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
Publication statusPublished - Jan 1 2016

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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

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