Optimization Methods In Metabolic Networks

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Optimization Methods In Metabolic Networks

Author : Costas D. Maranas
ISBN : 9781119028499
Genre : Science
File Size : 39.13 MB
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Provides a tutorial on the computational tools that use mathematical optimization concepts and representations for the curation, analysis and redesign of metabolic networks Organizes, for the first time, the fundamentals of mathematical optimization in the context of metabolic network analysis Reviews the fundamentals of different classes of optimization problems including LP, MILP, MLP and MINLP Explains the most efficient ways of formulating a biological problem using mathematical optimization Reviews a variety of relevant problems in metabolic network curation, analysis and redesign with an emphasis on details of optimization formulations Provides a detailed treatment of bilevel optimization techniques for computational strain design and other relevant problems
Category: Science

Applications Of Convex Optimization In Metabolic Network Analysis

Author : Mojtaba Tefagh
ISBN : OCLC:1104050842
Genre :
File Size : 20.13 MB
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Twenty years ago, the first genome-scale metabolic network reconstruction of the cellular metabolism of an organism was published, shortly after the first genome was sequenced. From that time on, the ever-increasing advances in the high-throughput omics technologies have allowed for the comprehensive reconstructions of exponentially growing sizes. However, the vast amount of data can be a two-edged sword which makes many essential tasks computationally intractable. To overcome the demands of systems biology, even while they are outpacing Moore's law, faster computational techniques are needed to enable the current methods to scale up to match the progress of data generation in a prospective manner. In this dissertation, we go over several different areas of systems biology from flux coupling analysis to context-specific reconstruction and propose efficient computational methods for several tasks separately. Then we work towards a more holistic approach and discuss the idea of a canonical metabolic network reduction to reduce the number of reactions for any general task. In analogy to the concept of lossless compression in information theory, we will show that the well-known emergent redundancies of flux distributions are the key concept. Additionally, we will derive the minimum reduced metabolic network and prove a converse that any further reduction loses some information on the elementary modes.

Stochastic Global Optimization Methods And Applications To Chemical Biochemical Pharmaceutical And Environmental Processes

Author : Ch Venkateswarlu
ISBN : 9780128173923
Genre :
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Stochastic global optimization methods and applications to chemical, biochemical, pharmaceutical and environmental processes presents various algorithms that include the genetic algorithm, simulated annealing, differential evolution, ant colony optimization, tabu search, particle swarm optimization, artificial bee colony optimization, and cuckoo search algorithm. The design and analysis of these algorithms is studied by applying them to solve various base case and complex optimization problems concerning chemical, biochemical, pharmaceutical, and environmental engineering processes. Design and implementation of various classical and advanced optimization strategies to solve a wide variety of optimization problems makes this book beneficial to graduate students, researchers, and practicing engineers working in multiple domains. This book mainly focuses on stochastic, evolutionary, and artificial intelligence optimization algorithms with a special emphasis on their design, analysis, and implementation to solve complex optimization problems and includes a number of real applications concerning chemical, biochemical, pharmaceutical, and environmental engineering processes. Presents various classical, stochastic, evolutionary, and artificial intelligence optimization algorithms for the benefit of the audience in different domains Outlines design, analysis, and implementation of optimization strategies to solve complex optimization problems of different domains Highlights numerous real applications concerning chemical, biochemical, pharmaceutical, and environmental engineering processes

Metabolic Network Analysis Of The Cell Factory Aspergillus Niger

Author : Guido Melzer
ISBN : 9783736934566
Genre : Science
File Size : 29.7 MB
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In the present work, a systems biology approach is presented, which enables the prediction of potential genetic targets and optimal pathways for protein production within a metabolic network, and thus, makes an important contribution to the rational strain optimization of micro-organisms. For this, elementary flux modes analysis was carried out using a metabolic model of Aspergillus niger, which was condensed from the genome based metabolic model. Hereby, a new approach was developed for the design of cell factories by the analysis of metabolic flux correlations between metabolic enzymes. This allowed the in silico prediction of deletion and amplification targets and thus provides an important prerequisite for rational strain optimization. The network analysis was carried out using various target products under varying nutrient conditions. The approach revealed that the success of identification of genetic targets depends on the differentiation of biological states, the growth-associated or non-growth associated production of the target proteins. Only a few targets, such as the pathways of protein glycosylation and protein biosynthesis can be identified as independent of the biological state. The growth-associated targets include inter alia the pentose-phosphate pathway (amplification target) and the reactions of the tricarboxylic acid cycle (attenuation target). The results of this systems biology approach could be validated by enzyme kinetic studies and analyses of intracellular metabolic fluxes using metabolite balancing and continuous cultivations. In addition, metabolic networks of several industrially relevant hosts were investigated using this in silico approach and essential differences were elaborated. Comparisons with experimental studies for rational strain optimization of Corynebacterium glutamicum for lysine production support the applicability of this novel in silico approach.
Category: Science

