Executable Biochemical Space for Specification and Analysis of Biochemical Systems

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14330%2F20%3A00114304" target="_blank" >RIV/00216224:14330/20:00114304 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1371/journal.pone.0238838" target="_blank" >http://dx.doi.org/10.1371/journal.pone.0238838</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1371/journal.pone.0238838" target="_blank" >10.1371/journal.pone.0238838</a>

Result language

angličtina

Original language name

Executable Biochemical Space for Specification and Analysis of Biochemical Systems

Original language description

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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/GA18-00178S" target="_blank" >GA18-00178S: Discrete Bifurcation Analysis of Reactive Systems</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

PLOS ONE

ISSN

1932-6203

e-ISSN

—

Volume of the periodical

15

Issue of the periodical within the volume

9

Country of publishing house

GB - UNITED KINGDOM

Number of pages

24

Pages from-to

1-23

UT code for WoS article

000571887500085

EID of the result in the Scopus database

2-s2.0-85090902980