PEtab-dev/PEtab

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PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

Stars: 66
Forks: 16
Open beginner issues: 0
Indexed issues: 22
Avg merge: 3h 2m
Merged PRs (30d): 10

Dominant language: No language data
License: MIT
Last GitHub push: Sep 8, 2026
Latest indexed: Sep 20, 2026
Contributing guide: Contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

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22 issues indexed so far

v2: Combining experiment and condition tables Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#657 · 1 comment · Opened Jan 1, 2026
Poisson and negative binomial distributions for parameter priors and noise models Open

v2

PEtab-dev/PEtab#653 · 3 comments · 1 reaction · 1 assignee · Opened Nov 12, 2025
v2: Add how-tos Open

documentation

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#637 · 1 comment · 1 reaction · Opened Jul 9, 2025
v2: add clarification sentence about simulation start time and end times Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

PEtab-dev/PEtab#626 · 4 comments · Opened May 7, 2025
Interaction of parameter bounds and parameter priors Open

question v1

Difficulty 5/5 Over a week Newbie friendliness 20/100

PEtab-dev/PEtab#591 · Opened Dec 11, 2024
Allow species in `yValues` of the visualization table Open

specification change visualization

Difficulty 4/5 3-5 days Newbie friendliness 35/100

PEtab-dev/PEtab#569 · 2 comments · 1 reaction · Opened Oct 20, 2023
PEtab extension for NLME Open

extension

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#566 · 20 comments · 5 reactions · Opened Aug 2, 2023
Clarification of condition table what happens if NaN is provided as a value Open

v1

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

PEtab-dev/PEtab#542 · Opened May 16, 2022
Clarification for condition table what happens if a parameter ID is provided as value Open

v1

Difficulty 1/5 Under an hour Newbie friendliness 55/100

PEtab-dev/PEtab#541 · 1 comment · Opened May 12, 2022
Condition table not specified for parameters governed by rate rules Open

v1

Difficulty 1/5 Under an hour Newbie friendliness 45/100

PEtab-dev/PEtab#539 · 3 comments · Opened Mar 30, 2022
Specification for formula format Open

specification change v1

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#522 · 1 comment · 3 reactions · Opened Apr 12, 2021
Clarify reinitialization for parameters in the condition table Open

v1

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#513 · 7 comments · Opened Mar 2, 2021
Visualization: add option to scale data Open

question specification change visualization

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#501 · Opened Jan 21, 2021
Specifying units Open

enhancement question specification change

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#500 · 1 comment · 4 reactions · Opened Jan 20, 2021
Visualization specification: Is tsv the right choice? Open

question specification change visualization

Difficulty 5/5 Over a week Newbie friendliness 20/100

PEtab-dev/PEtab#499 · 2 comments · Opened Jan 18, 2021
Visualization: allow grouping plots? Open

question specification change visualization

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#498 · 1 reaction · Opened Jan 18, 2021
Extension to correlated observables Open

enhancement specification change

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#495 · Opened Jan 8, 2021
Add support for non-SBML models Open

enhancement specification change

Difficulty 5/5 Over a week Newbie friendliness 20/100

PEtab-dev/PEtab#436 · 6 comments · Opened May 10, 2020
Add support for ordinal / qualitative data Open

specification change

Difficulty 5/5 Over a week Newbie friendliness 25/100

PEtab-dev/PEtab#425 · Opened Apr 2, 2020
uniform vs. logUniform prior Open

enhancement question v1

PEtab-dev/PEtab#402 · 30 comments · 10 assignees · Opened Mar 22, 2020
allow formulation of additional constraints Open

specification change

Difficulty 5/5 Over a week Newbie friendliness 30/100

PEtab-dev/PEtab#375 · 9 comments · Opened Mar 10, 2020
Can condition tables refer to parameters introduced in {observable,noise}Formula? Open

question specification change v1

Difficulty 5/5 Over a week Newbie friendliness 20/100

PEtab-dev/PEtab#362 · 2 comments · Opened Mar 2, 2020

PEtab-dev/PEtab

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