Skip to content

Implement PEtab v2 import #2662

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dweindl opened this issue Mar 13, 2025 · 1 comment
Open

Implement PEtab v2 import #2662

dweindl opened this issue Mar 13, 2025 · 1 comment
Assignees
Labels
enhancement PEtab PEtab-import related

Comments

@dweindl
Copy link
Member

dweindl commented Mar 13, 2025

We need to revise the PEtab import to handle the upcoming PEtab v2 format.

This implies:

  • New parameter mapping
    • instead of "preequilibration" and simulation, there will be a variable number of periods (at first, more than 2 conditions will only be supported through the JAX interface)
    • the mapped values will not be identifier or float, but could also be more complex math expressions
    • the values for reinitialization may depend on the model state and parameters (this also needs to be accounted for when computing sensitivities)
  • Auto-upconversion of PEtab v1 problems, to avoid duplicating the import logic
  • ...
@dweindl
Copy link
Member Author

dweindl commented Apr 4, 2025

The initial import implementation for sundials-based simulations will happen through translating experiments to events (PEtab-dev/libpetab-python#370).

To make that more robust, ideally #2185 should be continued, to support stopping at (constant) parameter-dependent fixed trigger times without root-finding.

Relevant issues:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement PEtab PEtab-import related
Projects
None yet
Development

No branches or pull requests

1 participant