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PEtab-dev

6 indexed repositories · View on GitHub

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

66 stars
libpetab-python
Python package for working with PEtab files

Python · 18 stars
petab_select
Model selection for PEtab

Python · 14 stars
petab_sciml
Exchangeable data format for training Scientific Machine Learning (SciML) models

Python · 11 stars
petab_test_suite
PEtab test suite

Python · 6 stars
petab_sciml_testsuite

Julia · 0 stars

Beginner friendly Everything

Open All

Improve model abstractions Open

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

PEtab-dev/libpetab-python#518 · Opened Sep 7, 2026
Consider extending the test suite to BNGL Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/petab_test_suite#117 · Opened Aug 14, 2026
Mapping table contributions to parameter table validation (SciML use case) Open

validation

Difficulty 5/5 Over a week Newbie friendliness 35/100

PEtab-dev/libpetab-python#494 · 1 comment · Opened Jun 26, 2026
Linter Open

PEtab-dev/petab_sciml#69 · 7 comments · 1 assignee · Opened Feb 24, 2026
Automatic hybridization of NN model inputs and outputs Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

PEtab-dev/petab_sciml#66 · Opened Feb 20, 2026
Add design principles page Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

PEtab-dev/petab_sciml#50 · 4 comments · Opened Jan 21, 2026
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
Include residuals and likelihoods in simulation tables Open

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

PEtab-dev/petab_test_suite#100 · Opened Dec 12, 2025
Support for discrete noise distributions Open

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

PEtab-dev/libpetab-python#466 · Opened Dec 3, 2025
Add tests for all noise distributions Open

new test case v2

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

PEtab-dev/petab_test_suite#95 · Opened Dec 2, 2025
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
DMM tutorial multiple simulation conditions Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

PEtab-dev/petab_sciml#40 · Opened Nov 5, 2025
Add CLI for petab v1->v2 conversion Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#453 · Opened Oct 29, 2025
Docs ways to inspect model selection results Open

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

PEtab-dev/petab_select#163 · Opened Oct 16, 2025
Doc unusual behavior of forward/backward methods Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

PEtab-dev/petab_select#162 · Opened Oct 16, 2025
Add goodness-of-fit and residual plots to visualization examples Open

documentation

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#439 · Opened Sep 19, 2025
API for renaming PEtab entities Open

enhancement

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

PEtab-dev/libpetab-python#438 · Opened Sep 19, 2025
Test suite TODO Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

PEtab-dev/petab_sciml_testsuite#9 · 3 comments · Opened Jul 24, 2025
Remove `v2.Problem.*_df` Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#409 · Opened Jul 21, 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: Visualization functions Open

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

PEtab-dev/libpetab-python#398 · Opened Jul 2, 2025
Document release process Open

documentation

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

PEtab-dev/libpetab-python#396 · Opened Jul 2, 2025
Documentation TODOs Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

PEtab-dev/petab_sciml#23 · 1 comment · Opened Jun 25, 2025
Subset priors Open

PEtab-dev/petab_select#159 · 1 reaction · 1 assignee · Opened Jun 15, 2025
v2: Handle multi-model problems Open

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

PEtab-dev/libpetab-python#392 · 2 comments · Opened Jun 5, 2025
Change RTD blue square to avoid clash with logo text Open

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

PEtab-dev/petab_select#158 · Opened May 20, 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
split standard and package into separate repos Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

PEtab-dev/petab_select#157 · Opened Apr 30, 2025
`analyze.compute_weights` does not permit a `str`-type criterion argument Open

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

PEtab-dev/petab_select#156 · Opened Apr 22, 2025
v2: Update validator Open

validation

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

PEtab-dev/libpetab-python#369 · Opened Mar 28, 2025
Add CLI to docs Open

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

PEtab-dev/petab_select#155 · Opened Mar 16, 2025
Update README Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

PEtab-dev/petab_select#154 · Opened Feb 23, 2025
Use different graph plotting library Open

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

PEtab-dev/petab_select#152 · Opened Feb 14, 2025
Manage state information more cleanly Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

PEtab-dev/petab_select#133 · Opened Jan 4, 2025
antlr runtime version Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

PEtab-dev/libpetab-python#344 · 4 comments · Opened Dec 18, 2024
PEtab SciML TODO Open

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

PEtab-dev/petab_sciml#11 · 6 comments · 1 reaction · Opened Dec 18, 2024
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
More introductory text in docs Open

fixed in next release

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

PEtab-dev/petab_select#118 · Opened Nov 19, 2024
`flatten_timepoint_specific_output_overrides` should not do anything if there are no timepoint-specific output parameters Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#314 · Opened Oct 17, 2024
Add functionality for computing posteriors Open

enhancement

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

PEtab-dev/libpetab-python#312 · 2 reactions · Opened Oct 15, 2024
Refactor priors Open

enhancement

PEtab-dev/libpetab-python#311 · 2 reactions · 1 assignee · Opened Oct 15, 2024
Feature to automate handling of replicate data Open

PEtab-dev/libpetab-python#310 · 1 comment · 1 assignee · Opened Oct 8, 2024
PEtab Simulator update_parameters Open

enhancement

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

PEtab-dev/libpetab-python#305 · 2 reactions · Opened Aug 15, 2024
Replace individual dataframe arguments by Problem objects Open

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

PEtab-dev/libpetab-python#301 · 1 reaction · Opened Jul 2, 2024
v2 validation: atomize checks Open

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

PEtab-dev/libpetab-python#289 · 1 reaction · Opened Jun 29, 2024
Integration of extensions Open

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

PEtab-dev/libpetab-python#273 · 2 comments · Opened Jun 25, 2024
Add test with multiple models Open

new test case v2

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

PEtab-dev/petab_test_suite#66 · Opened Jun 25, 2024
composite problem Open

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

PEtab-dev/libpetab-python#265 · 4 comments · Opened Jun 2, 2024
Add test case with parameters with initial assignments Open

new test case v1

Difficulty 3/5 1-2 days Newbie friendliness 25/100

PEtab-dev/petab_test_suite#61 · Opened Mar 5, 2024
Wrong plot_goodness_of_fit if different order of rows in measurement_df and simulation_df Open

bug visualization

Difficulty 3/5 1-2 days Newbie friendliness 45/100

PEtab-dev/libpetab-python#247 · 1 comment · 2 reactions · Opened Feb 27, 2024

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