petab
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Science Score: 44.0%
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Low similarity (15.3%) to scientific vocabulary
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Repository
PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
Basic Info
- Host: GitHub
- Owner: PEtab-dev
- License: mit
- Default Branch: main
- Homepage: https://petab.readthedocs.io
- Size: 11.4 MB
Statistics
- Stars: 60
- Watchers: 14
- Forks: 12
- Open Issues: 32
- Releases: 25
Topics
Metadata Files
README.md
PEtab -- a data format for specifying parameter estimation problems in systems biology
PEtab is a data format for specifying parameter estimation problems in systems biology. This repository contains the PEtab specifications and additional documentation.
About PEtab
PEtab is built around SBML and based on tab-separated values (TSV) files. It is meant as a standardized way to provide information for parameter estimation, which is out of the current scope of SBML. This includes, for example:
Specifying and linking measurements to models
- Defining model outputs
- Specifying noise models
Specifying parameter bounds for optimization
Specifying multiple simulation conditions with potentially shared parameters
Documentation
Documentation of the PEtab data format is available at https://petab.readthedocs.io/en/latest/.
Contributing to PEtab
To participate in PEtab editor elections, discussions on new PEtab developments, or PEtab-related events, please join our petab-discuss mailing list.
Any contributions and feedback to PEtab are very welcome, see our contribution guide.
Examples
A wide range of PEtab examples can be found in the systems biology parameter estimation benchmark problem collection.
PEtab support in systems biology tools
For a list of tools supporting PEtab, see the software support page.
Using PEtab
If you would like to use PEtab yourself, please have a look at:
- a PEtab tutorial going through the individual steps of setting up a parameter estimation problem in PEtab, independently of any specific software
- the PEtab format reference
- the example models provided in the benchmark collection.
- the tutorials provided with each of the softwares supporting PEtab
To convert your existing parameter estimation problem to the PEtab format, you will have to:
Specify your model in SBML.
Create a condition table.
Create a table of observables.
Create a table of measurements.
Create a parameter table.
Create a YAML file that lists the model and all of the tables above.
If you are using Python, some handy functions of the
PEtab library can help
you with that. This includes also a PEtab validator called petablint which
you can use to check if your files adhere to the PEtab standard. If you have
further questions regarding PEtab, feel free to post an
issue at our GitHub repository.
PEtab Python library
PEtab comes with a Python package for creating, checking, visualizing and working with PEtab files. This package is available at https://github.com/PEtab-dev/libpetab-python/.
PEtab R library
There is also an R package for PEtab in development, which currently supports: consistent manipulation of experimental conditions, measurements, and observables; and visualizing measurements. It also provides an interface to the PEtab Python library, and an interface to dMod that supports: conversion of dMod models to SBML; and simulation and visualization of results. The package is available at https://github.com/dlill/petab/.
Getting help
If you have any questions or problems with PEtab, feel free to post them at our GitHub issue tracker.
Owner
- Name: PEtab - an SBML and TSV-based data format for parameter estimation problems in systems biology
- Login: PEtab-dev
- Kind: organization
- Repositories: 6
- Profile: https://github.com/PEtab-dev
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: PEtab—Interoperable specification of parameter estimation problems in systems biology
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
license: MIT
authors:
-
family-names: "Schmiester"
given-names: "Leonard"
orcid: "https://orcid.org/0000-0001-7946-3232"
-
family-names: "Schälte"
given-names: "Yannik"
orcid: "https://orcid.org/0000-0003-1293-820X"
-
family-names: "Bergmann"
given-names: "Frank"
-
family-names: "Camba"
given-names: "Tacio"
-
family-names: "Dudkin"
given-names: "Erika"
-
family-names: "Egert"
given-names: "Janine"
-
family-names: "Fröhlich"
given-names: "Fabian"
orcid: "https://orcid.org/0000-0002-5360-4292"
-
family-names: "Fuhrmann"
given-names: "Lara"
-
family-names: "Hauber"
