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5 | 5 |
|
6 | | -# PEtab -- a data format for specifying parameter estimation problems in systems biology |
| 6 | +# petab - a Python package for handling PEtab files |
7 | 7 |
|
8 | | - |
9 | | - |
10 | | -*PEtab* is a data format for specifying parameter estimation problems in systems biology. |
11 | | -This repository provides extensive documentation and a Python library for easy |
12 | | -access and validation of *PEtab* files. |
13 | | - |
14 | | -## About PEtab |
15 | | - |
16 | | -PEtab is built around [SBML](http://sbml.org/) and based on tab-separated values |
17 | | -(TSV) files. It is meant as a standardized way to provide information for |
18 | | -parameter estimation, which is out of the current scope of SBML. This includes |
19 | | -for example: |
20 | | - |
21 | | - - Specifying and linking measurements to models |
22 | | - |
23 | | - - Defining model outputs |
24 | | - |
25 | | - - Specifying noise models |
26 | | - |
27 | | - - Specifying parameter bounds for optimization |
28 | | - |
29 | | - - Specifying multiple simulation condition with potentially shared parameters |
30 | | - |
31 | | - |
| 8 | +[PEtab](https://petab.readthedocs.io/) is a data format for specifying |
| 9 | +parameter estimation problems in systems biology. This repository provides |
| 10 | +the `petab` Python package for reading, writing and validating PEtab files. |
32 | 11 |
|
33 | 12 | ## Documentation |
34 | 13 |
|
35 | | -Documentation of the PEtab data format and Python library is available at |
| 14 | +Documentation of the `petab` Python package is available at |
| 15 | +[https://libpetab-python.readthedocs.io/en/latest/](https://libpetab-python.readthedocs.io/en/latest/). |
| 16 | +Documentation of the PEtab format in general is available at |
36 | 17 | [https://petab.readthedocs.io/en/latest/](https://petab.readthedocs.io/en/latest/). |
37 | 18 |
|
38 | | -## Examples |
39 | | - |
40 | | -A wide range of PEtab examples can be found in the systems biology parameter estimation |
41 | | -[benchmark problem collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab). |
42 | | - |
43 | | - |
44 | | -## PEtab support in systems biology tools |
45 | | - |
46 | | -Where PEtab is supported (in alphabetical order): |
47 | | - |
48 | | - |
49 | | - - [AMICI](https://github.com/ICB-DCM/AMICI/) |
50 | | - ([Example](https://github.com/ICB-DCM/AMICI/blob/master/python/examples/example_petab/petab.ipynb)) |
51 | | - |
52 | | - - A PEtab -> [COPASI](http://copasi.org/) |
53 | | - [converter](https://github.com/copasi/python-petab-importer) |
54 | | - |
55 | | - - [d2d](https://github.com/Data2Dynamics/d2d/) |
56 | | - ([HOWTO](https://github.com/Data2Dynamics/d2d/wiki/Support-for-PEtab)) |
57 | | - |
58 | | - - [dMod](https://github.com/dkaschek/dMod/) |
59 | | - ([HOWTO](https://github.com/dkaschek/dMod/wiki/Support-for-PEtab)) |
60 | | - |
61 | | - - [MEIGO](https://github.com/gingproc-IIM-CSIC/MEIGO64) |
62 | | - ([HOWTO](https://github.com/gingproc-IIM-CSIC/MEIGO64/tree/master/MEIGO/PEtabMEIGO)) |
63 | | - |
64 | | - - [parPE](https://github.com/ICB-DCM/parPE/) |
| 19 | +## Installation |
65 | 20 |
|
66 | | - - [pyABC](https://github.com/ICB-DCM/pyABC/) ([Example](https://pyabc.readthedocs.io/en/latest/examples/petab.html)) |
67 | | - |
68 | | - - [pyPESTO](https://github.com/ICB-DCM/pyPESTO/) |
69 | | - ([Example](https://pypesto.readthedocs.io/en/latest/example/petab_import.html)) |
70 | | - |
71 | | - - [SBML2Julia](https://github.com/paulflang/SBML2Julia) |
72 | | - ([Tutorial](https://sbml2julia.readthedocs.io/en/latest/python_api.html)) |
73 | | - |
74 | | -If your project or tool is using PEtab, and you would like to have it listed |
75 | | -here, please [let us know](https://github.com/PEtab-dev/PEtab/issues). |
76 | | - |
77 | | -### PEtab features supported in different tools |
78 | | - |
79 | | -The following list provides an overview of supported PEtab features in |
80 | | -different tools, based on passed test cases of the |
81 | | -[PEtab test suite](https://github.com/PEtab-dev/petab_test_suite): |
82 | | - |
83 | | - |
84 | | -| 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 | |
85 | | -|----|----------------------------------------------------------------|----------------------|--------|-----|------|-------|-----------------------|-------|------------------------|------------| |
86 | | -| 1 | Basic simulation | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
87 | | -| 2 | Multiple simulation conditions | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
88 | | -| 3 | Numeric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
89 | | -| 4 | Parametric observable parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
90 | | -| 5 | Parametric overrides in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
91 | | -| 6 | Time-point specific overrides in the measurement table | --- | --- | +++ | +++ | +++ | --- | --- | --- | +++ | |
92 | | -| 7 | Observable transformations to log10 scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ | +++ | |
93 | | -| 8 | Replicate measurements | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
94 | | -| 9 | Pre-equilibration | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
