Voozh

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++)
pyABC for distributed and scalable ABC-SMC (Approximate Bayesian Computation - Sequential Monte Carlo) for parameter estimation of complex stochastic models (Python)

pyABC Public

distributed, likelihood-free inference

Python 217 45
pyPESTO Public

python Parameter EStimation TOolbox

Python 269 47
parPE Public

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

C++ 21 4
PESTO Public

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

MATLAB 27 12

Showing 10 of 30 repositories

pyPESTO Public
python Parameter EStimation TOolbox

Python 269 BSD-3-Clause 47 131 (4 issues need help) 14 Updated
cOmicsArt Public
This is the code to run cOmicsArt! Want to use it without installation - check out the website:

HTML 8 1 50 (4 issues need help) 0 Updated
Shiny-Calorie-Wrapper Public
Electron Wrapper for Shiny-Calorie

JavaScript 0 0 0 6 Updated
pyABC Public
distributed, likelihood-free inference

Python 217 BSD-3-Clause 45 31 0 Updated
pyscat Public
Scatter search optimization in Python

Python 2 BSD-3-Clause 1 11 1 Updated
Tutorial_BCML_2026 Public
This repository contains the tutorial for AMICI, PEtab and pyPESTO presented in the 2nd Bonn Conference on Mathematical Life Sciences.

Jupyter Notebook 0 0 0 0 Updated
.github Public
Organization profile

0 0 0 0 Updated
custom_ci_image Public
Testing custom CI image for parPE

Shell 0 0 0 0 Updated
C-COMPASS Public
A Neural Network Tool for Multi-Omic Classification of Cell Compartments

Python 2 0 16 2 Updated
Extrinsic-apoptosis-Conversion-reaction-model Public
This is the reproducible code for the manuscript titled "Nonlinear Mixed-Effect Models and Tailored Parameterization Schemes Enable Integration of Single-Cell and Bulk Data," which covers both the extrinsic apoptosis and conversion reaction models.

MATLAB 0 MIT 0 0 0 Updated