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30 repositories

pyPESTO
Public
python Parameter EStimation TOolbox
python optimization systems-biology
python optimization systems-biology parameter-estimation hacktoberfest
Python
•
BSD 3-Clause "New" or "Revised" License
•47•269•131•12•Updated Apr 21, 2026Apr 21, 2026
cOmicsArt
Public
This is the code to run cOmicsArt! Want to use it without installation - check out the website:
HTML
•1•8•50•0•Updated Apr 16, 2026Apr 16, 2026
pyABC
Public
distributed, likelihood-free inference
abc parameter-inference approximate-bayesian-inference
abc parameter-inference approximate-bayesian-inference likelihood-free-inference
Python
•
BSD 3-Clause "New" or "Revised" License
•45•219•31•0•Updated Apr 14, 2026Apr 14, 2026
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 a…
MATLAB
•
MIT License
•0•0•0•0•Updated Apr 7, 2026Apr 7, 2026
Shiny-Calorie-Wrapper
Public
Electron Wrapper for Shiny-Calorie
r-shiny electronjs calorimetry
r-shiny electronjs calorimetry
JavaScript
•0•0•0•6•Updated Mar 31, 2026Mar 31, 2026
pyscat
Public
Scatter search optimization in Python
optimization ess metaheuristic
optimization ess metaheuristic scatter-search sacess
Python
•
BSD 3-Clause "New" or "Revised" License
•1•2•11•1•Updated Mar 19, 2026Mar 19, 2026
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 Mar 19, 2026Mar 19, 2026
.github
Public
Organization profile
0•0•0•0•Updated Mar 12, 2026Mar 12, 2026
custom_ci_image
Public
Testing custom CI image for parPE
Shell
•0•0•0•0•Updated Mar 9, 2026Mar 9, 2026
C-COMPASS
Public
A Neural Network Tool for Multi-Omic Classification of Cell Compartments
Python
•
Other
•0•2•16•2•Updated Mar 9, 2026Mar 9, 2026
parPE
Public
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
optimization systems-biology ode
optimization systems-biology ode high-performance-computing parameter-estimation hacktoberfest dynamical-modeling sbml petab amici
C++
•
MIT License
•4•21•57•5•Updated Dec 15, 2025Dec 15, 2025
fiddy
Public
Finite difference methods.
finite-differences hacktoberfest gradient-check
finite-differences hacktoberfest gradient-check amici
Python
•
BSD 3-Clause "New" or "Revised" License
•1•5•13•2•Updated Dec 15, 2025Dec 15, 2025
Shiny-Calorie
Public
Shiny-Calorie: A context-aware application for indirect calorimetry data analysis and visualization using R
shiny-r calorimetry
shiny-r calorimetry
R
•
MIT License
•0•1•0•0•Updated Sep 10, 2025Sep 10, 2025
FiguresMoSeS
Public
Python
•0•0•0•0•Updated Feb 6, 2025Feb 6, 2025
model_calibration_protocol
Public
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•3•5•0•0•Updated Nov 24, 2022Nov 24, 2022
SBMLimporter
Public
MATLAB toolbox to generate ODE models from SBML files
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Nov 2, 2022Nov 2, 2022
MEMOIR
Public
MATLAB toolbox for Mixed Effect Model InfeRence
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•1•2•2•0•Updated Aug 3, 2022Aug 3, 2022
SPToolbox
Public
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Jul 26, 2021Jul 26, 2021
lookahead-study
Public
Code for the pyABC dynamic look-ahead scheduling study
Jupyter Notebook
•
MIT License
•0•3•2•0•Updated Jun 18, 2021Jun 18, 2021
tumor2d
Public
Python bindings to a C++ implementation of the source code accompanying: Jagiella, Rickert, Theis, Hasenauer "Parallelization and high-performance computing ena…
C++
•
BSD 3-Clause "New" or "Revised" License
•0•1•2•0•Updated Dec 6, 2020Dec 6, 2020
solverstudy
Public
Python
•
MIT License
•0•2•1•0•Updated Nov 23, 2020Nov 23, 2020
CS_Signalling_ERBB_RAS_AKT
Public
Model and data from FroehlichKes2018
Jupyter Notebook
•
MIT License
•0•2•3•0•Updated Jul 27, 2020Jul 27, 2020
PESTO
Public
PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.
optimization matlab systems-biology
optimization matlab systems-biology parameter-estimation uncertainty-quantification profile-likelihood
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•12•27•42•0•Updated Mar 2, 2020Mar 2, 2020
Study-DFO
Public
Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology.
C
•1•2•0•0•Updated Jan 8, 2020Jan 8, 2020
ODEMM
Public
MATLAB Toolbox for ODE constrained mixture models
systems-biology single-cell mixture-modeling
systems-biology single-cell mixture-modeling ode-model
MATLAB
•
BSD 3-Clause "New" or "Revised" License
•1•3•0•0•Updated Jul 29, 2019Jul 29, 2019
NullModels
Public
Code for Null Models used in Sinzger et al. (2019) Scientific Reports, 9, 3002
bliss drug-combination null-model
bliss drug-combination null-model loewe tallarida highest-single-agent
MATLAB
•0•0•0•0•Updated Mar 14, 2019Mar 14, 2019
delos
Public
DeLOS is a toolbox for local optimization using mini batching ideas from the Deep Learning community
MATLAB
•0•0•4•0•Updated Sep 10, 2018Sep 10, 2018
LNAplusplus
Public
LNA++: a Fast C++ Implementation of the Linear Noise Approximation with first- and second-order sensitivities
C++
•
BSD 3-Clause "New" or "Revised" License
•0•2•3•0•Updated Jun 12, 2018Jun 12, 2018
NOODLES
Public
NOn-convex Optimization by high-order Derivative Learning and Exploiting Schemes
MATLAB
•0•0•1•0•Updated Mar 20, 2018Mar 20, 2018
pABC-SMC
Public
pABC-SMC scripts & data and model code for tumor growth example
C++
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GNU General Public License v3.0
•1•1•0•0•Updated Jun 8, 2016Jun 8, 2016

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Data-driven Computational Modelling

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All

30 repositories

pyPESTO

cOmicsArt

pyABC

Extrinsic-apoptosis-Conversion-reaction-model

Shiny-Calorie-Wrapper

pyscat

Tutorial_BCML_2026

.github

custom_ci_image

C-COMPASS

parPE

fiddy

Shiny-Calorie

FiguresMoSeS

model_calibration_protocol

SBMLimporter

MEMOIR

SPToolbox

lookahead-study

tumor2d

solverstudy

CS_Signalling_ERBB_RAS_AKT

PESTO

Study-DFO

ODEMM

NullModels

delos

LNAplusplus

NOODLES

pABC-SMC

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All

Repositories list

30 repositories