This is a fully featured CombineArchive demonstrating the concepts and best practices.
This CombineArchive represents the study described by Calzone et. al. in Dynamical modeling of syncytial mitotic cycles in Drosophila embryos, Mol Syst Biol. 2007; 3: 131. I decided for that study because
- the corresponding article is published as open access (Creative Commons Attribution‐NonCommercial‐NoDerivs),
- the study is already available in SBML format (BIOMD0000000144),
- the study is already available in CellML format (exposure),
- I've been working with that model before.
The files of the simulation study are organised in folders:
- documentation: Files describing the model and its behaviour, such as the article published in 2007.
- model: Files that describe and encode the biological system, such as the model in SBML/CellML format and figures.
- experiment: Files which encode the actual experimental setup, such as SED-ML simulation descriptions.
- result: Files that were obtained by running the in silico experiment, such as graphs and tables.
Please note, that this structure is not mandatory.
To conveniently explore the contents of this CombineArchive you may open it in the CombineArchive WebInterface. Just import it using the following link:
You can of course also clone this repository or download the latest version of this archive.
The archive is published as A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos in f1000Research and available from Figshare.