Directory structure of Zip file

The Zip file submitted to CellCircuits web site should contain the publication information, the network model images presented in the publication, their thumbnail images (in small scale), and sif files corresponding to the network models. Optionally, the zip file can contain PDF file of the publication, cover image of the publish journal, supplement materials, URL to supplemental material, and legends for frequently asked questions (FAQ) about the models.

All the data in zip file must conform the format defined by CellCircuits web site, so that they can be loaded into CellCircuits database automatically. If the model images are exported from Cytoscape, it is highly recommended to use Cytoscape plugin  “SessionForWeb” to export the session directly into a Zip file. Cytoscape plugin SessionForWeb can be installed through the plugin manager of Cytoscape. After installation of the plugin, there will be a menu item under File->Export->Session for CellCircuits web site.

The exported zip file from "Sesion for CellCircuits web site" privides a base to publish the models in the CellCircuits website. The Zip file should be unzipped and include all othe data, such as publication information, PDF files, and supplemental material. And it should then be zipped again, so that the directory structure in the ZIP file conform the format defined by CellCircuits website. If there is no new data added, the exported ZIP file should still be unzipped and zipped again, so that the directory structure within the new ZIP file will conform the format defined by CellCircuits website.

The following is an example of Zip file, which contain two models, in the CellCircuit defined format. Note that the SIF files are in the subdirectories named after the species of the corresponding models. A sif file must have at least one species. In cases there are more than one species associated with a sif file, all species must be specified.

File name: Any file name with extension .zip

MyModelData/
     img/
          Fig5B_1.jpeg
          Fig5B_2.jpeg

    thum_img/
          Fig5B_1.jpeg
          Fig5B_2.jpeg
     sif/
          Saccharomyces_cerevisiae_Homo_sapiens/
              Fig5B_1.sif
              Fig5B_2.sif
     legends/ (optional)
          Legend_FAQ.html
          Fig5_small.jpg
     coverImage.gif (optional)
     myPaper.pdf (optional)
     publication_url.txt
     supplement_material.doc (optional)
     supplement_url.txt (optional)

Download a smaple zip file Here