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insilicoCell : an integrated platform for biological model development and analysis

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

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insilicoCell : an integrated platform for biological model development and analysis

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  1. insilicoCell: an integrated platform for biological model development and analysis Thai Quang Tung Korea Institute of Science and Technology Information (KISTI)

  2. Dept. of Cyber environment, KISTI • Development of Next-Generation Cyber Research Environment • Development of an Advanced Science Education Hub • Development of Science Cloud Technology

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

  4. System biology • Target systems: organisms, organs, tissues, signaling networks (molecular level)

  5. Why modeling? • Comprehend information • Reduce complexity, help understanding real systems • Explain biological phenomena • Virtual laboratory • Generating new hypotheses • Design new experiments

  6. Modeling process

  7. What computer can help? • Knowledge management • Search literature database (PubMed) for system interactions • Search gene/protein database for specific gene/protein functions • Computer simulation tools • Validate the model • Edit/create models • Dynamical analysis tools • Parameter estimation • Sensitivity analysis • Bifurcation analysis

  8. insilicoCell • System biologists need: • multiple tools, some are complex to used (command line) • literature, database searching • Tools are developed for desktop environment Interaction, reaction database Kinetic parameter database Systems biology workbench Biological model database • insilicoCellbrings: • Integration • Intuitive GUI • High performance computing SBML editor Model converter Time-course simulation Local sensitivity analysis Parameter estimation Global sensitivity analysis, robustness analysis Biological system modelers Bifurcation analysis

  9. System architecture

  10. Computational engine

  11. ezBioNet GUI

  12. Demo

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