PEtab-GUI: A graphical user interface to create, edit and inspect PEtab parameter estimation problems Article Swipe
Jost, Paul Jonas
,
Bergmann, Frank T.
,
Weindl, Daniel
,
Hasenauer, Jan
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2511.11515
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.48550/arxiv.2511.11515
Motivation: Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful community standard to encode parameter estimation problems, promoting interoperability and reusability. However, its reliance on multiple interlinked files - often edited manually - can introduce inconsistencies, and new users often struggle to navigate them. Here, we present PEtab-GUI, an open-source Python application designed to streamline the creation, editing, and validation of PEtab problems through an intuitive graphical user interface. PEtab-GUI integrates all PEtab components, including SBML models and tabular files, into a single environment with live error-checking and customizable defaults. Interactive visualization and simulation capabilities enable users to inspect the relationship between the model and the data. PEtab-GUI lowers the barrier to entry for specifying standardized parameter estimation problems, making dynamic modeling more accessible, especially in educational and interdisciplinary settings. Availability and Implementation: PEtab-GUI is implemented in Python, open-source under a 3-Clause BSD license. The code, designed to be modular and extensible, is hosted on https://github.com/PEtab-dev/PEtab-GUI and can be installed from PyPI. Key words: Parameter Estimation, Python, Graphical User Interface, Systems Biology
Related Topics
Concepts
SBML
Computer science
Graphical user interface
Interoperability
Python (programming language)
Modular design
Visualization
Interoperation
Estimation theory
User interface
Human–computer interaction
Graphical display
Interface (matter)
Data visualization
Key (lock)
Data mining
Graphical model
ENCODE
Interfacing
Software engineering
Graphical user interface testing
Plug-in
Programming language
User modeling
Interactive visualization
Markup language
Modular programming
File format
Estimation
Computer graphics (images)
Theoretical computer science
Distributed computing
Metadata
- Type
- preprint
- Landing Page
- https://doi.org/10.48550/arxiv.2511.11515
- OA Status
- green
- OpenAlex ID
- https://openalex.org/W7105919342
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W7105919342Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.48550/arxiv.2511.11515Digital Object Identifier
- Title
-
PEtab-GUI: A graphical user interface to create, edit and inspect PEtab parameter estimation problemsWork title
- Type
-
preprintOpenAlex work type
- Publication year
-
2025Year of publication
- Publication date
-
2025-11-14Full publication date if available
- Authors
-
Jost, Paul Jonas, Bergmann, Frank T., Weindl, Daniel, Hasenauer, JanList of authors in order
- Landing page
-
https://doi.org/10.48550/arxiv.2511.11515Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.48550/arxiv.2511.11515Direct OA link when available
- Concepts
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SBML, Computer science, Graphical user interface, Interoperability, Python (programming language), Modular design, Visualization, Interoperation, Estimation theory, User interface, Human–computer interaction, Graphical display, Interface (matter), Data visualization, Key (lock), Data mining, Graphical model, ENCODE, Interfacing, Software engineering, Graphical user interface testing, Plug-in, Programming language, User modeling, Interactive visualization, Markup language, Modular programming, File format, Estimation, Computer graphics (images), Theoretical computer science, Distributed computingTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
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| abstract_inverted_index.graphical | 89 |
| abstract_inverted_index.including | 97 |
| abstract_inverted_index.installed | 182 |
| abstract_inverted_index.introduce | 57 |
| abstract_inverted_index.intuitive | 88 |
| abstract_inverted_index.parameter | 37, 139 |
| abstract_inverted_index.problems, | 39, 141 |
| abstract_inverted_index.promoting | 40 |
| abstract_inverted_index.settings. | 152 |
| abstract_inverted_index.Interface, | 192 |
| abstract_inverted_index.PEtab-GUI, | 70 |
| abstract_inverted_index.accessible | 20 |
| abstract_inverted_index.especially | 147 |
| abstract_inverted_index.estimation | 2, 38, 140 |
| abstract_inverted_index.integrates | 93 |
| abstract_inverted_index.interface. | 91 |
| abstract_inverted_index.simulation | 116 |
| abstract_inverted_index.specifying | 137 |
| abstract_inverted_index.streamline | 77 |
| abstract_inverted_index.validation | 82 |
| abstract_inverted_index.Estimation, | 188 |
| abstract_inverted_index.Interactive | 113 |
| abstract_inverted_index.Motivation: | 0 |
| abstract_inverted_index.accessible, | 146 |
| abstract_inverted_index.application | 74 |
| abstract_inverted_index.components, | 96 |
| abstract_inverted_index.cornerstone | 5 |
| abstract_inverted_index.data-driven | 7 |
| abstract_inverted_index.educational | 149 |
| abstract_inverted_index.environment | 106 |
| abstract_inverted_index.established | 28 |
| abstract_inverted_index.extensible, | 174 |
| abstract_inverted_index.implemented | 158 |
| abstract_inverted_index.interlinked | 49 |
| abstract_inverted_index.open-source | 72, 161 |
| abstract_inverted_index.Availability | 153 |
| abstract_inverted_index.capabilities | 117 |
| abstract_inverted_index.challenging. | 23 |
| abstract_inverted_index.constructing | 13 |
| abstract_inverted_index.customizable | 111 |
| abstract_inverted_index.relationship | 123 |
| abstract_inverted_index.reproducible | 18 |
| abstract_inverted_index.reusability. | 43 |
| abstract_inverted_index.standardized | 138 |
| abstract_inverted_index.visualization | 114 |
| abstract_inverted_index.error-checking | 109 |
| abstract_inverted_index.Implementation: | 155 |
| abstract_inverted_index.inconsistencies, | 58 |
| abstract_inverted_index.interoperability | 41 |
| abstract_inverted_index.interdisciplinary | 151 |
| abstract_inverted_index.https://github.com/PEtab-dev/PEtab-GUI | 178 |
| cited_by_percentile_year | |
| countries_distinct_count | 0 |
| institutions_distinct_count | 4 |
| citation_normalized_percentile |