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Achievements

Achievement: QuickdrawAchievement: Pair Extraordinairex4Achievement: YOLOAchievement: Pull Sharkx4Achievement: StarstruckAchievement: Arctic Code Vault Contributor

Achievements

Achievement: QuickdrawAchievement: Pair Extraordinairex4Achievement: YOLOAchievement: Pull Sharkx4Achievement: StarstruckAchievement: Arctic Code Vault Contributor

Highlights

  • Pro

Organizations

@ICB-DCM @Benchmarking-Initiative @PeriNAA @PEtab-dev @AMICI-dev @biosimulators

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dweindl/README.md

About me

Hi 👋, I'm Daniel, a Computational Biologist at the Interdisciplinary Research Unit Mathematics and Life Sciences / Life & Medical Sciences Institute at the University of Bonn. I am mostly active in dynamical modeling and parameter estimation. My papers are listed on Google Scholar.

I am developer / regular contributor / maintainer of a number of tools around efficient simulation and parameter estimation for dynamic models in systems biology. The main projects are:

  • 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))
  • pypesto for parameter estimation in Python
  • parPE for parameter estimation for ordinary differential equation models on high-performance computing cluster (C++)

Other projects in rather early stage:

📫 How to reach me

Some stats

Pinned Loading

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

    Advanced Multilanguage Interface to CVODES and IDAS

    Jupyter Notebook 112 31

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

    python Parameter EStimation TOolbox

    Python 225 47

  3. PEtab-dev/PEtab PEtab-dev/PEtab Public

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

    60 12

  4. ICB-DCM/parPE ICB-DCM/parPE Public

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

    C++ 20 4

  5. mia mia Public

    Mass isotopolome analyzer - GUI-based non-targeted analysis of stable isotope labeling mass spectrometry data

    C++ 4 1

  6. sbmlmath sbmlmath Public

    SBML MathML <-> SymPy

    Python 8