Issues

• simulate.py imports are incompatible with current AMICI main

  Benchmarking-Initiative/Benchmark-Models-PEtab#334 · Filter by author dweindl opened on Oct 14, 2026

• v1/v2 equivalence of problems with priors on log-scaled parameters

  Benchmarking-Initiative/Benchmark-Models-PEtab#333 · Filter by author dweindl opened on Oct 13, 2026

• Add Weckel_PLOSComputBiol2026

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#329 · Filter by author dweindl opened on Oct 9, 2026

• Perelson uses digitised rather than Hulin Wu's data release

  Benchmarking-Initiative/Benchmark-Models-PEtab#322 · Filter by author FFroehlich opened on Sep 14, 2026
  3

  

• Format of simulation tables

  Benchmarking-Initiative/Benchmark-Models-PEtab#280 · Filter by author dweindl opened on Oct 21, 2025

• Validate simulation tables

  Benchmarking-Initiative/Benchmark-Models-PEtab#278 · Filter by author dweindl opened on Oct 20, 2025
  1

• Bachmann_MSB2011

  Benchmarking-Initiative/Benchmark-Models-PEtab#268 · Filter by author dilpath opened on Jun 24, 2025
  2

  

• Add Hoepfl_PLOSComputBiol2025

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#263 · Filter by author dweindl opened on May 15, 2025
  1

  

• Include objective function values and gradients at nominal parameter values

  Benchmarking-Initiative/Benchmark-Models-PEtab#259 · Filter by author dweindl opened on Dec 18, 2024
  4

• add Steinbrecht_MolSystBiol2024

  Benchmarking-Initiative/Benchmark-Models-PEtab#256 · Filter by author m-philipps opened on Dec 3, 2024

• Add Cook et al. (2022)

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#229 · Filter by author dilpath opened on Jul 17, 2024
  

• Add Montjourides et al 2024

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#227 · Filter by author dweindl opened on Jul 3, 2024

• Roadmap for the next PEtab version

  Benchmarking-Initiative/Benchmark-Models-PEtab#208 · Filter by author dilpath opened on Apr 18, 2024
  1

• add Burbano et al. (2024)

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#201 · Filter by author plakrisenko opened on Feb 7, 2024

• add Hiemstra et al. (2022)

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#200 · Filter by author plakrisenko opened on Feb 7, 2024

• Add Mishra_MetabEng2023

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#199 · Filter by author plakrisenko opened on Feb 7, 2024
  1

  

• Issues with Crauste Model

  Benchmarking-Initiative/Benchmark-Models-PEtab#183 · Filter by author FFroehlich opened on May 5, 2023
  2

• Add Millard et al. (2017)

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#182 · Filter by author dweindl opened on Mar 20, 2023

• Zheng_PNAS2012: measurements matches simulation

  Benchmarking-Initiative/Benchmark-Models-PEtab#181 · Filter by author dilpath opened on Feb 22, 2023
  1

• Add Ildefonso et al. (2023)

  new model
  Benchmarking-Initiative/Benchmark-Models-PEtab#176 · Filter by author C-Peiter opened on Jan 31, 2023

• Errors in Chen_MSB2009 benchmark

  Benchmarking-Initiative/Benchmark-Models-PEtab#175 · Filter by author FFroehlich opened on Jan 18, 2023
  4

  

• mislabeling Giordano_Nature2020

  Benchmarking-Initiative/Benchmark-Models-PEtab#170 · Filter by author FFroehlich opened on Dec 13, 2022
  

• Add CITATION.cff

  Benchmarking-Initiative/Benchmark-Models-PEtab#164 · Filter by author dweindl opened on Jul 21, 2022
  1

• Add missing visualization files

  Benchmarking-Initiative/Benchmark-Models-PEtab#156 · Filter by author dilpath opened on Feb 21, 2022
  3

• Change <model> metaid in all models

  Benchmarking-Initiative/Benchmark-Models-PEtab#155 · Filter by author dilpath opened on Feb 15, 2022