NIHBA: A Network Interdiction Approach for Metabolic Engineering Design release_uokyr5vb5rgjvaekp25ilptc24

by Shouyong Jiang, Yong Wang, Marcus Kaiser, Natalio Krasnogor

Published in Bioinformatics by Oxford University Press (OUP).

2020   Volume 36, Issue 11, p3482-3492

Abstract

<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> Flux balance analysis (FBA) based bilevel optimisation has been a great success in redesigning metabolic networks for biochemical overproduction. To date, many computational approaches have been developed to solve the resulting bilevel optimisation problems. However, most of them are of limited use due to biased optimality principle, poor scalability with the size of metabolic networks, potential numeric issues, or low quantity of design solutions in a single run. </jats:sec> <jats:sec> <jats:title>Results</jats:title> Here, we have employed a network interdiction (NI) model free of growth optimality assumptions, a special case of bilevel optimisation, for computational strain design and have developed a hybrid Benders algorithm (HBA) that deals with complicating binary variables in the model, thereby achieving high efficiency without numeric issues in search of best design strategies. More importantly, HBA can list solutions that meet users' production requirements during the search, making it possible to obtain numerous design strategies at a small runtime overhead (typically ∼1 hour for examples studied in this paper). </jats:sec> <jats:sec> <jats:title>Availability</jats:title> Source code implemented in the MATALAB Cobratoolbox is freely available at https://github.com/chang88ye/NIHBA. </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> Supplementary data are available at Bioinformatics online. </jats:sec>
In application/xml+jats format

Archived Files and Locations

application/pdf  1.2 MB
file_ta5tiav5jfhp7mhggaj5rosace
eprint.ncl.ac.uk (web)
web.archive.org (webarchive)
application/pdf  1.2 MB
file_hldew75u2ratbc5u5qdlybom5a
watermark.silverchair.com (web)
web.archive.org (webarchive)
application/pdf  1.2 MB
file_hhjegqm7wfcfrfpo4cvr23jsjq
aura.abdn.ac.uk (web)
web.archive.org (webarchive)
Read Archived PDF
Preserved and Accessible
Type  article-journal
Stage   published
Date   2020-03-13
Language   en ?
Container Metadata
Not in DOAJ
In Keepers Registry
ISSN-L:  1367-4803
Work Entity
access all versions, variants, and formats of this works (eg, pre-prints)
Catalog Record
Revision: 418436f7-94b3-4712-92f6-9543b53145ff
API URL: JSON