Detailed Information on Publication Record
2020
Executable Biochemical Space for Specification and Analysis of Biochemical Systems
TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIMBasic information
Original name
Executable Biochemical Space for Specification and Analysis of Biochemical Systems
Authors
TROJÁK, Matej (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Lukrécia MERTOVÁ (703 Slovakia, belonging to the institution) and Luboš BRIM (203 Czech Republic, belonging to the institution)
Edition
PLOS ONE, Public Library of Science, 2020, 1932-6203
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 3.240
RIV identification code
RIV/00216224:14330/20:00114304
Organization unit
Faculty of Informatics
UT WoS
000571887500085
Keywords in English
rule-based; modelling; static analysis
Tags
International impact, Reviewed
Změněno: 29/4/2021 08:02, RNDr. Pavel Šmerk, Ph.D.
Abstract
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.
Links
| GA18-00178S, research and development project |
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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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