Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Strain design tools

Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms. Existing approaches relying solely on stoichiometry and rudimentary…
BeReTa
Desktop

BeReTa Beneficial Regulator Targeting

An algorithm for prioritization of transcriptional regulator (TR) manipulation…

An algorithm for prioritization of transcriptional regulator (TR) manipulation targets, which makes use of unintegrated network models. BeReTa identifies TR manipulation targets by evaluating…

MOST
Desktop

MOST Metabolic Optimization and Simulation Tool

Allows users to create constraint-based models of metabolism and load, edit and…

Allows users to create constraint-based models of metabolism and load, edit and save existing models. MOST is a software packages for constraint-based modeling that implements genetic design through…

Biopathway…
Desktop

Biopathway Predictor

A computational tool implemented in Genomatica's SimPheny platform for…

A computational tool implemented in Genomatica's SimPheny platform for enumerating and evaluating networks of enzyme-catalyzed reactions, with the goal of identifying novel pathways for…

cRegMCSs
Desktop

cRegMCSs constrained regulatory MCSs

Generalizes the minimal cut sets (MCS)-based framework to constrained…

Generalizes the minimal cut sets (MCS)-based framework to constrained regulatory MCSs. cRegMCSs has been integrated as a new functionality in the CellNetAnalyzer package, a MATLAB toolbox for…

OptStrain
Desktop

OptStrain

A hierarchical computational framework aimed at guiding pathway modifications,…

A hierarchical computational framework aimed at guiding pathway modifications, through reaction additions and deletions, of microbial networks for the overproduction of targeted compounds. These…

GCM
Dataset

GCM Global Catalogue of Microorganisms

Allows members to organize, make public, and explore their data resources. GCM…

Allows members to organize, make public, and explore their data resources. GCM is an online catalogue and a data management system that contains information from (i) culture collection staff, (ii)…

GDLS
Desktop

GDLS Genetic Design through Local Search

A scalable, heuristic, algorithmic method that employs an approach based on…

A scalable, heuristic, algorithmic method that employs an approach based on local search with multiple search paths, which results in effective, low-complexity search of the space of genetic…

Redirector
Desktop

Redirector

A Flux Balance Analysis-based framework for identifying engineering targets to…

A Flux Balance Analysis-based framework for identifying engineering targets to optimize metabolite production in complex pathways. Previous optimization frameworks have modeled metabolic alterations…

EMILiO
Algorithm

EMILiO

An algorithm that increases the scope of strain design to include reactions…

An algorithm that increases the scope of strain design to include reactions with individually optimized fluxes. Unlike existing approaches that would experience an explosion in complexity to solve…

k-OptForce
Algorithm

k-OptForce

Integrates the available kinetic descriptions of metabolic steps with…

Integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving the bio-production of a chemical of…

LASER
Dataset

LASER Learning Assisted Strain EngineeRing

A repository for metabolic engineering strain designs and a formal standard for…

A repository for metabolic engineering strain designs and a formal standard for disseminating designs to metabolic engineers. LASER, provides an immense resource of metabolic engineering knowledge…

RobustKnock
Desktop

RobustKnock

A constraint-based method that predicts gene deletion strategies that lead to…

A constraint-based method that predicts gene deletion strategies that lead to the over-production of chemicals of interest, by accounting for the presence of competing pathways in the network.…

GDBB
Desktop

GDBB Genetic Design through Branch and Bound

A computational design tool for metabolic engineering. GDBB uses an efficient…

A computational design tool for metabolic engineering. GDBB uses an efficient truncated branch and bound approach to identify favorable genetic designs from flux-balance metabolic models.

OptForce
Desktop

OptForce

Identifies all possible engineering interventions by classifying reactions in…

Identifies all possible engineering interventions by classifying reactions in the metabolic model depending upon whether their flux values must increase, decrease or become equal to zero to meet a…

Optknock
Desktop

Optknock

Suggests gene deletion strategies leading to the overproduction of a…

Suggests gene deletion strategies leading to the overproduction of a pre-specified metabolite using the provided metabolic model. A nested optimization framework identifies the gene deletions by…

CosMos
Algorithm

CosMos

A strain design method with continuous modifications that provides strategies…

A strain design method with continuous modifications that provides strategies for deletions, downregulations, and upregulations of fluxes that will lead to the production of the desired products. The…

BiMOMA
Algorithm

BiMOMA

Uses minimization of metabolic adjustment to predict knockout behavior in a…

Uses minimization of metabolic adjustment to predict knockout behavior in a mixed-integer programming (MIP)-based bi-level problem. BiMOMA will facilitate the strain design process and extend the…

SimOptStrain
Algorithm

SimOptStrain

Simultaneously considers gene deletion and non-native reaction addition from a…

Simultaneously considers gene deletion and non-native reaction addition from a universal database. Conceptually, adding a non-native reaction to a host network is equivalent to adding all non-native…

ReacKnock
Algorithm

ReacKnock

Identifies reaction deletion strategies for microbial strain optimization based…

Identifies reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network. Compared to the previous methods, ReacKnock is fast, stable and reliable to find the…

BAFBA
Algorithm

BAFBA Bees Algorithm and Flux Balance Analysis

An algorithm to solve the local minima problem and to predict optimal sets of…

An algorithm to solve the local minima problem and to predict optimal sets of gene deletion for maximizing the growth rate of certain metabolite. BAFBA shows better results compared to the other…

Natural…
Desktop

Natural Computation Algorithms for In Silico Metabolic Engineering

Algorithms proposed for in silico metabolic engineering, for example, to…

Algorithms proposed for in silico metabolic engineering, for example, to identify sets of gene deletions towards maximization of a desired physiological objective function. In this approach, each…

OptORF
Algorithm

OptORF

An effective method to systematically integrate transcriptional regulatory…

An effective method to systematically integrate transcriptional regulatory networks and metabolic networks. This allows for the formulation of linear optimization problems that search for metabolic…

CiED
Algorithm

CiED Cipher of Evolutionary Design

Identifies genetic perturbations, such as gene deletions and other network…

Identifies genetic perturbations, such as gene deletions and other network modifications, that result in optimal phenotypes for the production of end products, such as recombinant natural products.…

FSEOF
Algorithm

FSEOF Flux Scanning based on Enforced Objective Flux

A strategy to identify gene amplification targets. FSEOF scans all the…

A strategy to identify gene amplification targets. FSEOF scans all the metabolic fluxes in the metabolic model and selects fluxes that increase when the flux toward product formation is enforced as…

OptSwap
Desktop

OptSwap

Predicts bioprocessing strain designs by identifying optimal modifications of…

Predicts bioprocessing strain designs by identifying optimal modifications of the cofactor binding specificities of oxidoreductase enzyme and complementary reaction knockouts. The OptSwap formulation…

MESSI
Web

MESSI Metabolic Engineering target Selection and best Strain Identification tool

Predicts efficient chassis and regulatory components for yeast bio-based…

Predicts efficient chassis and regulatory components for yeast bio-based production. MESSI provides an integrative platform for users to analyse ready-to-use public high-throughput metabolomic data,…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.