Towards human cell simulation

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

Risultato della ricerca: Chapter

1 Citazione (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

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Cells
Cell
Emergent Behavior
Simulation
Cellular Systems
Multiple Scales
Model Reduction
Systems Biology
Faithful
Parameterization
Parameter estimation
Parameter Estimation
Complex Systems
Simulator
Extremes
Infrastructure
High Performance
Simulators
Kinetics
Mathematical Model

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cita questo

Vitabile, S., Oplatková, Z. K., Senkerik, R., Zamuda, A., Stojanovic, N., Nobile, M. S., ... 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).

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

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. pag. 221-249 (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE).

Risultato della ricerca: Chapter

Vitabile, S, Oplatková, ZK, Senkerik, R, Zamuda, A, Stojanovic, N, Nobile, MS, Viktorin, A, Kadavy, T, Spolaor, S, 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). LECTURE NOTES IN ARTIFICIAL INTELLIGENCE, pagg. 221-249.
Vitabile S, Oplatková ZK, Senkerik R, Zamuda A, Stojanovic N, Nobile MS e altri. Towards human cell simulation. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. pag. 221-249. (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE).
Vitabile, Salvatore ; Oplatková, Zuzana Komínková ; Senkerik, Roman ; Zamuda, Aleš ; Stojanovic, Natalija ; Nobile, Marco S. ; Viktorin, Adam ; Kadavy, Tomas ; Spolaor, Simone ; Gribaudo, Marco ; Turunen, Esko ; Iacono, Mauro ; Mauri, Giancarlo ; Pllana, Sabri. / Towards human cell simulation. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2019. pagg. 221-249 (LECTURE NOTES IN ARTIFICIAL INTELLIGENCE).
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