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Administative Overview
Abel Hodelin Hernandez edited this page Jul 4, 2021
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Name: Bachmann-Modell as a Fully Featured COMBINE Archive
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Title: COMBACH
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Description:
To provide the Bachmann model as a Fully Featured COMBINE Archive we need different working groups, here is our proposal:
- Group 1: Review of existing materials; composition of COMBINE archive; documentation template; review of intermediate results.
- Group 2: Comparison of the provided SBML models, selection and provision of detailed metadata
- Group 3: Provision of the SBGN model (graphical representation)
- Group 4: Provision of at least one SED-ML script (if necessary several)
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Duration (start/end): 15.06.2021 - 04.07.2021
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Research sponsor and program or self-financing: BIDS Study
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License: CC0-1.0
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Coordination: Abel Hodelin Hernandez
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Supervisor: Prof. Dr. Dagmar Waltemath
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