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@ICB-DCM

Data-driven Computational Modelling

Hasenauer Lab @ University of Bonn (formerly at Helmholtz Munich)
README.md

Hi there 👋

This is the GitHub organization of the Hasenauer Lab at University of Bonn, Germany.

For our research in computational biology, we developed a number of tools, mostly around simulation of dynamical models and parameter inference.

The highlights are:

  • pypesto for parameter estimation in Python
  • PEtab for specifying parameter estimation problems in systems biology in an efficient and interoperable manner
  • AMICI for scalable simulation and sensitivity analysis (Python / C++)
  • pyABC for distributed and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo) for parameter estimation of complex stochastic models (Python)

Pinned Loading

  1. pyABC pyABC Public

    distributed, likelihood-free inference

    Python 221 46

  2. pyPESTO pyPESTO Public

    python Parameter EStimation TOolbox

    Python 281 49

  3. parPE parPE Public

    Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

    C++ 21 4

  4. PESTO PESTO Public

    PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.

    MATLAB 27 12

Repositories

Showing 10 of 33 repositories
  • pyPESTO Public

    python Parameter EStimation TOolbox

    ICB-DCM/pyPESTO's past year of commit activity
    Python 281 BSD-3-Clause 49 134 (4 issues need help) 17 Updated Sep 11, 2026
  • fiddy Public

    Finite difference methods.

    ICB-DCM/fiddy's past year of commit activity
    Python 5 BSD-3-Clause 1 10 1 Updated Sep 10, 2026
  • pyABC Public

    distributed, likelihood-free inference

    ICB-DCM/pyABC's past year of commit activity
    Python 221 BSD-3-Clause 46 27 2 Updated Sep 8, 2026
  • pyscat Public

    Scatter search optimization in Python

    ICB-DCM/pyscat's past year of commit activity
    Python 2 BSD-3-Clause 1 11 1 Updated Sep 3, 2026
  • cOmicsArt Public

    This is the code to run cOmicsArt! Want to use it without installation - check out the website:

    ICB-DCM/cOmicsArt's past year of commit activity
    HTML 8 1 52 (5 issues need help) 1 Updated Aug 25, 2026
  • C-COMPASS Public

    A Neural Network Tool for Multi-Omic Classification of Cell Compartments

    ICB-DCM/C-COMPASS's past year of commit activity
    Python 3 0 16 2 Updated Aug 10, 2026
  • parPE Public

    Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.

    ICB-DCM/parPE's past year of commit activity
    C++ 21 MIT 4 57 (1 issue needs help) 5 Updated Jul 14, 2026
  • optimizer-benchmark-2026-suppl-code-and-data Public

    Supplementary code and data for the 2026 optimizer benchmarking manuscript

    ICB-DCM/optimizer-benchmark-2026-suppl-code-and-data's past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jul 10, 2026
  • custom_ci_image Public

    Testing custom CI image for parPE

    ICB-DCM/custom_ci_image's past year of commit activity
    Shell 0 0 0 0 Updated Jun 23, 2026
  • ACT_melanoma_neutrophil Public

    This is the reproducible code for the manuscript "Longitudinal spatial neutrophil profiling during ACT in murine melanoma reveals distinct lymph node infiltration patterns", which explores neutrophil and CD8 T cell kinetics and spatial organisation in tumor-draining vs non-draining lymph nodes in murine melanoma under adoptive T cell therapy.

    ICB-DCM/ACT_melanoma_neutrophil's past year of commit activity
    Python 1 MIT 0 0 0 Updated Jun 12, 2026
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