Spolaor, S., Gribaudo, M., Iacono, M., Kadavy, T., Oplatková, Z., Mauri, G., et al. (2019). Towards human cell simulation. In Kolodziej J., Gonzalez-Vélez H. (a cura di), High-Performance Modelling and Simulation for Big Data Applications (pp. 221-249). Springer Verlag [10.1007/978-3-030-16272-6_8].

Towards human cell simulation

Spolaor, Simone
Primo
;
Mauri, Giancarlo;Nobile, Marco S.
Ultimo
2019

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.
Capitolo o saggio
Agent-based simulation; Big data; Biochemical simulation; Computational intelligence; Constraint-based modeling; Fuzzy logic; High-performance computing; Model reduction; Multi-scale modeling; Parameter estimation; Reaction-based modeling; Systems biology;
English
High-Performance Modelling and Simulation for Big Data Applications
Kolodziej J.; Gonzalez-Vélez H.
2019
978-3-030-16271-9
11400
Springer Verlag
221
249
Spolaor, S., Gribaudo, M., Iacono, M., Kadavy, T., Oplatková, Z., Mauri, G., et al. (2019). Towards human cell simulation. In Kolodziej J., Gonzalez-Vélez H. (a cura di), High-Performance Modelling and Simulation for Big Data Applications (pp. 221-249). Springer Verlag [10.1007/978-3-030-16272-6_8].
none
File in questo prodotto:
Non ci sono file associati a questo prodotto.

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10281/231024
Citazioni
  • Scopus 11
  • ???jsp.display-item.citation.isi??? ND
Social impact