Programmatic access to logical models in the Cell Collective modeling environment via a REST API

Bryan M. Kowal, Travis R. Schreier, Joseph T. Dauer, Tomáš Helikar

Research output: Contribution to journalArticle

Abstract

Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. Availability and implementation: The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective ( http://thecellcollective.org). Contact: thelikar2@unl.edu. Supplementary information: Technical user documentation: https://goo.gl/U52GWo.

Original languageEnglish (US)
Pages (from-to)12-16
Number of pages5
JournalBioSystems
Volume139
DOIs
StatePublished - Jan 1 2016

Fingerprint

Application programming interfaces (API)
Programming
Cell
Modeling
Model
Programming Languages
Biological Models
Biological systems
Biological Systems
Documentation
Computer programming languages
Web-based
Web services
Web Services
Annotation
Availability
Contact
Output
Processing
Simulation

Keywords

  • Boolean models
  • Logical models
  • REST API
  • Systems biology

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Applied Mathematics

Cite this

Programmatic access to logical models in the Cell Collective modeling environment via a REST API. / Kowal, Bryan M.; Schreier, Travis R.; Dauer, Joseph T.; Helikar, Tomáš.

In: BioSystems, Vol. 139, 01.01.2016, p. 12-16.

Research output: Contribution to journalArticle

Kowal, Bryan M. ; Schreier, Travis R. ; Dauer, Joseph T. ; Helikar, Tomáš. / Programmatic access to logical models in the Cell Collective modeling environment via a REST API. In: BioSystems. 2016 ; Vol. 139. pp. 12-16.
@article{b042fb05a09e4450a160d86c8c1683e9,
title = "Programmatic access to logical models in the Cell Collective modeling environment via a REST API",
abstract = "Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. Availability and implementation: The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective ( http://thecellcollective.org). Contact: thelikar2@unl.edu. Supplementary information: Technical user documentation: https://goo.gl/U52GWo.",
keywords = "Boolean models, Logical models, REST API, Systems biology",
author = "Kowal, {Bryan M.} and Schreier, {Travis R.} and Dauer, {Joseph T.} and Tom{\'a}š Helikar",
year = "2016",
month = "1",
day = "1",
doi = "10.1016/j.biosystems.2015.11.005",
language = "English (US)",
volume = "139",
pages = "12--16",
journal = "BioSystems",
issn = "0303-2647",
publisher = "Elsevier Ireland Ltd",

}

TY - JOUR

T1 - Programmatic access to logical models in the Cell Collective modeling environment via a REST API

AU - Kowal, Bryan M.

AU - Schreier, Travis R.

AU - Dauer, Joseph T.

AU - Helikar, Tomáš

PY - 2016/1/1

Y1 - 2016/1/1

N2 - Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. Availability and implementation: The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective ( http://thecellcollective.org). Contact: thelikar2@unl.edu. Supplementary information: Technical user documentation: https://goo.gl/U52GWo.

AB - Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. Availability and implementation: The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective ( http://thecellcollective.org). Contact: thelikar2@unl.edu. Supplementary information: Technical user documentation: https://goo.gl/U52GWo.

KW - Boolean models

KW - Logical models

KW - REST API

KW - Systems biology

UR - http://www.scopus.com/inward/record.url?scp=84947996867&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84947996867&partnerID=8YFLogxK

U2 - 10.1016/j.biosystems.2015.11.005

DO - 10.1016/j.biosystems.2015.11.005

M3 - Article

C2 - 26589448

AN - SCOPUS:84947996867

VL - 139

SP - 12

EP - 16

JO - BioSystems

JF - BioSystems

SN - 0303-2647

ER -