Table 1. Content of the fully featured COMBINE archive.
The table lists all files included in the presented COMBINE archive together with formats and descriptions. The indentation indicates the directory structure used to organise the files in the archive.
| File | Format | Description |
|---|---|---|
| manifest.xml | Omex | Skeleton, automatically generated by WebCAT |
| metadata.rdf | Omex | Skeleton, automatically generated by WebCAT |
| README.md | Markdown | Human readable information for users stumbling upon the archive |
| model/ | ||
| BIOMD0000000144.xml | SBML L2V1 | origin: www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000144 |
| calzone_2007.svg | SVG | origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 |
| calzone_2007.ai | Illustrator | origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 |
| calzone_2007.png | PNG | origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 |
| calzone_thieffry_tyson_novak_2007.cellml | CellML 1.0 | origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 |
| sbgn/Calzone2007.gml | GML | SBGN compliant figure generated using SBGN-ED |
| sbgn/Calzone2007.graphml | GraphML | SBGN compliant figure generated using SBGN-ED |
| sbgn/Calzone2007.pdf | SBGN compliant figure generated using SBGN-ED | |
| sbgn/Calzone2007.png | PNG | SBGN compliant figure generated using SBGN-ED |
| sbgn/Calzone2007.sbgn | SBGN-ML | SBGN-ML encoded figure generated using SBGN-ED |
| experiment/ | ||
| Calzone2007-default-simulation.xml | SED-ML L1V1 | Simulation description generated using SED-ML Web Tools |
| Calzone2007-simulation-figure-1B.xml | SED-ML L1V1 | Simulation description generated using SED-ML Web Tools based on
Calzone2007-default-simulation.xml |
| documentation/ | ||
| Calzone2007.pdf | Scientific publication
“Dynamical modeling of syncytial mitotic cycles in
Drosophila embryos” obtained from msb.embopress.org/content/3/1/131 |
|
| Calzone2007-supplementary-material.pdf | Supplementary information for the publication obtained from
msb.embopress.org/content/3/1/131 |
|
| result/ | ||
| Fig1B-bottom-COPASI.svg | SVG | Image generated by executing Calzone2007-simulation-figure-1B.xml on
BIOMD0000000144.xml in COPASI |
| Fig1B-top-COPASI.svg | SVG | Image generated by executing Calzone2007-simulation-figure-1B.xml on
BIOMD0000000144.xml in COPASI |
| Fig1B-bottom-webtools.png | PNG | Image generated by executing Calzone2007-simulation-figure-1B.xml on
BIOMD0000000144.xml in SED-ML Web Tools |
| Fig1B-top-webtools.png | PNG | Image generated by executing Calzone2007-simulation-figure-1B.xml on
BIOMD0000000144.xml in SED-ML Web Tools |