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FFroehlich/README.md

About Me

I am a Early Career Group Leader at the Francis Crick Instute, where I head the Dynamics of Living Systems (https://github.com/frohlich-lab). For more information, you can follow me on twitter or read my papers.

Estimation Pipeline

Over the years, I have developed and contributed to several toolboxes that permit the efficient formulation, simulation and calibration of kinetic models of cellular signaling. All toolboxes are modular and interoperable, allowing the flexible definition of customizable analysis pipelines.

  • Formulate your model using pysb
  • Define your estimation problem using PEtab
  • Solve your estimation problem using pyPESTO
  • Use the efficient optimizers implemented in fides
  • Use the scalable simulate and sensitivity computation methods implemented in AMICI

Pinned Loading

  1. AMICI-dev/AMICI AMICI-dev/AMICI Public

    Advanced Multilanguage Interface to CVODES and IDAS

    Jupyter Notebook 108 31

  2. ICB-DCM/pyPESTO ICB-DCM/pyPESTO Public

    python Parameter EStimation TOolbox

    Python 219 47

  3. fides-dev/fides fides-dev/fides Public

    Trust Region Optimization in Python

    Python 26 4

  4. PEtab-dev/PEtab PEtab-dev/PEtab Public

    PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology

    60 12

  5. pysb/pysb pysb/pysb Public

    Python framework for Systems Biology modeling

    Python 168 71