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2021-10-15Zeitschriftenartikel DOI: 10.3390/pr9101830
SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
dc.contributor.authorYamada, Takahiro
dc.contributor.authorIi, Kaito
dc.contributor.authorKönig, Matthias
dc.contributor.authorFeierabend, Martina
dc.contributor.authorDräger, Andreas
dc.contributor.authorFunahashi, Akira
dc.contributor.editorBudman, Hector
dc.date.accessioned2021-12-16T14:28:38Z
dc.date.available2021-12-16T14:28:38Z
dc.date.issued2021-10-15none
dc.date.updated2021-11-04T22:14:23Z
dc.identifier.urihttp://edoc.hu-berlin.de/18452/24450
dc.description.abstractIn 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.eng
dc.language.isoengnone
dc.publisherHumboldt-Universität zu Berlin
dc.rights(CC BY 4.0) Attribution 4.0 Internationalger
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectSBMLeng
dc.subjectkinetic modelseng
dc.subjecttime-course simulationeng
dc.subjectsteady-state simulationeng
dc.subjectparameter estimationeng
dc.subjectmodel calibrationeng
dc.subjectsoftwareeng
dc.subjectweb applicationeng
dc.subject.ddc570 Biologienone
dc.titleSBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Modelsnone
dc.typearticle
dc.identifier.urnurn:nbn:de:kobv:11-110-18452/24450-3
dc.identifier.doi10.3390/pr9101830none
dc.identifier.doihttp://dx.doi.org/10.18452/23792
dc.type.versionpublishedVersionnone
local.edoc.container-titleProcesses : open access journalnone
local.edoc.pages10none
local.edoc.type-nameZeitschriftenartikel
local.edoc.institutionLebenswissenschaftliche Fakultätnone
local.edoc.container-typeperiodical
local.edoc.container-type-nameZeitschrift
local.edoc.container-publisher-nameMDPInone
local.edoc.container-publisher-placeBaselnone
local.edoc.container-volume9none
local.edoc.container-issue10none
dc.description.versionPeer Reviewednone
local.edoc.container-articlenumber1830none
dc.identifier.eissn2227-9717

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