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cplex linear programming solver  (Tomlab Optimization)

 
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    Tomlab Optimization cplex linear programming solver
    Cplex Linear Programming Solver, supplied by Tomlab Optimization, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cplex+linear+programming+solver/cplex/pmc03261703-189-7-1
    Average 90 stars, based on 1 article reviews
    cplex linear programming solver - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Optimal Model for Local Energy Community Scheduling Considering Peer to Peer Electricity Transactions
    Article Snippet: TOMLAB optimization platform with the solver CPLEX has been used.

    Article Title: Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling
    Article Snippet: Tomlab CPLEX (Tomlab Optimization Inc., San Diego, CA) and Gurobi (Gurobi Optimization Inc., Houston, TX) were used for solving the linear programming problems.

    Article Title: Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
    Article Snippet: Flux balance analysis (FBA) [ ] for pairwise simulations was performed using the optimization solver CPLEX through the Tomlab (Tomlab, Inc.) interface for MATLAB.

    Article Title: Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism.
    Article Snippet: CPLEX from Tomlab 185 (http://tomopt.com) was used for the LP and QP solvers.

    Article Title: Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
    Article Snippet: All scripts were implemented in MATLAB scripting language (MATLAB Release 2015a, The MathWorks, Inc., Natick, Massachusetts, United States ) under usage of the COBRA toolbox 2 and the cplex-solver provided by the TOMLAB Optimization Environment by Tomlab Optimization .

    Article Title: Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy
    Article Snippet: All computations were done locally on a 64-bit machine and optimization was done using a CPLEX solver (version 7, Tomlab) in MATLAB.

    Article Title: Computational identification of gene over-expression targets for metabolic engineering of taxadiene production
    Article Snippet: Optimization was undertaken using the CPLEX (version 11.0) algorithm of the TOMLAB TM Optimization Environment (TOMLAB TM /CPLEX) interfaced with the COBRA Toolbox and MATLAB ® 7.4.



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    The running time for both the <t>PSAMM</t> overall function (blue) and the PSAMM problem-solving steps (red) were calculated, and the running time for COBRA only included the problem-solving step (green). Each value represents a median of seven simulation runs using the same specifications, and the error bars indicate the 25th and the 75th percentiles.
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    The running time for both the PSAMM overall function (blue) and the PSAMM problem-solving steps (red) were calculated, and the running time for COBRA only included the problem-solving step (green). Each value represents a median of seven simulation runs using the same specifications, and the error bars indicate the 25th and the 75th percentiles.

    Journal: PLoS Computational Biology

    Article Title: PSAMM: A Portable System for the Analysis of Metabolic Models

    doi: 10.1371/journal.pcbi.1004732

    Figure Lengend Snippet: The running time for both the PSAMM overall function (blue) and the PSAMM problem-solving steps (red) were calculated, and the running time for COBRA only included the problem-solving step (green). Each value represents a median of seven simulation runs using the same specifications, and the error bars indicate the 25th and the 75th percentiles.

    Article Snippet: The simulations were carried out on the model iJO1366 [ ] with the Cplex linear programming solver for PSAMM (version 0.17) and COBRA (version 12.6, IBM academic release for PSAMM and TOMLAB release for COBRA), and with the MOSEK solver for RAVEN (version 7.1.0.36).

    Techniques: Combined Bisulfite Restriction Analysis Assay

    The five main components include: (1) user interface, (2) model input/output, (3) model representation, (4) linear programming utilities, and (5) model checking/simulation. Connections among these components form the internal workflow of PSAMM.

    Journal: PLoS Computational Biology

    Article Title: PSAMM: A Portable System for the Analysis of Metabolic Models

    doi: 10.1371/journal.pcbi.1004732

    Figure Lengend Snippet: The five main components include: (1) user interface, (2) model input/output, (3) model representation, (4) linear programming utilities, and (5) model checking/simulation. Connections among these components form the internal workflow of PSAMM.

    Article Snippet: The simulations were carried out on the model iJO1366 [ ] with the Cplex linear programming solver for PSAMM (version 0.17) and COBRA (version 12.6, IBM academic release for PSAMM and TOMLAB release for COBRA), and with the MOSEK solver for RAVEN (version 7.1.0.36).

    Techniques:

    List of commands supported in the psamm-model program. Additional parameters can be specified for the commands, for example to select a specific implementation among multiple algorithms, enable/disable thermodynamic constraints, or select linear programming solvers, etc . Details about these parameters are available through the -h or -- help options for each command.

    Journal: PLoS Computational Biology

    Article Title: PSAMM: A Portable System for the Analysis of Metabolic Models

    doi: 10.1371/journal.pcbi.1004732

    Figure Lengend Snippet: List of commands supported in the psamm-model program. Additional parameters can be specified for the commands, for example to select a specific implementation among multiple algorithms, enable/disable thermodynamic constraints, or select linear programming solvers, etc . Details about these parameters are available through the -h or -- help options for each command.

    Article Snippet: The simulations were carried out on the model iJO1366 [ ] with the Cplex linear programming solver for PSAMM (version 0.17) and COBRA (version 12.6, IBM academic release for PSAMM and TOMLAB release for COBRA), and with the MOSEK solver for RAVEN (version 7.1.0.36).

    Techniques:

    (a) This diagram shows an example of the YAML model format, which includes a central model definition (model.yaml) and multiple annotation files. Each box indicates a file with a possible filename indicated above the box, and the text within is a snapshot of the file content. (b) An example showing how changes can be tracked in a PSAMM YAML file (biomass.yaml) using the Git version control system in command line. The text highlighted in red indicates the stoichiometry of the compound arg-L in an old version of the biomass function, while the text highlighted in green indicates the updated value in a new version of the model. Additional examples of applying Git version control on the YAML format are provided in the supplemental materials ( – Texts).

    Journal: PLoS Computational Biology

    Article Title: PSAMM: A Portable System for the Analysis of Metabolic Models

    doi: 10.1371/journal.pcbi.1004732

    Figure Lengend Snippet: (a) This diagram shows an example of the YAML model format, which includes a central model definition (model.yaml) and multiple annotation files. Each box indicates a file with a possible filename indicated above the box, and the text within is a snapshot of the file content. (b) An example showing how changes can be tracked in a PSAMM YAML file (biomass.yaml) using the Git version control system in command line. The text highlighted in red indicates the stoichiometry of the compound arg-L in an old version of the biomass function, while the text highlighted in green indicates the updated value in a new version of the model. Additional examples of applying Git version control on the YAML format are provided in the supplemental materials ( – Texts).

    Article Snippet: The simulations were carried out on the model iJO1366 [ ] with the Cplex linear programming solver for PSAMM (version 0.17) and COBRA (version 12.6, IBM academic release for PSAMM and TOMLAB release for COBRA), and with the MOSEK solver for RAVEN (version 7.1.0.36).

    Techniques: Control