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Open-Systems-Pharmacology / OSMOSES

Open-Source MOdeling framework for automated quality control and management of complex life Science systEms modelS (OSMOSES)
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WP2 use case: Extendinig the spatial structure #4

Closed PavelBal closed 1 week ago

PavelBal commented 4 years ago

Extending the spatial structure (SS) on the example of a tumor organ.

Module structure:

  1. SS with an organ "Tumor".
  2. Neighborhoods from "Interstitial", "Plasma", and "BloodCells" to the rest of the organism.
  3. Container "Tumor" having a property "Parent container path = Organism".
  4. IC and LP with entries for molecules from all PK-Sim modules in physical containers of the tumor organ. By default, these values are populated based on the definied rules (default "IsPresent" and "NegativeValuesAllowed" that can be selected for each container, default IC is 0 in most cases).

Model configuration

  1. The user selects a PK-Sim module and the extension module "Tumor".
  2. The container "Tumor" is added to the SS of the PK-Sim module under the node "Organism".
  3. Additional neighborhoods are created based on the list the Tumor-modulle. If a neighbor that is defined in the "Tumor" module is not found in the root module, the build configuration is created and warnings are displayed ("WARNING: The neighborhood "Tumor_pls_Head_pls" was not created, as the neighbor "Organism|Head|Plasma" is not present!").
  4. LP and IC BBs of the PK-Sim module are extended by the entries in the tumor extension module.
  5. The user can explore the structure of the model configuratioin as is it shown currently in MoBi for the simulation structure.
  6. The user can edit the LP and IC BBs (includes "Import from CSV").
  7. The user can save the LP and IC BBs as pkml.
  8. The user can now creation model from the model configuration. Each model will have a distinct name.
  9. The user can change values of parameters and initial conditions of a simulation.