Helpers

In order to generate Oris input files, the zipero plugin is used as follows:

TODO: This section is provided by Viviam.

Instructions, usage examples, and ZIP generation details should be placed here.

Once generated, the resulting file is a ZIP archive containing all the information required to run Oris in any of its modes. The internal directory structure is as follows:

  • Models/ Contains the Gitsbe-generated Boolean models in BNET format.

  • src/ Contains auxiliary files used throughout the Oris pipeline:

    • drugpanel Defines drug identifiers, modes of action, and target nodes. Used to generate perturbed model instances (see Oris Modes).

    • training Calibration data used by Gitsbe to fit Boolean models to experimental profiles. Used in Oris to incorporate initial conditions (see Initial Conditions).

    • modeloutputs Specifies the nodes used as viability proxies and assigns them weights:

      • +1 for pro-survival / positive regulators.

      • -1 for pro-death / negative regulators.

      Required in the synergy and full modes (see Oris Modes).

    • perturbations Defines the set of single and double perturbations to be simulated. Used across all modes (see Oris Modes).