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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++ (/ Matlab))
  • 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 Public

    distributed, likelihood-free inference

    Python 209 44

  2. pyPESTO Public

    python Parameter EStimation TOolbox

    Python 237 47

  3. 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 Public

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

    MATLAB 26 12

Repositories

Showing 10 of 25 repositories
  • cOmicsArt Public

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

    HTML 2 0 56 (1 issue needs help) 3 Updated Mar 21, 2025
  • C-COMPASS Public

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

    Python 2 0 16 0 Updated Mar 20, 2025
  • pyPESTO Public

    python Parameter EStimation TOolbox

    Python 237 BSD-3-Clause 47 122 (4 issues need help) 7 Updated Mar 13, 2025
  • parPE Public

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

    C++ 21 MIT 4 56 (1 issue needs help) 5 Updated Feb 19, 2025
  • FiguresMoSeS Public
    Python 0 0 0 0 Updated Feb 6, 2025
  • fiddy Public

    Finite difference methods.

    Python 4 BSD-3-Clause 1 11 2 Updated Nov 10, 2024
  • pyABC Public

    distributed, likelihood-free inference

    Python 209 BSD-3-Clause 44 39 0 Updated Oct 30, 2024
  • custom_ci_image Public

    Testing custom CI image for parPE

    Shell 0 0 0 0 Updated Oct 12, 2024
  • .github Public

    Organization profile

    0 0 0 0 Updated Aug 8, 2024
  • model_calibration_protocol Public
    Jupyter Notebook 3 BSD-3-Clause 2 0 0 Updated Nov 24, 2022
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