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GDLS specifications


Unique identifier OMICS_06469
Alternative name Genetic Design through Local Search
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for Genetic Design through Local Search

GDLS citations


Genome scale model driven strain design for dicarboxylic acid production in Yarrowia lipolytica

BMC Syst Biol
PMCID: 5861505
PMID: 29560822
DOI: 10.1186/s12918-018-0542-5

[…] GDLS strain design algorithm [] was implemented in COBRA toolbox in Matlab, searching up to maximum of 5 knockout reactions with the outer objective of maximizing DDDA exchange flux. […]


Growth coupled overproduction is feasible for almost all metabolites in five major production organisms

Nat Commun
PMCID: 5489714
PMID: 28639622
DOI: 10.1038/ncomms15956

[…] , studies on feasibility of growth-coupled product synthesis focused on single products or/and on a single organism (E. coli) only. Furthermore, although other used methods such as OptKnock, OptGene, GDLS and FastPros demand only weak coupling, which is easier to achieve than strong coupling demanded in this work, an almost unlimited feasibility of coupling under aerobic conditions in E. coli as p […]


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

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

[…] roduction 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 one or more mixed-i […]


Reconstruction and applications of consensus yeast metabolic network based on RNA sequencing

FEBS Open Bio
PMCID: 4821349
PMID: 27239440
DOI: 10.1002/2211-5463.12033

[…] The metabolic models were analyzed by using multiple methods in COBRA toolbox (V 2.0.2) , including flux balance analysis (FBA) , minimization of metabolic adjustment (MOMA) , and Genetic Design through Local Search (GDLS) .These methods provide important tools for harnessing the knowledge encoded in the reconstructed metabolic model. FBA predicts metabolic flux distributions a […]


Multi Target Analysis and Design of Mitochondrial Metabolism

PLoS One
PMCID: 4574446
PMID: 26376088
DOI: 10.1371/journal.pone.0133825

[…] networks with a large number of components [].In the past, FBA models have been chosen for analysis aimed to synthetic biology. For instance, OptKnock [] implements a bi-level programming framework, GDLS [] proposes a local optimization algorithm, and GDMO [] performs optimization based on genetic algorithms, where bacterial cells are optimized and computationally designed in terms of gene knocko […]


Genome Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

PLoS One
PMCID: 3906188
PMID: 24489927
DOI: 10.1371/journal.pone.0087494

[…] In-silico strains which enhance ethanol production were obtained via optimization-based approach by using Genetic Design through Local Search (GDLS) algorithm (COBRA function GDLS). All solutions were checked to be unique and whether they were coupled or non-coupled to growth by using COBRA function analyseOptKnock, non-unique solutions wer […]


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GDLS institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Department of Mathematics and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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