Toward Full-Stack <i>In Silico</i> Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation
Savas Konur, Laurenţiu Mierlă, Harold Fellermann, Christophe Ladroue, Bradley Brown, Anil Wipat, Jamie Twycross, Boyang Peter Dun, Sara Kalvala, Marian Gheorghe, Natalio Krasnogor
Abstract
analyses. This novel approach offers seamless interoperability across different tools as well as compatibility with SBOL and SBML frameworks and removes the burden of doing manual translations for standalone applications. We demonstrate the features, usability, and effectiveness of IBW and IBL using well-established synthetic biological circuits.
Topics & Concepts
Computer scienceWorkflowProgramming languageSynthetic biologyInteroperabilityUsabilityWorkbenchSBMLIn silicoScalabilitySoftware engineeringComputer architectureMarkup languageDatabaseBioinformaticsData miningXMLOperating systemVisualizationBiologyBiochemistryGeneChemistryGene Regulatory Network AnalysisMicrobial Metabolic Engineering and BioproductionDNA and Biological Computing