Sbmlwebapp: Web-based simulation, steady-state analysis, and parameter estimation of systems biology models

Takahiro Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, Akira Funahashi

Research output: Contribution to journalArticlepeer-review

Abstract

In systems biology, biological phenomena are often modeled by Ordinary Differential Equations (ODEs) and distributed in the de facto standard file format SBML. The primary analyses performed with such models are dynamic simulation, steady-state analysis, and parameter estimation. These methodologies are mathematically formalized, and libraries for such analyses have been published. Several tools exist to create, simulate, or visualize models encoded in SBML. However, setting up and establishing analysis environments is a crucial hurdle for non-modelers. Therefore, easy access to perform fundamental analyses of ODE models is a significant challenge. We developed SBMLWebApp, a web-based service to execute SBML-based simulation, steady-state analysis, and parameter estimation directly in the browser without the need for any setup or prior knowledge to address this issue. SBMLWebApp visualizes the result and numerical table of each analysis and provides a download of the results. SBMLWebApp allows users to select and analyze SBML models directly from the BioModels Database. Taken together, SBMLWebApp provides barrier-free access to an SBML analysis environment for simulation, steady-state analysis, and parameter estimation for SBML models. SBMLWebApp is implemented in Java™ based on an Apache Tomcat® web server using COPASI, the Systems Biology Simulation Core Library (SBSCL), and LibSBMLSim as simulation engines. SBMLWebApp is licensed under MIT with source code freely available. At the end of this article, the Data Availability Statement gives the internet links to the two websites to find the source code and run the program online.

Original languageEnglish
Article number1830
JournalProcesses
Volume9
Issue number10
DOIs
Publication statusPublished - 2021 Oct

Keywords

  • Kinetic models
  • Model calibration
  • Parameter esti-mation
  • SBML
  • Software
  • Steady-state simulation
  • Time-course simulation
  • Web application

ASJC Scopus subject areas

  • Bioengineering
  • Chemical Engineering (miscellaneous)
  • Process Chemistry and Technology

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