Data analysis pipeline from laboratory to MP models

Castellini, Alberto; Franco, Giuditta; Pagliarini, Roberto

doi:10.1007/s11047-010-9200-6

Cited by 15 publications

(7 citation statements)

References 22 publications

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“…Another significant application of Metabolic P system in chemistry is the Non Photochemical Quenching (NPQ) process. An example of rules and regulators of one particular NPQ MP system are as follows (Castellini et al 2011b):…”

Section: Reactionsmentioning

confidence: 99%

Research of Metabolic P System Field Programmable Gate Array Implementation

Kulakovskis¹

2019

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Disertacija rengta 2014-2019 metais Vilniaus Gedimino technikos universitete. Vadovas prof. dr. Dalius NAVAKAUSKAS (Vilniaus Gedimino technikos universitetas, elektros ir elektronikos inžinerija-T 001). Vilniaus Gedimino technikos universiteto Elektros ir elektronikos inžinerijos mokslo krypties disertacijos gynimo taryba: Pirmininkas prof. dr. Vytautas URBANAVIČIUS (Vilniaus Gedimino technikos universitetas, elektros ir elektronikos inžinerija-T 001). Nariai: prof. dr. Algirdas BAŠKYS (Vilniaus Gedimino technikos universitetas, elektros ir elektronikos inžinerija-T 001), prof. habil. dr. Gintautas DZEMYDA (Vilniaus universitetas, informatikos inžinerija-T 007), dr. Ofer HADAR (Negevo Ben-Guriono universitetas, Izraelis, elektros ir elektronikos inžinerija-T 001), prof. dr. Jurij NOVICKIJ (Vilniaus Gedimino technikos universitetas, elektros ir elektronikos inžinerija-T 001). Disertacija bus ginama viešame Elektros ir elektronikos inžinerijos mokslo krypties disertacijos gynimo tarybos posėdyje 2019 m. gegužės 31 d. 13 val. Vilniaus Gedimino technikos universiteto senato posėdžių salėje.

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Section: Reactionsmentioning

confidence: 99%

Research of Metabolic P System Field Programmable Gate Array Implementation

Kulakovskis¹

2019

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“…NPQ MP system has been iteratively improved many times and has numerous variations of MP grammar that have been tested is different cases [22]. For the research of automated implementation in FPGA, a single type of NPQ MP system was selected.…”

Section: Mp System Description -Case Bmentioning

confidence: 99%

“…For the research of automated implementation in FPGA, a single type of NPQ MP system was selected. The rules and regulators of the particular NPQ MP system are as follows [23]: [ {"add": {"G": 1}, "sub": {}}, {"add": {}, "sub": {"G": 1}}, {"add": {"I": 1}, "sub": {}}, {"add": {}, "sub": {"I": 1}} ], "constants": {"f1c1": 0.6, "f2c1": 0.12, "f2c2": 0.0000016, "f3c1": 49.9, "f3c2": 0.1, "f4c1": 0.84}, "fluxes": [ ["f1c1"], ["f2c1", "*", "G", "+", "f2c2", "*", "G", "*", "G", "*", "I"],…”

Section: Mp System Description -Case Bmentioning

confidence: 99%

“…However, other parameters are not equal. The implementation with the highest number of bits (23) for the fractional part surprisingly uses the least amount of FPGA resources (slices and LUTs). In a very close second place is the implementation with 21 bits, and the automatically selected (closest to the 1 % error) implementation with 22 bits uses the most of FPGA resources.…”

Section: Parameters For the Evaluation Of Mp Implementationsmentioning

confidence: 99%

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Automated Metabolic P System Placement in FPGA

Kulakovskis

Navakauskas

2016

Electrical, Control and Communication Engineering

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“…and t is the number of observations [2,4]. The methodology here presented enables to synthesize polynomial regulation functions.…”

Section: Mp System Modelingmentioning

confidence: 99%

A genetic approach for synthesizing metabolic models from time series

Castellini

Manca

Zucchelli

et al. 2012

Proceedings of the 14th Annual Conference Companion on Genetic and Evolutionary Computation

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In this paper we introduce a new approach, based on genetic algorithms and multiple linear regression, for the synthesis of flux regulation functions in metabolic models from observed time series. Genetic algorithms are used as a variable selection technique to identify the best primitive functions for flux regulation, and multiple linear regression is employed to compute primitive function coefficients. Our methodology is here successfully applied to synthesize a set of regulation functions able to regenerate an observed dynamics for the mitotic oscillator in early amphibian embryos.

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Data analysis pipeline from laboratory to MP models

Cited by 15 publications

References 22 publications

Research of Metabolic P System Field Programmable Gate Array Implementation

Research of Metabolic P System Field Programmable Gate Array Implementation

Automated Metabolic P System Placement in FPGA

A genetic approach for synthesizing metabolic models from time series

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