95 | | -| 10 | Partial pre-equilibration | +++ | --- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
96 | | -| 11 | Numeric initial concentration in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
97 | | -| 12 | Numeric initial compartment sizes in condition table | --- | +-- | +++ | +++ | +++ | --- | --- | --- | +++ | |
98 | | -| 13 | Parametric initial concentrations in condition table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
99 | | -| 14 | Numeric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
100 | | -| 15 | Parametric noise parameter overrides in measurement table | +++ | +-- | +++ | +++ | +++ | --+ | +++ | +++ | +++ | |
101 | | -| 16 | Observable transformations to log scale | +-+ | +-- | +++ | ++- | +++ | --+ | +-+ | +-+ | +++ | |
102 | | - |
103 | | -Legend: |
104 | | -* First character indicates whether computing simulated data is supported and simulations are correct (+) or not (-). |
105 | | -* Second character indicates whether computing chi2 values of residuals are supported and correct (+) or not (-). |
106 | | -* Third character indicates whether computing likelihoods is supported and correct (+) or not (-). |
107 | | - |
108 | | -## Using PEtab |
109 | | - |
110 | | -If you would like to use PEtab yourself, please have a look at: |
111 | | - |
112 | | -* [a PEtab tutorial](https://petab.readthedocs.io/en/latest/tutorial.html) |
113 | | - going through the individual steps of setting up a parameter estimation |
114 | | - problem in PEtab, independently of any specific software |
115 | | -* [the PEtab format reference](https://petab.readthedocs.io/en/stable/documentation_data_format.html) |
116 | | -* the example models provided in the |
117 | | - [benchmark collection](https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab). |
118 | | -* the tutorials provided with each of the softwares supporting PEtab |
119 | | - |
120 | | -To convert your existing parameter estimation problem to the PEtab format, you |
121 | | -will have to: |
122 | | - |
123 | | -1. Specify your model in SBML. |
124 | | - |
125 | | -1. Create a condition table. |
126 | | - |
127 | | -1. Create a table of observables. |
128 | | - |
129 | | -1. Create a table of measurements. |
130 | | - |
131 | | -1. Create a parameter table. |
132 | | - |
133 | | -If you are using Python, some handy functions of the |
134 | | -[PEtab library](https://petab.readthedocs.io/en/latest/modules.html) can help |
135 | | -you with that. This include also a PEtab validator called `petablint` which |
136 | | -you can use to check if your files adhere to the PEtab standard. If you have |
137 | | -further questions regarding PEtab, feel free to post an |
138 | | -[issue](https://github.com/PEtab-dev/PEtab/issues) at our github repository. |
139 | | - |
140 | | -## PEtab Python library |
141 | | - |
142 | | -PEtab comes with a Python package for creating, checking, visualizing and |
143 | | -working with PEtab files. This library is available on |
144 | | -[pypi](https://pypi.org/project/petab/) and the easiest way to install |
145 | | -it is running |
| 21 | +The PEtab library is available on [pypi](https://pypi.org/project/petab/) |
| 22 | +and the easiest way to install it is running |
146 | 23 |
|
147 | 24 | pip3 install petab |
148 | 25 |
|
149 | 26 | It will require Python>=3.7.1 to run. |
150 | 27 |
|
151 | 28 | Development versions of the PEtab library can be installed using |
152 | 29 |
|
153 | | - pip3 install https://github.com/PEtab-dev/PEtab/archive/develop.zip |
| 30 | + pip3 install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip |
154 | 31 |
|
155 | 32 | (replace `develop` by the branch or commit you would like to install). |
156 | 33 |
|
|
168 | 45 | - `petab.create_combine_archive` to create a |
169 | 46 | [COMBINE Archive](https://combinearchive.org/index/) from PEtab files |
170 | 47 |
|
171 | | -### Library examples |
| 48 | +## Examples |
172 | 49 |
|
173 | 50 | Examples for PEtab Python library usage: |
174 | 51 |
|
175 | | -* [Validation](https://github.com/PEtab-dev/PEtab/blob/master/doc/example/example_petablint.ipynb) |
176 | | -* [Visualization](https://github.com/PEtab-dev/PEtab/blob/master/doc/example/example_visualization.ipynb) |
| 52 | +* [Validation](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_petablint.ipynb) |
| 53 | +* [Visualization](https://github.com/PEtab-dev/libpetab-python/blob/master/doc/example/example_visualization.ipynb) |
177 | 54 |
|
178 | 55 |
|
179 | 56 | ## Getting help |
180 | 57 |
|
181 | | -If you have any question or problems with PEtab, feel free to post them at |
182 | | -our GitHub [issue tracker](https://github.com/PEtab-dev/PEtab/issues/). |
| 58 | +If you have any question or problems with this package, feel free to post them |
| 59 | +at our GitHub [issue tracker](https://github.com/PEtab-dev/libpetab-python/issues/). |
183 | 60 |
|
184 | | -## Contributing to PEtab |
| 61 | +## Contributing |
185 | 62 |
|
186 | | -Contributions and feedback to PEtab are very welcome, see our |
| 63 | +Contributions and feedback to this package are very welcome, see our |
187 | 64 | [contribution guide](CONTRIBUTING.md). |
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