Data-driven Computational Modelling

pyPESTO

python Parameter EStimation TOolbox

pyABC

distributed, likelihood-free inference

PESTO

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

parPE

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

fiddy

Finite difference methods.

lookahead-study

Code for the pyABC dynamic look-ahead scheduling study

ODEMM

MATLAB Toolbox for ODE constrained mixture models

CS_Signalling_ERBB_RAS_AKT

Model and data from FroehlichKes2018

LNAplusplus

LNA++: a Fast C++ Implementation of the Linear Noise Approximation with first- and second-order sensitivities

MEMOIR

MATLAB toolbox for Mixed Effect Model InfeRence

model_calibration_protocol

Study-DFO

Evaluation of Derivative-Free Optimizers for Parameter Estimation in Systems Biology.

SBMLimporter

MATLAB toolbox to generate ODE models from SBML files

solverstudy

SPToolbox

custom_ci_image

Testing custom CI image for parPE

delos

DeLOS is a toolbox for local optimization using mini batching ideas from the Deep Learning community

NOODLES

NOn-convex Optimization by high-order Derivative Learning and Exploiting Schemes

NullModels

Code for Null Models used in Sinzger et al. (2019) Scientific Reports, 9, 3002

pABC-SMC

pABC-SMC scripts & data and model code for tumor growth example

tumor2d

Python bindings to a C++ implementation of the source code accompanying: Jagiella, Rickert, Theis, Hasenauer "Parallelization and high-performance computing enables automated statistical inference of multiscale models" (2017)