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cs_signalling_erbb_ras_akt

Model and data from FroehlichKes2018

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

fiddy

Finite difference methods.

lnaplusplus

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

lookahead-study

Code for the pyABC dynamic look-ahead scheduling study

memoir

MATLAB toolbox for Mixed Effect Model InfeRence

model_calibration_protocol

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

odemm

MATLAB Toolbox for ODE constrained mixture models

pabc-smc

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

parpe

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

pesto

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

pyabc

distributed, likelihood-free inference

pypesto

python Parameter EStimation TOolbox

sbmlimporter

MATLAB toolbox to generate ODE models from SBML files

solverstudy

sptoolbox

study-dfo

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

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)