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About me

Hi 👋, I'm Daniel, a Computational Biologist at the Computational Health Center at Helmholtz Munich. 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++)

📫 How to reach me

Some stats

Daniel Weindl's Projects

amici icon amici

Advanced Multilanguage Interface to CVODES and IDAS

biosimulators_amici icon biosimulators_amici

AMICI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container

exhale icon exhale

Automatic C++ library api documentation generation: breathe doxygen in and exhale it out.

fides icon fides

Trust Region Optimization in Python

isrene icon isrene

Isotopologue reaction networks in Python

mia icon mia

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

microblog icon microblog

A microblogging web application written in Python and Flask that I developed as part of my Flask Mega-Tutorial series.

pandas icon pandas

Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more

pypesto icon pypesto

python Parameter EStimation TOolbox

pysb icon pysb

Python framework for Systems Biology modeling

staged-recipes icon staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

sympy icon sympy

A computer algebra system written in pure Python

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