insilicoCell : an integrated platform for biological model development and analysis

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insilicoCell : an integrated platform for biological model development and analysis. Thai Quang Tung Korea Institute of Science and Technology Information (KISTI). Dept . of Cyber environment, KISTI. Development of Next-Generation Cyber Research Environment - PowerPoint PPT Presentation

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insilicoCell: an integrated platform for biological model development and analysis

insilicoCell: an integrated platform for biological model development and analysisThai Quang TungKorea Institute of Science and Technology Information (KISTI)Dept. of Cyber environment, KISTI

Development of Next-Generation Cyber Research EnvironmentDevelopment of an Advanced Science Education HubDevelopment of Science Cloud Technology

System biologySystem biology aims at a (sub)system level understanding of biological process and networks

System biology

Target systems: organisms, organs, tissues, signaling networks (molecular level)Why modeling?Comprehend informationReduce complexity, help understanding real systemsExplain biological phenomenaVirtual laboratoryGenerating new hypothesesDesign new experiments

Modeling process

What computer can help?Knowledge managementSearch literature database (PubMed) for system interactionsSearch gene/protein database for specific gene/protein functionsComputer simulation toolsValidate the modelEdit/create modelsDynamical analysis toolsParameter estimationSensitivity analysisBifurcation analysisinsilicoCellSystem biologists need:multiple tools, some are complex to used (command line)literature, database searchingTools are developed for desktop environmentSystems biology workbenchBiological system modelers

Interaction, reaction databaseKinetic parameter databaseBiological model databaseSBML editorTime-course simulationLocal sensitivity analysisModel converterParameter estimationGlobal sensitivity analysis, robustness analysisBifurcation analysisinsilicoCell brings:IntegrationIntuitive GUIHigh performance computing

System architecture

Computational engine

ezBioNet GUI

Demo

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