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  4. Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 3
 
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Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 3

Choudhury, Subham  
•
Narayanan, Bharath
•
Moret, Michael
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2023
Zenodo

Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" by S. Choudhury et al (https://doi.org/10.1101/2023.02.21.529387) - Part 3 The code to use with these data and reproduce the manuscript results is available at  https://github.com/EPFL-LCSB/renaissance and https://gitlab.com/EPFL-LCSB/renaissance. The execution of parts of this code is dependent on the SkimPy toolbox (https://github.com/EPFL-LCSB/skimpy). Refer to the readme files on the RENAISSANCE code repositories for more details. The dataset contains the following files: Distribution_comparison - contains 2 folders No integration test - 10 repeats of RENAISSANCE generated models with 25 generations each with maximal eigenvalues All integration test - 5 repeats of RENAISSANCE with 108 Kms integrate with 25 generations each with maximal eigenvalues Shikki bioreactor -contains 350000 RENAISSANCe generated parameter sets with the corresponding bioreactor simulation solutions.  Slow and steady - contains 30 sampled slow steady states and their RENAISSANCE achieved maximal eigenvalues (originally sampled from index 1586 to 1581 from 5000 smaples already provided)

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Type
dataset
DOI
10.5281/zenodo.10391802
ACOUA ID

1e8a7545-5ac6-40af-acbb-ec0c83e835cf

Author(s)
Choudhury, Subham  
Narayanan, Bharath
Moret, Michael
Hatzimanikatis, Vassily  
Miskovic, Ljubisa  
Date Issued

2023

Version

v1

Publisher

Zenodo

Subjects

metabolism

•

integration of omics

•

data large-scale and genome-scale kinetic models

•

machine learning

•

evolution strategies

•

E. coli

•

kinetic parameters

•

nonlinear dynamics

FunderGrant NO

EU funding

SHIKIFACTORY100 – Modular cell factories for the production of 100 compounds from the shikimate pathway (814408)

FNS

Computational Methods for modeling and analysis of large-scale metabolic networks (163423)

Other government funding

A new paradigm for versatile cell factories (2016-06160)

RelationRelated workURL/DOI

IsNewVersionOf

https://doi.org/10.5281/zenodo.10391801

IsSupplementTo

https://infoscience.epfl.ch/record/302975
Available on Infoscience
January 19, 2024
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/203055
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