2020
Executable Biochemical Space for Specification and Analysis of Biochemical Systems
TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ a Luboš BRIMZákladní údaje
Originální název
Executable Biochemical Space for Specification and Analysis of Biochemical Systems
Autoři
TROJÁK, Matej (703 Slovensko, domácí), David ŠAFRÁNEK (203 Česká republika, garant, domácí), Lukrécia MERTOVÁ (703 Slovensko, domácí) a Luboš BRIM (203 Česká republika, domácí)
Vydání
PLOS ONE, Public Library of Science, 2020, 1932-6203
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10201 Computer sciences, information science, bioinformatics
Stát vydavatele
Velká Británie a Severní Irsko
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 3.240
Kód RIV
RIV/00216224:14330/20:00114304
Organizační jednotka
Fakulta informatiky
UT WoS
000571887500085
Klíčová slova anglicky
rule-based; modelling; static analysis
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 29. 4. 2021 08:02, RNDr. Pavel Šmerk, Ph.D.
Anotace
V originále
Computational systems biology provides multiple formalisms for modelling of biochemical processes among which the rule-based approach is one of the most suitable. Its main advantage is a compact and precise mechanistic description of complex processes. However, state-of-the-art rule-based languages still suffer several shortcomings that limit their use in practice. In particular, the elementary (low-level) syntax and semantics of rule-based languages complicate model construction and maintenance for users outside computer science. On the other hand, mathematical models based on differential equations (ODEs) still make the most typical used modelling framework. In consequence, robust re-interpretation and integration of models are difficult, thus making the systems biology paradigm technically challenging. Though several high-level languages have been developed at the top of rule-based principles, none of them provides a satisfactory and complete solution for semi-automated description and annotation of heterogeneous biophysical processes integrated at the cellular level. We present the second generation of a rule-based language called Biochemical Space Language (BCSL) that combines the advantages of different approaches and thus makes an effort to overcome several problems of existing solutions. BCSL relies on the formal basis of the rule-based methodology while preserving user-friendly syntax of plain chemical equations. BCSL combines the following aspects: the level of abstraction that hides structural and quantitative details but yet gives a precise mechanistic view of systems dynamics; executable semantics allowing formal analysis and consistency checking at the level of the language; universality allowing the integration of different biochemical mechanisms; scalability and compactness of the specification; hierarchical specification and composability of chemical entities; and support for genome-scale annotation.
Návaznosti
| GA18-00178S, projekt VaV |
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| MUNI/A/0945/2015, interní kód MU |
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| MUNI/A/1050/2019, interní kód MU |
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| MUNI/A/1076/2019, interní kód MU |
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