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@ICB-DCM

Data-driven Computational Modelling

Hasenauer Lab @ University of Bonn / 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 pyABC Public

    distributed, likelihood-free inference

    Python 206 44

  2. pyPESTO pyPESTO Public

    python Parameter EStimation TOolbox

    Python 228 47

  3. parPE parPE Public

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

    C++ 20 4

  4. PESTO PESTO Public

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

    MATLAB 26 12

Repositories

Showing 10 of 23 repositories
  • 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 1 0 49 (9 issues need help) 1 Updated Dec 19, 2024
  • 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++ 20 MIT 4 55 (1 issue needs help) 5 Updated Dec 19, 2024
  • pyPESTO Public

    python Parameter EStimation TOolbox

    ICB-DCM/pyPESTO’s past year of commit activity
    Python 228 BSD-3-Clause 47 131 (4 issues need help) 13 Updated Dec 18, 2024
  • fiddy Public

    Finite difference methods.

    ICB-DCM/fiddy’s past year of commit activity
    Python 4 BSD-3-Clause 1 11 2 Updated Nov 10, 2024
  • pyABC Public

    distributed, likelihood-free inference

    ICB-DCM/pyABC’s past year of commit activity
    Python 206 BSD-3-Clause 44 38 0 Updated Oct 30, 2024
  • 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 Oct 12, 2024
  • .github Public

    Organization profile

    ICB-DCM/.github’s past year of commit activity
    0 0 0 0 Updated Aug 8, 2024
  • model_calibration_protocol Public
    ICB-DCM/model_calibration_protocol’s past year of commit activity
    Jupyter Notebook 2 BSD-3-Clause 2 0 0 Updated Nov 24, 2022
  • SBMLimporter Public

    MATLAB toolbox to generate ODE models from SBML files

    ICB-DCM/SBMLimporter’s past year of commit activity
    MATLAB 1 BSD-3-Clause 0 0 0 Updated Nov 2, 2022
  • MEMOIR Public

    MATLAB toolbox for Mixed Effect Model InfeRence

    ICB-DCM/MEMOIR’s past year of commit activity
    MATLAB 2 BSD-3-Clause 1 2 0 Updated Aug 3, 2022
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