| TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. PLOS ONE. Public Library of Science, 2020, vol. 15, No 9, p. 1-23, 24 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0238838. |
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@article{1678155,
author = {Troják, Matej and Šafránek, David and Mertová, Lukrécia and Brim, Luboš},
article_number = {9},
doi = {http://dx.doi.org/10.1371/journal.pone.0238838},
keywords = {rule-based; modelling; static analysis},
language = {eng},
issn = {1932-6203},
journal = {PLOS ONE},
title = {Executable Biochemical Space for Specification and Analysis of Biochemical Systems},
url = {http://dx.doi.org/10.1371/journal.pone.0238838},
volume = {15},
year = {2020}
}
TY - JOUR
ID - 1678155
AU - Troják, Matej - Šafránek, David - Mertová, Lukrécia - Brim, Luboš
PY - 2020
TI - Executable Biochemical Space for Specification and Analysis of Biochemical Systems
JF - PLOS ONE
VL - 15
IS - 9
SP - 1-23
EP - 1-23
PB - Public Library of Science
SN - 19326203
KW - rule-based
KW - modelling
KW - static analysis
UR - http://dx.doi.org/10.1371/journal.pone.0238838
N2 - 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.
ER -
TROJÁK, Matej, David ŠAFRÁNEK, Lukrécia MERTOVÁ and Luboš BRIM. Executable Biochemical Space for Specification and Analysis of Biochemical Systems. \textit{PLOS ONE}. Public Library of Science, 2020, vol.~15, No~9, p.~1-23, 24 pp. ISSN~1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0238838.
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