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Integration_COMBINE
JessicaVasseur123 edited this page Jun 30, 2021
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SED-ML files (including the associated , output files (plots and tables) and validation results were bundled together and stored in a fully featured COMBINE archive using the Webcat tool.
List of SED-ML files (./experiment)
- DefaultSimulation.sedml
- Fig3.sedml (generated with SEDML_Fig3_v2.ipynb)
- Fig4.sedml (generated with SEDML_Fig4_v3.ipynb)
- Fig5.sedml (generated with SEDML_Fig5_v2.ipynb)
- SuppFig9.sedml (generated with SEDML_SuppFig9_v3.ipynb)
- SuppFig9_COPASI.sedml
List of outputs (./result)
- DefaultSimulation
- Fig3
- Fig4
- Fig5
- SuppFig9
- SuppFig9_COPASI
- Validation
- Test_COPASI_2021-06-28
- Test_SWT_2021-06-28
Bioinformatics & Systems biology SS 2021
- Synopsis Group 1
- Sources of Bachmann model
- Software tools for simulation
- How to build a Fully Featured COMBINE Archive?
- Communication channels
- Provision of a template for documentation
- Schedule (draft)
- Review of results
- COMBINE Archive (Testversion!)
- Synopsis Group 2
- Finding of SBML models
- Comparison of SBML models
- The chosen one
- Simulation tools
- Metadata
- Improving metadata annotations
- Synopsis Group 3
- SBGN Maps for Bachmann model
- Choice of SBGN language
- Tool to draw the SBGN Map
- SBGN-Map Drawing, Validation & Beautification
- Integration into COMBINE Archive
- Synopsis Group 4
- Selection of experiments
- Selection of SED-ML tool(s)
- Generation of SED-ML file(s)
- Integration into COMBINE Archive
- Test of SED-ML files and COMBINE Archive