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Merge pull request #490 from PEtab-dev/release_0.1.12
Release 0.1.12 * Documentation update: * Added SBML2Julia to list of tools supporting PEtab * Extended PEtab introduction * Tutorial for creating PEtab files * Minor fix: Default argument for optional 'model' parameter in `petab.lint.check_condition_df`` (#477)
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‎CHANGELOG.md‎

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## 0.1 series
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### 0.1.12
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* Documentation update:
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* Added SBML2Julia to list of tools supporting PEtab
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* Extended PEtab introduction
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* Tutorial for creating PEtab files
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* Minor fix: Default argument for optional 'model' parameter in
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`petab.lint.check_condition_df`` (#477)
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### 0.1.11
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* Function for generating synthetic data (#472)
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* Minor documentation updates (#470)
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### 0.1.10
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*Fixed deployment setup, no further changes.*
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* Fixed deployment setup, no further changes.*
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### 0.1.9
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‎README.md‎

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- [pyPESTO](https://github.com/ICB-DCM/pyPESTO/)
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([Example](https://pypesto.readthedocs.io/en/latest/example/petab_import.html))
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- [SBML2Julia](https://github.com/paulflang/SBML2Julia)
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([Tutorial](https://sbml2julia.readthedocs.io/en/latest/python_api.html))
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If your project or tool is using PEtab, and you would like to have it listed
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here, please [let us know](https://github.com/PEtab-dev/PEtab/issues).
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[PEtab test suite](https://github.com/PEtab-dev/petab_test_suite):
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| ID | Test | AMICI<br>`>=0.10.20` | Copasi | D2D | dMod | MEIGO | parPE<br>`develop` | pyABC<br>`>=0.10.1` | pyPESTO<br>`>=0.0.11` |
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|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|-----------------------|-------|------------------------|
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| 1 | Basic simulation | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 2 | Multiple simulation conditions | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 3 | Numeric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 4 | Parametric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 5 | Parametric overrides in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 6 | Time-point specific overrides in the measurement table | --- | --- | +++ | +++ | +++ | --- | --- | --- |
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| 7 | Observable transformations to log10 scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ |
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| 8 | Replicate measurements | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 9 | Pre-equilibration | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 10 | Partial pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 11 | Numeric initial concentration in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 12 | Numeric initial compartment sizes in condition table | --- | +-- | +++ | +++ | +++ | --- | --- | --- |
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| 13 | Parametric initial concentrations in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 14 | Numeric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 15 | Parametric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ |
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| 16 | Observable transformations to log scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ |
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| ID | Test | AMICI<br>`>=0.10.20` | Copasi | D2D | dMod | MEIGO | parPE<br>`develop` | pyABC<br>`>=0.10.1` | pyPESTO<br>`>=0.0.11` | SBML2Julia |
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|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|-----------------------|-------|------------------------|------------|
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| 1 | Basic simulation | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 2 | Multiple simulation conditions | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 3 | Numeric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 4 | Parametric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 5 | Parametric overrides in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 6 | Time-point specific overrides in the measurement table | --- | --- | +++ | +++ | +++ | --- | --- | --- | +++ |
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| 7 | Observable transformations to log10 scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ | +++ |
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| 8 | Replicate measurements | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 9 | Pre-equilibration | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 10 | Partial pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 11 | Numeric initial concentration in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 12 | Numeric initial compartment sizes in condition table | --- | +-- | +++ | +++ | +++ | --- | --- | --- | +++ |
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| 13 | Parametric initial concentrations in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 14 | Numeric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 15 | Parametric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ |
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| 16 | Observable transformations to log scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ | +++ |
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Legend:
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* First character indicates whether computing simulated data is supported and simulations are correct (+) or not (-).
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## Using PEtab
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If you would like to use PEtab yourself, please have a look at
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[doc/documentation_data_format.rst](doc/documentation_data_format.rst) or at
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the example models provided in the
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[benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
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If you would like to use PEtab yourself, please have a look at:
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* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html)
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going through the individual steps of setting up a parameter estimation
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problem in PEtab, independently of any specific software
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* [the PEtab format reference](https://petab.readthedocs.io/en/stable/documentation_data_format.html)
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* the example models provided in the
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[benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab).
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* the tutorials provided with each of the softwares supporting PEtab
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To convert your existing parameter estimation problem to the PEtab format, you
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will have to:

‎doc/compile_tutorial.sh‎

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#!/bin/sh
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# Build a pdflatex document from the tutorial
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pandoc tutorial.rst \
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-o tutorial.pdf \
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-V geometry:margin=1.5in -V geometry:a4paper -V fontsize=10pt \
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-V urlcolor=cyan \
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--toc \
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--pdf-engine pdflatex

‎doc/documentation_data_format.rst‎

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(ODE) models.
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Scope
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-----
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The scope of PEtab is the full specification of parameter estimation problems
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in typical systems biology applications. In our experience, a typical setup of
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data-based modeling starts either with (i) the model of a biological system
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that is to be calibrated, or with (ii) experimental data that are to be
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integrated and analyzed using a computational model.
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Measurements are linked to the biological model by an observation and noise
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model. Often, measurements are taken after some perturbations have been
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applied, which are modeled as derivations from a generic model
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(Figure 1A). Therefore, one goal was to specify such a setup in the
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least redundant way. Furthermore, we wanted to establish an intuitive, modular,
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machine- and human-readable and -writable format that makes use of existing
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standards.
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.. figure:: gfx/petab_scope_and_files.png
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:alt: A common setup for data-based modeling studies and its representation in PEtab.
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:scale: 80%
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**Figure 1: A common setup for data-based modeling studies and its representation in PEtab.**
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Overview
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The PEtab data format specifies a parameter estimation problem using a number
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of text-based files (`Systems Biology Markup Language (SBML) <http://sbml.org>`_
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`Tab-Separated Values (TSV) <https://www.iana.org/assignments/media-types/text/tab-separated-values>`_),
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i.e.
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`Tab-Separated Values (TSV) <https://www.iana.org/assignments/media-types/text/tab-separated-values>`_)
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(Figure 2), i.e.
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- An SBML model [SBML]
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- (optional) A visualization file, which contains specifications how the data
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.. image:: gfx/petab_files.png
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.. figure:: gfx/petab_files.png
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:alt: Files constituting a PEtab problem
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**Figure 2: Files constituting a PEtab problem.**
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Figure 1B shows how those files relate to a common setup for
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data-based modeling studies.
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The following sections will describe the minimum requirements of those
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**General remarks**
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- All model entities, column names and row names are case-sensitive
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- All identifiers must consist only of upper and lower case letters, digits and
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underscores, and must not start with a digit.
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- Fields in "[]" are optional and may be left empty.
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Unique identifier for the simulation/experimental condition, to be referenced
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by the measurement table described below.
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by the measurement table described below. Must consist only of upper and
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lower case letters, digits and underscores, and must not start with a digit.
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Any identifier which would be a valid identifier in SBML. This is referenced
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any existing model entity or parameter introduced elsewhere.
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Unique identifier for the given observable. Must consist only of upper and
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lower case letters, digits and underscores, and must not start with a digit.
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This is referenced by the ``observableId`` column in the measurement table.
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* [``observableName``] [STRING, OPTIONAL]
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‎doc/gfx/petab_scope_and_files.pdf‎

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