scholarly journals MOFA: Multi-Objective Flux Analysis for the COBRA Toolbox

2021 ◽  
Author(s):  
Marc Griesemer ◽  
Ali Navid
Keyword(s):  
Flux Analysis ◽  
E Coli ◽  
Multi Objective ◽  
Trade Offs ◽  
Quantitative Examination ◽  
Genome Scale ◽  
Cobra Toolbox ◽  
Normalized Normal Constraint ◽  
Constraint Based Models ◽  
Biological Organisms

Multi-objective Optimization (MO) is an important tool for quantitative examination of the trade-offs faced by biological organisms. Using genome-scale constraint-based models of metabolism (GSMs),Multi-Objective Flux Analysis (MOFA) allows MO analyses of trade-offs among key biological tasks. The leading software package for conducting a plethora of different types of constraint-based analyses using GSMs is the COBRA Toolbox for MATLAB. We have developed a new add-on tool for this toolbox using Normalized Normal Constraint (NNC) that performs MOFA for a number of objectives only limited by computation power (n≤10). This development will facilitate MOFA analyses by COBRA's large user base and allow greater multi-faceted examination of metabolic trade-offs in complicated biological systems. Availability and Implementation: The MOFA software is freely available for download from https://bbs.llnl.gov under the GPL v2 license. The program runs on MATLAB with the COBRA software on Windows, Linux, and MacOS. It includes a detailed manual explaining the input and output of a simulation, a listing of the code's functions, and an example MOFA run using a well-curated GSM model of E. coli.

scholarly journals A Comparison of Genetic Representations and Initialisation Methods for the Multi-objective Shortest Path Problem on Multigraphs

2021 ◽  
Vol 2 (3) ◽  
Author(s):  
Lilla Beke ◽  
Michal Weiszer ◽  
Jun Chen
Keyword(s):  
Shortest Path ◽  
Time Budget ◽  
Exact Algorithm ◽  
Simple Graph ◽  
Shortest Path Problem ◽  
Future Application ◽  
Multi Objective ◽  
Trade Offs ◽  
Conflicting Objectives ◽  
Problem Instances

AbstractThis paper compares different solution approaches for the multi-objective shortest path problem (MSPP) on multigraphs. Multigraphs as a modelling tool are able to capture different available trade-offs between objectives for a given section of a route. For this reason, they are increasingly popular in modelling transportation problems with multiple conflicting objectives (e.g., travel time and fuel consumption), such as time-dependent vehicle routing, multi-modal transportation planning, energy-efficient driving, and airport operations. The multigraph MSPP is more complex than the NP-hard simple graph MSPP. Therefore, approximate solution methods are often needed to find a good approximation of the true Pareto front in a given time budget. Evolutionary algorithms have been successfully applied for the simple graph MSPP. However, there has been limited investigation of their applications to the multigraph MSPP. Here, we extend the most popular genetic representations to the multigraph case and compare the achieved solution qualities. Two heuristic initialisation methods are also considered to improve the convergence properties of the algorithms. The comparison is based on a diverse set of problem instances, including both bi-objective and triple objective problems. We found that the metaheuristic approach with heuristic initialisation provides good solutions in shorter running times compared to an exact algorithm. The representations were all found to be competitive. The results are encouraging for future application to the time-constrained multigraph MSPP.

scholarly journals Multi-Objective Optimization of Autonomous Microgrids with Reliability Consideration

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4466
Author(s):  
Maël Riou ◽  
Florian Dupriez-Robin ◽  
Dominique Grondin ◽  
Christophe Le Loup ◽  
Michel Benne ◽  
...  
Keyword(s):  
Power Systems ◽  
Rural Areas ◽  
Energy System ◽  
Design Stage ◽  
Multi Objective Optimization ◽  
Renewable Energy Resources ◽  
Nsga Ii ◽  
Renewable Integration ◽  
Multi Objective ◽  
Trade Offs

Microgrids operating on renewable energy resources have potential for powering rural areas located far from existing grid infrastructures. These small power systems typically host a hybrid energy system of diverse architecture and size. An effective integration of renewable energies resources requires careful design. Sizing methodologies often lack the consideration for reliability and this aspect is limited to power adequacy. There exists an inherent trade-off between renewable integration, cost, and reliability. To bridge this gap, a sizing methodology has been developed to perform multi-objective optimization, considering the three design objectives mentioned above. This method is based on the non-dominated sorting genetic algorithm (NSGA-II) that returns the set of optimal solutions under all objectives. This method aims to identify the trade-offs between renewable integration, reliability, and cost allowing to choose the adequate architecture and sizing accordingly. As a case study, we consider an autonomous microgrid, currently being installed in a rural area in Mali. The results show that increasing system reliability can be done at the least cost if carried out in the initial design stage.

A Spectral Optimization Algorithm for Multi-Objective Prototype Selection

1995 ◽  
Author(s):  
Andy Dong ◽  
Alice M. Agogino
Keyword(s):  
Optimization Algorithm ◽  
Parametric Design ◽  
Selection Process ◽  
Objective Evaluation ◽  
Design Synthesis ◽  
Multi Objective ◽  
Trade Offs ◽  
Spectral Optimization ◽  
The Right ◽  
Selection Of

Abstract In design synthesis, engineering prototypes make an ideal representation medium for preliminary designs. Unlike parametric design wherein a pre-specified design is parametrically varied, design synthesis demands artistic creativity and engineering experience to transform the previously known components, relationships and designs into a new form. The process compels the designer to ascertain which prototypes will, in some sense, best satisfy the design task. The challenge in this assignment lies in selecting the “right” design prototype. This selection process typically entails an objective evaluation of different designs that perform the same functions or have similar intended behavior and comparing trade-offs between alternate designs. This paper introduces a multi-objective spectral optimization algorithm for the selection of design prototypes based upon their functional representations. The optimization algorithm returns an index of rank, scoring the functional similarity of the proposed design to the goal design. Two illustrative examples apply the algorithm to the selection of a heat fin and beam.