given-names: "Adrian"
-
family-names: "Kemmer"
given-names: "Svenja"
-
family-names: "Lakrisenko"
given-names: "Polina"
-
family-names: "Loos"
given-names: "Carolin"
-
family-names: "Merkt"
given-names: "Simon"
-
family-names: "Müller"
given-names: "Wolfgang"
-
family-names: "Pathirana"
given-names: "Dilan"
orcid: "https://orcid.org/0000-0001-7000-2659"
-
family-names: "Raimúndez"
given-names: "Elba"
-
family-names: "Refisch"
given-names: "Lukas"
-
family-names: "Rosenblatt"
given-names: "Marcus"
-
family-names: "Stapor"
given-names: "Paul"
-
family-names: "Städter"
given-names: "Philipp"
-
family-names: "Wang"
given-names: "Dantong"
-
family-names: "Wieland"
given-names: "Franz-Georg"
-
family-names: "Banga"
given-names: "Julio"
-
family-names: "Timmer"
given-names: "Jens"
-
family-names: "Villaverde"
given-names: "Alejandro"
-
family-names: "Sahle"
given-names: "Sven"
-
family-names: "Kreutz"
given-names: "Clemens"
-
family-names: "Hasenauer"
given-names: "Jan"
orcid: "https://orcid.org/0000-0002-4935-3312"
-
family-names: "Weindl"
given-names: "Daniel"
orcid: "https://orcid.org/0000-0001-9963-6057"
repository-code: 'https://github.com/PEtab-dev/PEtab'
preferred-citation:
type: article
title: "PEtab—Interoperable specification of parameter estimation problems in systems biology"
doi: 10.1371/journal.pcbi.1008646
journal: "PLOS Computational Biology"
year: 2021
month: 1
start: 1
end: 10
volume: 17
number: 1
authors:
-
family-names: "Schmiester"
given-names: "Leonard"
orcid: "https://orcid.org/0000-0001-7946-3232"
-
family-names: "Schälte"
given-names: "Yannik"
orcid: "https://orcid.org/0000-0003-1293-820X"
-
family-names: "Bergmann"
given-names: "Frank"
-
family-names: "Camba"
given-names: "Tacio"
-
family-names: "Dudkin"
given-names: "Erika"
-
family-names: "Egert"
given-names: "Janine"
-
family-names: "Fröhlich"
given-names: "Fabian"
orcid: "https://orcid.org/0000-0002-5360-4292"
-
family-names: "Fuhrmann"
given-names: "Lara"
-
family-names: "Hauber"
given-names: "Adrian"
-
family-names: "Kemmer"
given-names: "Svenja"
-
family-names: "Lakrisenko"
given-names: "Polina"
-
family-names: "Loos"
given-names: "Carolin"
-
family-names: "Merkt"
given-names: "Simon"
-
family-names: "Müller"
given-names: "Wolfgang"
-
family-names: "Pathirana"
given-names: "Dilan"
orcid: "https://orcid.org/0000-0001-7000-2659"
-
family-names: "Raimúndez"
given-names: "Elba"
-
family-names: "Refisch"
given-names: "Lukas"
-
family-names: "Rosenblatt"
given-names: "Marcus"
-
family-names: "Stapor"
given-names: "Paul"
-
family-names: "Städter"
given-names: "Philipp"
-
family-names: "Wang"
given-names: "Dantong"
-
family-names: "Wieland"
given-names: "Franz-Georg"
-
family-names: "Banga"
given-names: "Julio"
-
family-names: "Timmer"
given-names: "Jens"
-
family-names: "Villaverde"
given-names: "Alejandro"
-
family-names: "Sahle"
given-names: "Sven"
-
family-names: "Kreutz"
given-names: "Clemens"
-
family-names: "Hasenauer"
given-names: "Jan"
orcid: "https://orcid.org/0000-0002-4935-3312"
-
family-names: "Weindl"
given-names: "Daniel"
orcid: "https://orcid.org/0000-0001-9963-6057"
GitHub Events
Total
- Create event: 26
- Commit comment event: 3
- Issues event: 32
- Watch event: 3
- Delete event: 22
- Issue comment event: 103
- Push event: 147
- Pull request review comment event: 243
- Pull request review event: 246
- Pull request event: 50
Last Year
- Create event: 26
- Commit comment event: 3
- Issues event: 32
- Watch event: 3
- Delete event: 22
- Issue comment event: 103
- Push event: 147
- Pull request review comment event: 243
- Pull request review event: 246
- Pull request event: 50
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 20
- Total pull requests: 30
- Average time to close issues: over 1 year
- Average time to close pull requests: 28 days
- Total issue authors: 6
- Total pull request authors: 6
- Average comments per issue: 3.15
- Average comments per pull request: 0.73
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 13
- Pull requests: 29
- Average time to close issues: 2 months
- Average time to close pull requests: 12 days
- Issue authors: 5
- Pull request authors: 5
- Average comments per issue: 2.08
- Average comments per pull request: 0.31
- Merged pull requests: 17
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dweindl (13)
- FFroehlich (5)
- matthiaskoenig (3)
- dilpath (3)
- fbergmann (1)
- LeonardSchmiester (1)
- jvanhoefer (1)
- tinop99 (1)
- leodarrigade (1)
- MA-Kochen (1)
Pull Request Authors
- dweindl (27)
- dilpath (3)
- sebapersson (2)
- matthiaskoenig (1)
- fbergmann (1)
- FFroehlich (1)