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This public repository is the collaborative work of the participants of the module "Bioinformatik und Systembiologie" in the Master Program BIDS, organized by the Graduate School Rhein-Neckar in cooperation with MIRACUM, a consortium of the Medizininformatik-Initiative.
Our goal is to provide the Bachmann Model, a showcase biomodel, as a fully-featured COMBINE archive, a standardized container for data files related to biological simulation studies, for instance described by Scharm & Waltemath in "A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos" [2].
Figure 1: Elements of a COMBINE-Archive from [1]. Besides the actual modeling information the archive contains metadata (e.g. publication references, used taxonomies, and plotting information).
We use this Wiki as a tool for the data management, documentation and easy understanding COMBINE archive created in this project. The core concepts and results of this wiki are summarized in the executive summary. You will find a short summary of each group's work in the synopsis of each group. We have laid out all relevant documentation steps on individual Wiki pages accessible from the Wiki sidebar.
We need teamwork to build the Bachmann Model as a fully featured COMBINE archive. Each team of two or three members has a different function and contributed to different aspects of the final COMBINE archive.
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Group 1: Review of existing materials; composition of the COMBINE archive; documentation template; review of intermediate results.
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Group 2: Comparison of provided SBML models, selection and provision of detailed metadata.
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Group 3: Provision of the SBGN model (graphical representation).
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Group 4: Provision of at least one SED-ML script (more than one if necessary).
!No comprende nada? Please check out our glossary.
[1] the COMBINE community (2017): COMBINE archive. Online verfügbar unter https://combinearchive.org/index/.
[2] Scharm, M. and Waltemath, D. A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5, 2421 (2016). https://doi.org/10.12688/f1000research.9379.1
This project was created under the guidance, monitoring and continuous review of Prof. Dr. Dagmar Waltemath