Multi-objective optimization for safety and reliability trade-off: Optimization and results processing

2018 ◽  
Vol 232 (6) ◽  
pp. 661-676
Author(s):  
Cristina Johansson ◽  
Johan Ölvander ◽  
Micael Derelöv
Keyword(s):  
Decision Making ◽  
Solid Base ◽  
Multi Objective Optimization ◽  
Specific System ◽  
Multi Objective ◽  
Trade Offs ◽  
Design Alternatives ◽  
Safety And Reliability ◽  
Potential Issue ◽  
Selection Of

In early design phases, it is vital to be able to screen the design space for a set of promising design alternatives for further study. This article presents a method able to balance several objectives of different mathematical natures, with high impact on the design choices. The method (MOSART) handles multi-objective optimization for safety and reliability trade-offs. The article focuses on optimization problem approach and processing of results as a base for decision-making. The output of the optimization step is the selection of specific system elements obtaining the best balance between the targets. However, what is a good base for decision can easily transform into too much information and overloading of the decision-maker. To solve this potential issue, from a set of Pareto optimal solutions, a smaller sub-set of selected solutions are visualized and filtered out using preference levels of the objectives, yielding a solid base for decision-making and valuable information on potential solutions. Trends were observed regarding each system element and discussed while processing the results of the analysis, supporting the decision of one final best solution.

scholarly journals Exploring the associations between transcript levels and fluxes in constraint-based models of metabolism

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Neeraj Sinha ◽  
Evert M. van Schothorst ◽  
Guido J. E. J. Hooiveld ◽  
Jaap Keijer ◽  
Vitor A. P. Martins dos Santos ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Transcript Levels ◽  
Proportionality Constant ◽  
Model Predictions ◽  
Physiological Information ◽  
Highly Expressed Genes ◽  
Transcriptomics Data ◽  
Genome Scale ◽  
The Impact ◽  
Constraint Based Models

Abstract Background Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distributions. Even though existing methods use transcript abundances as a proxy for enzyme activity, each method uses a different hypothesis and assumptions. Most methods implicitly assume a proportionality between transcript levels and flux through the corresponding function, although these proportionality constant(s) are often not explicitly mentioned nor discussed in any of the published methods. E-Flux is one such method and, in this algorithm, flux bounds are related to expression data, so that reactions associated with highly expressed genes are allowed to carry higher flux values. Results Here, we extended E-Flux and systematically evaluated the impact of an assumed proportionality constant on model predictions. We used data from published experiments with Escherichia coli and Saccharomyces cerevisiae and we compared the predictions of the algorithm to measured extracellular and intracellular fluxes. Conclusion We showed that detailed modelling using a proportionality constant can greatly impact the outcome of the analysis. This increases accuracy and allows for extraction of better physiological information.

scholarly journals Metabolic control of nitrogen fixation in rhizobium-legume symbioses

2021 ◽  
Vol 7 (31) ◽  
pp. eabh2433
Author(s):  
Carolin C. M. Schulte ◽  
Khushboo Borah ◽  
Rachel M. Wheatley ◽  
Jason J. Terpolilli ◽  
Gerhard Saalbach ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
Tricarboxylic Acid Cycle ◽  
Oxygen Demand ◽  
Metabolic Model ◽  
Redox Balance ◽  
Ammonia Assimilation ◽  
Nodule Formation ◽  
Flux Analysis ◽  
Carbon And Nitrogen ◽  
Genome Scale

Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.

scholarly journals Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

2020 ◽  
Author(s):  
Colton J. Lloyd ◽  
Jonathan Monk ◽  
Laurence Yang ◽  
Ali Ebrahim ◽  
Bernhard O. Palsson
Keyword(s):  
Amino Acids ◽  
Growth Conditions ◽  
Anaerobic Growth ◽  
Metabolic Phenotype ◽  
E Coli ◽  
Scale Models ◽  
Protein Components ◽  
K 12 ◽  
Genome Scale ◽  
Prosthetic Groups

AbstractSustaining a robust metabolic network requires a balanced and fully functioning proteome. In addition to amino acids, many enzymes require cofactors (coenzymes and engrafted prosthetic groups) to function properly. Extensively validated genome-scale models of metabolism and gene expression (ME-models) have the unique ability to compute an optimal proteome composition underlying a metabolic phenotype, including the provision of all required cofactors. Here we use the ME-model for Escherichia coli K-12 MG1655 to computationally examine how environmental conditions change the proteome and its accompanying cofactor usage. We found that: (1) The cofactor requirements computed by the ME model mostly agree with the standard biomass objective function used in models of metabolism alone (M models); (2) ME-model computations reveal non-intuitive variability in cofactor use under different growth conditions; (3) An analysis of ME-model predicted protein use in aerobic and anaerobic conditions suggests an enrichment in the use of prebiotic amino acids in the proteins used to sustain anaerobic growth (4) The ME-model could describe how limitation in key protein components affect the metabolic state of E. coli. Genome-scale models have thus reached a level of sophistication where they reveal intricate properties of functional proteomes and how they support different E. coli lifestyles.

scholarly journals A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0171744 ◽  
Author(s):  
Marko Budinich ◽  
Jérémie Bourdon ◽  
Abdelhalim Larhlimi ◽  
Damien Eveillard
Keyword(s):  
Multi Objective ◽  
Microbial Ecosystems ◽  
Genome Scale
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