Data-driven Computational Modelling

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29 repositories

pyPESTO
Public
python Parameter EStimation TOolbox
python optimization systems-biology
python optimization systems-biology parameter-estimation hacktoberfest
Python
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BSD 3-Clause "New" or "Revised" License
•47•266•131•11•Updated Mar 5, 2026Mar 5, 2026
C-COMPASS
Public
A Neural Network Tool for Multi-Omic Classification of Cell Compartments
Python
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Other
•0•2•16•2•Updated Mar 2, 2026Mar 2, 2026
pyABC
Public
distributed, likelihood-free inference
abc parameter-inference approximate-bayesian-inference
abc parameter-inference approximate-bayesian-inference likelihood-free-inference
Python
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BSD 3-Clause "New" or "Revised" License
•46•217•32•0•Updated Feb 26, 2026Feb 26, 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
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MIT License
•0•0•0•0•Updated Feb 22, 2026Feb 22, 2026
pyscat
Public
Scatter search optimization in Python
optimization ess metaheuristic
optimization ess metaheuristic scatter-search sacess
Python
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BSD 3-Clause "New" or "Revised" License
•1•2•11•0•Updated Feb 12, 2026Feb 12, 2026
Shiny-Calorie-Wrapper
Public
Electron Wrapper for Shiny-Calorie
r-shiny electronjs calorimetry
r-shiny electronjs calorimetry
JavaScript
•0•0•0•5•Updated Feb 10, 2026Feb 10, 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++
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MIT License
•4•22•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
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BSD 3-Clause "New" or "Revised" License
•1•5•13•2•Updated Dec 15, 2025Dec 15, 2025
custom_ci_image
Public
Testing custom CI image for parPE
Shell
•0•0•0•0•Updated Nov 24, 2025Nov 24, 2025
cOmicsArt
Public
This is the code to run cOmicsArt! Want to use it without installation - check out the website:
HTML
•1•8•54•1•Updated Sep 24, 2025Sep 24, 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
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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
.github
Public
Organization profile
0•0•0•0•Updated Aug 8, 2024Aug 8, 2024
model_calibration_protocol
Public
Jupyter Notebook
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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
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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
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BSD 3-Clause "New" or "Revised" License
•1•2•2•0•Updated Aug 3, 2022Aug 3, 2022
SPToolbox
Public
MATLAB
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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
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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++
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BSD 3-Clause "New" or "Revised" License
•0•1•2•0•Updated Dec 6, 2020Dec 6, 2020
solverstudy
Public
Python
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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
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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
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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
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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++
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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