Releases · Benchmarking-Initiative/Benchmark-Models-PEtab

What's Changed

Overview table: discontinuities by @dweindl in #241

Set parameters and compartments to constant Perelson model by @sebapersson in #245

Fix typo in overview.py regarding discontinuities by @dilpath in #246

Update How to Cite information by @dilpath in #244

add Armistead_CellDeathDis2024 by @m-philipps in #249

update simulated data by @m-philipps in #251

What's Changed

Fix pre-commit config by @dweindl in #187
Add links to SBML4Humans for model inspection by @dweindl in #186
README how to cite by @dilpath in #185
Require recent libpetab by @dweindl in #188
Fixed wrong reference to research article from Laske model by @C-Peiter in #173
Update README by @dilpath in #189
update Boehm parameters table by @m-philipps in #190
fix Isensee model visualization spec by @plakrisenko in #192
Isensee visualization fix by @plakrisenko in #193
add benchmark collection references by @plakrisenko in #194
Add model Raia_CancerResearch2011 by @m-philipps in #191
another Isensee visualization fix by @plakrisenko in #196
Fix RaiaCancerResearch2011 by @m-philipps in #197
one more Isensee visualization fix by @plakrisenko in #198
Fix Froehlich_CellSystems2018 ref by @dilpath in #204
Update readme table automatically by @dilpath in #205
Checklist for new submissions by @dilpath in #206
Fix PR template; remove duplicated contributing info by @dilpath in #207
Add Lang_PLOSComputBiol2024 by @paulflang in #202
Fix #212, annotation fix invalid sbml Lang by @matthiaskoenig in #213
removing empty annotations by @matthiaskoenig in #215
Fix dataset id in Schwen_PONE2014 by @m-philipps in #216
Add get_problem_yaml_path by @dweindl in #223
Require newer PEtab, use petab.v1 by @dweindl in #225
Fix visualization specification for Zhao. by @stephanmg in #217
Bertozzi_PNAS2020: update to match Table 1 of paper by @dilpath in #222
Update Lang_PLOSComputBiol2024 to fix petablint errors by @dilpath in #228
GHA: Enable dependabot for action upgrades by @dweindl in #224
Bump actions/checkout from 2 to 4 by @dependabot in #231
Bump actions/setup-python from 1 to 5 by @dependabot in #230
Fix tsv format in parameters_Schwen_PONE2014.tsv by @dweindl in #234
Consolidate scripts and python package by @dweindl in #238
Fix parameter ID typo in Giordano_Nature2020 by @dweindl in #237
Fix Fiedler_BMCSystBiol2016 ID by @m-philipps in #240
Use setuptools_scm for package versions by @dweindl in #243

New Contributors

@m-philipps made their first contribution in #190
@paulflang made their first contribution in #202
@matthiaskoenig made their first contribution in #213
@stephanmg made their first contribution in #217
@dependabot made their first contribution in #231

Full Changelog: v2023.07.17...v2024.10.15

Smith_BMCSystBiol2013 (#180) * add draft implementation * fix time & model id * fix concentration vs amount * fix Ins concentration * fix conc/amount * fix scaling factors nominal value * add insulin injection event, add simulation test * Update MODEL1212210000_Ins_events.xml * Update MODEL1212210000_Ins_events.xml * fixup event * don't use infinite parameter values * fix test problem * fix compartment observables * add indicator functions for different model compositions * Update experimentalCondition_Smith_BMCSystBiol2013.tsv * conditionalize k4, kminus4, k_irs1_basal_syn, fix test conditions * workaround E2F1 * revert to original model to avoid amount/conc snafu * ??? * remove null obs * update version * fix conditions * fix conditions * correct tx rate for 2H * remove debug stuff, add reference * add E2F1 condition * parametrize fig2h fixes * fix readme * use URLs instead of copying files * add readme * added simulated data file * fixes + visualization table * reenable linting