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Genomica File Repositories

Genomica file repository defines a workspace of files. It does not contain the actual files but references to them. You can define a repository for each of your projects, which will include the files relevant to the project. These files can be loaded to genomica via the repository window, which makes your work on the project much more convenient. Currently the repository supports gene sets (.gxa files) and chromosome tracks (.gxt files). In the future support for expression files will be added.

You can define your own repository or use one of the repositories we supply in the repository packages.

Edit a repository

You can open the repository dialog from Tools -> File Repository.

Click the Browse ... button to load an existing repository. To create a new repository click the Browse ... button and type the name of the new repository file. Genomica Repository file extension is .gxr. The last repository files in use apear in the File Repository: combo box. Selecting a repository file from that list will load it.
The entries that the repository contains are displayed in an hierarchical manner at the center of the dialog in 4 lists:
  • File type
  • Organism
  • Attribute (Gene namespace for gene sets and genome version for chromosome tracks).
  • File

Clicking on an entry in each list will update the displayed information accordingly. You can Remove the selected files from the repository (notice that this does not delete the actual file, only the reference to it from the repository), Edit a selected file or Add new files to the repository. Clicking the Edit or the Add buttons will open the File Repository Element Properties dialog:

The Organism and Gene Namespace/Genome Version (depends on the file type) are combo boxes that have the current values that the repository contains, in the specific context (of the selected file type and/or organism). You can type a new value in those combo boxes. The Source field should point to the file. You can enter either an absolute file path or a path relative to the repository file itself. Once a file is selected other fields will be updated automatically according to the information inside it (See the Name, Description and GeneNamespace/GenomeVersion fields in the gxa and gxt sample files).
The Description field accepts either plain text or HTML format. In case of HTML, you should regard the description as a standalone HTML document (include the <html>, <head>, <body> tags etc.).

Load files

As before, you must load an expression file before loading a gene set or a chromosome track is possible. After the expression data is loaded, to load one or more gene sets from the repository you should open the repository dialog from Sets -> Load Gene Sets From Repository.... Select the requested gene sets and click the OK button.
Similarly, load a chromosome track from Chromosomes -> Load Track From Repository... menu. In both cases the repository dialog will be opened in the context of the selected file type (Gene sets or chromosome tracks), and you will be able to see and add only files of the same file type.

Ready-made Repository Packages

A repository package is a zip file containing the repository configuration file and the actual files it is pointing to. Currently we supply repositories of chromosome tracks and gene sets for human and for yeast.
Go to the Download Data page to download the repository packages.