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Group 1
The function of the group 1 included the setup of a documentation platform. A poll was conducted prior to the project start to determine whether to use a Fairdomhub (1 vote) or a Github (7 votes) on day 0. As Github provides an intuitive and easy to customize environment the project was started right away on day 0 providing both a concise documentation hub as well as a working stage for the development of the COMBINE archive.
To achieve these goals we should research the literatur about the Bachmann model and the COMBINE Archive, along with SBML and extra file formats, checking the reproducibility of the COMBINE structure and software tools that hade been used. It is also part of the group's function to set up this GitHub repository and analyze how a Fully Featured COMBINE archive is built. In addition, this group should establish communication channels, develop a rough schedule, provide a template for documentation, and periodically review intermediate deliverables. At the end we should create a test version of a COMBINE Archive with the Bachmann model.
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