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Improving dynamic predictions with ensembles of observable models (supplementary information)

Authors: Massonis, Gemma; Villaverde, Alejandro F.; Banga, Julio R.;

Improving dynamic predictions with ensembles of observable models (supplementary information)

Abstract

This repository contains the accompanying code to the paper "Improving dynamic predictions with ensembles of observable models", by Gemma Massonis, Alejandro F. Villaverde, and Julio R. Banga (gemma.massonis@csic.es, afvillaverde@uvigo.gal, j.r.banga@csic.es), which presents a method for building ensembles of dynamic models. The repository contains four folders, one for each case study considered in the paper. Each folder contains: A Matlab Live Script that analyses the case study, provided in two formats: as .html files, for convenient visualization, and as .mlx files that can be executed in Matlab. Auxiliary files including model definitions, simulated data, and others. In order to run the Live Scripts, the following software is needed and must be in the Matlab path: MATLAB (tested with version R2020b), including the following toolboxes and packages: Statistics Toolbox FanChart, from the Matlab file exchange (https://es.mathworks.com/matlabcentral/fileexchange/48006-fanchart-visualize-percentiles-of-time-series-data) gramm (https://github.com/piermorel/gramm) AMICI (tested with version 0.11.12) (https://github.com/AMICI-dev/AMICI/releases/tag/v0.11.12) MEIGO (tested with version V18JAN2018) (https://github.com/gingproc-IIM-CSIC/MEIGO64) AMIGO2 (tested with AMIGO2_R2019b) (https://sites.google.com/site/amigo2toolbox/)

Keywords

dynamic modelling, ensemble modelling, observability, uncertainty quantification, systems biology, identifiability

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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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