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RobustKnock specifications

Information


Unique identifier OMICS_06466
Name RobustKnock
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for RobustKnock

RobustKnock citations

 (11)
library_books

Yeast metabolic chassis designs for diverse biotechnological products

2016
Sci Rep
PMCID: 4949481
PMID: 27430744
DOI: 10.1038/srep29694

[…] analysis (FBA)-based growth-product coupling; ii) MiMBl-based growth-product coupling and iii) flux variability analysis (FVA). The FBA-based approach was implemented as a variant of the OptKnock and RobustKnock algorithms. In brief, we calculated, for each of the simulated mutants, the minimal product secretion while constraining the growth to its maximum possible limit. To identify growth-produc […]

library_books

Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications

2016
Metab Eng Com
PMCID: 5779729
PMID: 29468116
DOI: 10.1016/j.meteno.2016.03.003

[…] knock-outs for EPS production were calculated. These growth-coupled designs could be difficult to achieve and may require multiple knock-outs. A number of algorithms, such as OptKnock (), OptGene (), RobustKnock (), and GDLS (), have been proposed for designing production strains through gene knock-outs. Still, the search for knock-out phenotypes is computationally extensive, since the solution of […]

library_books

Designing minimal microbial strains of desired functionality using a genetic algorithm

2015
PMCID: 4687386
PMID: 26697103
DOI: 10.1186/s13015-015-0060-6

[…] e is no guarantee that the predicted optimum will be achieved. In a similar vein, the method presented here has advantages over other methods which use a biased biological objective like OptKnock [], RobustKnock [] and tilting of the objective function [].Boghigian et al. [] also use a GA and EFMs to design strains with higher product yields. Their approach however differs from the method presente […]

library_books

Flux sum analysis identifies metabolite targets for strain improvement

2015
BMC Syst Biol
PMCID: 4625974
PMID: 26510838
DOI: 10.1186/s12918-015-0198-3

[…] es ranging from simple in silico simulation of gene deletions [, ], to more sophisticated computational techniques such as OptKnock [], OptReg [], OptStrain [], OptGene [], flux response analysis [], RobustKnock [], flux scanning based on enforced objective flux [], OptForce [] and most recently, cofactor modification analysis [] for identifying valid gene knockout, up-, down-regulation and cofact […]

library_books

Computational Methods for Modification of Metabolic Networks

2015
Comput Struct Biotechnol J
PMCID: 4477032
PMID: 26106462
DOI: 10.1016/j.csbj.2015.05.004

[…] bioengineering objective in the outer problem, and the cellular objective in the inner problem , where the upper bound of the number of removed reactions is given as in the above. On the other hand, RobustKnock maximizes the minimal possible rate of the bioengineering objective in the outer max–min problem, while the cellular objective is maximized in the inner min–max structure . […]

library_books

RobOKoD: microbial strain design for (over)production of target compounds

2015
PMCID: 4371745
PMID: 25853130
DOI: 10.3389/fcell.2015.00017

[…] eely-accessible solvers, extensively validated COBRA Toolbox methods, and standardized model formats such as SBML.A necessary future direction for both RobOKoD and existing tools such as OptKnock and RobustKnock will be to move to making predictions regarding knockouts, over-expressions, etc. at the level of the gene, rather than, as currently, at the level of the reaction. Due to the presence of […]

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RobustKnock institution(s)
Department of Computer Science, Technion-IIT, Haifa, Israel

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