PEtab-dev / PEtab-dev/PEtab

PEtab extension for NLME

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Description

Which problem would you like to address? Please describe.
Currently, PEtab does not allow to express nonlinear mixed effects models (i.e containing fixed (population) and random (patient-specific) effects). These models are very common to represent inter-patient variability in pharmacological models. IIUC, such models are often represented in software like NONMEM, which was developed in the late 70s. I believe the field could benefit from a software independent model storage and exchange format.

Describe the solution you would like
In this spreadsheet, I have summarised a suggestion for a PEtab extension to introduce random effects in addition to the current format, which only allows to express fixed effects (happy to jump on a brief call to discuss in person).

Describe alternatives you have considered
There is a format called PharmML (Fig 2 here), which can express mixed effects, too. However, I don't think it is widely used yet, perhaps because the XML format is hard for humans to read and understand.

Additional context
I have no experience with NLME. While I have briefly discussed the suggestion linked in the spreadsheet with NLME experts, it would be good to get broader insight into a variety of use cases.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the linked Google spreadsheet and the PEtab format context in this issue; no repository files or tests are identified. Clarify supported NLME use cases and agree on the extension's scope before locating implementation and validation work.

Written by the indexing model from the issue text.

Assessment

Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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