Machine Learning And Optimization Methods To Engineer Microbes

Author : Prashant Kumar
ISBN : OCLC:1139321068
Genre :
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Microbes are a rich source of numerous industrially relevant chemicals. During my Ph.D., I worked on developing machine learning and optimization methods to engineer microbes. There are primarily three research projects and a review study mentioned in this work. I contributed to a book chapter on metabolic modeling for design of cell factories. In Chapter 2, I have described the work done on reconstructing the genome-scale metabolic model of two strains of Gluconacetobacter, namely hansenii ATCC 53582 and xylinus 399. I designed strains of these two strains with four and five gene knockouts to enhance the biocellulose yields from them. In Chapter 3, I describe a method, iRegMet which can make predictions about the cellular behavior under perturbation using the integrated regulatory and metabolic network of microbes. iRegMet was used to make predictions of transcription factor knockout gene expressions and cellular growth. In Chapter 4, I have described ActiveOpt, an active learning, and machine learning driven design of experiments tool. ActiveOpt was successfully validated on two separate datasets.

Aiche Symposium Series

Author : American Institute of Chemical Engineers
ISBN : UOM:39015047888345
Genre : Chemical engineering
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Category: Chemical engineering

Iee Proceedings

Author :
ISBN : UCSD:31822032911596
Genre : Bioinformatics
File Size : 20.36 MB
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Category: Bioinformatics

1996 Biennial Conference Of The North American Fuzzy Information Processing Society Nafips

Author : North American Fuzzy Information Processing Society. Conference
ISBN : 0780332253
Genre : Computers
File Size : 30.6 MB
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The theme of this year's conference is New Frontiers in Fuzzy Logic and Soft Computing. The past few years have witnessed a crystallization of soft computing as a distinct body of concepts and techniques which is orientated toward the conception and design of intelligent systems. Soft computing is not a single methodology. Rather it is a partnership of fuzzy logic, neurocomputing and probabilistic reasoning, with the latter subsuming genetic algorithms, chaotic systems, belief networks and parts of learning theory.
Category: Computers

Methods In Bioengineering

Author : Arul Jayaraman
ISBN : 9781596934061
Genre : Science
File Size : 64.15 MB
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"This cutting-edge volume provides a detailed look at the two main aspects of systems biology: the design of sophisticated experimental methods and the development of complex models to analyze the data. Focusing on methods that are being used to solve current problems in biomedical science and engineering, this comprehensive, richly illustrated resource shows you how to: design of state-of-the art methods for analyzing biological systems Implement experimental approaches for investigating cellular behavior in health and disease; use algorithms and modeling techniques for quantitatively describing biomedical problems; and integrate experimental and computational approaches for a more complete view of biological systems." --Book Jacket.
Category: Science

Computer Applications In Biotechnology 1998

Author : International Federation of Automatic Control
ISBN : CORNELL:31924085460156
Genre : Science
File Size : 75.32 MB
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The 7th International Conference on Computer Applications in Biotechnology (CAB7) was held in Osaka on May 31- June 4, 1998. CAB7 was the continuation of a successful series of conferences which addressed all major areas in which computers are used to aid process analysis, synthesis, supervision, diagnosis, operation, optimization, control and other biotechnological procedures. Essential bioprocess system engineering aspects ranging from metabolic engineering to the control of bioproduction plants were covered. CAB7 was supported by the International Federation of Automatic Control, the European Federation of Biotechnology, and the Society of Fermentation and Bioengineering, Japan. The scientific program was arranged in several sessions. Titles of the sessions were: Modeling, simulation, design and optimization of bioprocesses; Robotics in biotechnology; Knowledge engineering approaches for bioprocess operation; Computer application in metabolic engineering; Instrumentation and data processing; Cell culture engineering and clinical application; and Application to environmental engineering. Leading international figures in their fields presented papers of the latest information. All papers selected were reviewed with the assistance of the international organizing committee (IPC). In total, 94 high quality papers are complied in this volume.
Category: Science