petab_timecourse's Introduction

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]

Examples

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

File formats

Timecourse table

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.

TODO

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

Timecourse parameters table

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

petab_timecourse's People

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petab_timecourse's Issues

it should be possible to run the package without pypest / amici

I needed the following changes to have the package run for me:

diff --git a/petab_timecourse/__init__.py b/petab_timecourse/__init__.py
index 4f77a5b..b38cd07 100644
--- a/petab_timecourse/__init__.py
+++ b/petab_timecourse/__init__.py
@@ -22,14 +22,17 @@ from .misc import (
 )
 
 
-from . import amici
-from .amici import (
-    simulate_timecourse,
-)
-
-from .pypesto import (
-    TimecourseObjective,
-)
+try: 
+    from . import amici
+    from .amici import (
+        simulate_timecourse,
+    )
+
+    from .pypesto import (
+        TimecourseObjective,
+    )
+except ImportError:
+    pass
 
 from .problem import Problem
 
diff --git a/petab_timecourse/simulator.py b/petab_timecourse/simulator.py
index fb7a9bf..249b06d 100644
--- a/petab_timecourse/simulator.py
+++ b/petab_timecourse/simulator.py
@@ -23,11 +23,15 @@ from petab.C import (
 from .C import (
     PERIODS,
 )
-from .amici import (
-    precreate_edata_periods,
-    precreate_parameter_mapping_periods,
-    add_output_timepoints_if_missing,
-)
+try:
+    from .amici import (
+        precreate_edata_periods,
+        precreate_parameter_mapping_periods,
+        add_output_timepoints_if_missing,
+    )
+except ImportError:
+    pass
+
 from .misc import (
     get_timecourse,
     subset_petab_problem,