PEtab timecourse

This is an example implementation of an extension of PEtab, for the specification of time-dependent conditions.

Installation

Clone this repository then install it into your Python (virtual) environment.

git clone --recurse-submodules https://github.com/dilpath/petab_timecourse
cd petab_timecourse
pip install -e .[examples]

The examples depend on AMICI for simulation and pyPESTO for optimization, but these are independent of the PEtab extension.

A TSV with sequences of experimental conditions/dosing regimes/etc.

`timecourseId`	`timecourse`
(Unique) [string]	[string]
dummyId	0:c0;5:c1;50:c2

timecourseId: An ID for the timecourse.
timecourse: A semicolon-delimited sequence of times and experimental conditions.
- in the example, the timecourse starts at time t=0 with experimental condition c0. At t=5, experimental condition switches to c1. From t=50 onwards, experimental condition c2 is used.

How to specify parameter estimation problem when estimating time?

a lot of possible flexibility...
- use objectivePrior... to apply constraints to the values that each estimated time point can take
- for consecutively estimated time periods
  - the lower bound of the next period should match the upper bound of the previous period
  - handle via PEtab Control

WIP

all columns from normal PEtab parameters table
timecourseIds
conditionIds
type
- time to estimate the start time of the period
  - then ignore parameterId etc?!
- value to estimate the value that the parameter takes during the period