A Comprehensive Web-based Platform For Domain-Specific
Biological Models

D 2013

A Comprehensive Web-based Platform For Domain-Specific Biological Models

KLEMENT, Matej, David ŠAFRÁNEK, Tadeáš DĚD, Aleš PEJZNOCH, Ladislav NEDBAL et. al.

Basic information

Original name

A Comprehensive Web-based Platform For Domain-Specific Biological Models

Authors

KLEMENT, Matej (703 Slovakia, belonging to the institution), David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution), Tadeáš DĚD (203 Czech Republic, belonging to the institution), Aleš PEJZNOCH (203 Czech Republic, belonging to the institution), Ladislav NEDBAL (203 Czech Republic), Ralf STEUER (276 Germany), Jan ČERVENÝ (203 Czech Republic) and Stefan MUELLER (40 Austria)

Edition

Neuveden, Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13), p. 61-67, 7 pp. 2013

Publisher

Elsevier

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/13:00068771

Organization unit

Faculty of Informatics

ISSN

DOI

http://dx.doi.org/10.1016/j.entcs.2013.11.006

UT WoS

000216920700006

Keywords in English

systems biology; modelling; mode repository; database

Abstract

V originále

A Comprehensive Modeling Platform, that is, a general framework for public sharing, annotation, and visualization of domain-specific biological models, is presented. For a selected organism, the framework is instantiated as a web-based application which allows to capture several aspects of biological models represented as biochemical reaction networks or ordinary differential equations. The key feature of the instantiation for a given organism relies on mapping kinetic models to a precise textual and a schematic graphical representation of the related biological knowledge, thereby supporting the systems biological view of the modeled organism. Besides model repository and annotation, the platform includes basic model analysis features such as simulation and static analysis.

Links

EE2.3.20.0256, research and development project

Name: Vytvoření výzkumného týmu a mezinárodního konzorcia pro počítačový model buňky sinice

Citovat

KLEMENT, Matej, David ŠAFRÁNEK, Tadeáš DĚD, Aleš PEJZNOCH, Ladislav NEDBAL, Ralf STEUER, Jan ČERVENÝ and Stefan MUELLER. A Comprehensive Web-based Platform For Domain-Specific Biological Models. Online. In Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13). Neuveden: Elsevier, 2013, p. 61-67. ISSN 1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2013.11.006.

@inproceedings{1114457,
   author = {Klement, Matej and Šafránek, David and Děd, Tadeáš and Pejznoch, Aleš and Nedbal, Ladislav and Steuer, Ralf and Červený, Jan and Mueller, Stefan},
   address = {Neuveden},
   booktitle = {Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13)},
   doi = {http://dx.doi.org/10.1016/j.entcs.2013.11.006},
   keywords = {systems biology; modelling; mode repository; database},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Neuveden},
   pages = {61-67},
   publisher = {Elsevier},
   title = {A Comprehensive Web-based Platform For Domain-Specific Biological Models},
   url = {http://dx.doi.org/10.1016/j.entcs.2013.11.006},
   year = {2013}
}

TY  - JOUR
ID  - 1114457
AU  - Klement, Matej - Šafránek, David - Děd, Tadeáš - Pejznoch, Aleš - Nedbal, Ladislav - Steuer, Ralf - Červený, Jan - Mueller, Stefan
PY  - 2013
TI  - A Comprehensive Web-based Platform For Domain-Specific Biological Models
PB  - Elsevier
CY  - Neuveden
KW  - systems biology
KW  - modelling
KW  - mode repository
KW  - database
UR  - http://dx.doi.org/10.1016/j.entcs.2013.11.006
L2  - http://dx.doi.org/10.1016/j.entcs.2013.11.006
N2  - A Comprehensive Modeling Platform, that is, a general framework for public sharing, annotation, and visualization of domain-specific biological models, is presented. For a selected organism, the framework is instantiated as a web-based application which allows to capture several aspects of biological models represented as biochemical reaction networks or ordinary differential equations. The key feature of the instantiation for a given organism relies on mapping kinetic models to a precise textual and a schematic graphical representation of the related biological knowledge, thereby supporting the systems biological view of the modeled organism. Besides model repository and annotation, the platform includes basic model analysis features such as simulation and static analysis.
ER  -

KLEMENT, Matej, David ŠAFRÁNEK, Tadeáš DĚD, Aleš PEJZNOCH, Ladislav NEDBAL, Ralf STEUER, Jan ČERVENÝ and Stefan MUELLER. A Comprehensive Web-based Platform For Domain-Specific Biological Models. Online. In \textit{Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13)}. Neuveden: Elsevier, 2013, p.~61-67. ISSN~1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2013.11.006.

Detailed Information on Publication Record