-
Notifications
You must be signed in to change notification settings - Fork 1
Synopsis Group 1
To set the stage for the remaining group effort, we initiated the Git Hub Repo and set up a (documentation template), as well as the overall structure of the projects Repository, laid out in the Wiki and it's sidebar (wiki). We set up and circulated (communication channels) to be used in the group project. We translated the tasks into issues and added a Kanban Board for better overview. We also initiated several meetings to discuss and plan the project progress. For a fast overview, we included an executive ([summary page])(https://github.com/ahodelin/Bachmann_Archive/wiki/Executive-Summary) where all groups summarized their part of the project.
We reviewed the available resources and identified six (SBML-Bachmann models). One of these models is in support of the original publication ([Bachmann et. al.])
We outlined several (software tools for simulation), reviewed the structure and components of a (COMBINE-ARCHIVE) and finally provided a (Final COMBINE-ARCHIVE of this project)
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