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  • Biochemistry and Biotechnology  (3)
  • decision trees  (1)
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  • 1
    Electronic Resource
    Electronic Resource
    Formal modeling of approximate relations in biochemical systems (1989)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 34 (1989), S. 196-206 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Aiming to satisfy the need for the formalization of semiquantitative reasoning in the analysis of biochemical systems, the O[M] formalism for reasoning with orders of magnitude and approximate relations has been developed. It is based on seven primitive relations among quantities and compound relations which are formed as implicit disjunctions of primitives. O[M] can perform inferences by using formal approximate relations, algebraic equations, inequalities, if-then rules, assumptions, and goals. The applications discussed include Michaelis-Menten kinetics, different modes of inhibition of an enzymatic reaction, analysis of fluxes in biochemical networks, and identification of rate-limiting steps of biochemical pathways. In these applications, O[M] provides a medium for acquisition and formalization of previously informal concepts, analysis of systems at the order-of-magnitude level of detail, and automation of commonsense reasoning.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260340208
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Computer-aided synthesis of biochemical pathways (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 36 (1990), S. 1119-1132 
    Details
    ISSN: 0006-3592
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The synthesis of biochemical pathways satisfying stoichiometric constraints is discussed. Stoichiometric constraints arise primarily from designating compounds as required or allowed reactants, and required or allowed products of the pathways; they also arise from similar restrictions on intermediate metabolites and bioreactions participating in the pathways. An algorithm for the complete and correct solution of the problem is presented; the algorithm satisfies each constraint by recursively transforming a base-set of pathways. The algorithm is applied to the problem of lysine synthesis from glucose and ammonia. In addition to the established synthesis routes, the algorithm constructs several alternative pathways that bypass key enzymes, such as malate dehydrogenase and pyruvate dehydrogenase. Apart from the construction of pathways with desired characteristics, the systematic synthesis of pathways can also uncover fundamental constraints in a particular problem, by demonstrating that no pathways exist to meet certain sets of specifications. In the case of lysine, the algorithm shows that oxaloacetate is a necessary intermediate in all pathways leading to lysine from glucose, and that the yield of lysine over glucose cannot exceed 67% in the absence of enzymatic recovery of carbon dioxide.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260361107
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    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Fermentation database mining by pattern recognition (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 53 (1997), S. 443-452 
    Details
    ISSN: 0006-3592
    Keywords: fermentation ; database mining ; pattern recognition ; dbminer© ; decision trees ; wavelets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: A large volume of data is routinely collected during the course of typical fermentation and other processes. Such data provide the required basis for process documentation and occasionally are also used for process analysis and improvement. The information density of these data is often low, and automatic condensing, analysis, and interpretation (“database mining”) are highly desirable. In this article we present a methodology whereby process variables are processed to create a database of derivative process quantities representative of the global patterns, intermediate trends, and local characteristics of the process. A powerful search algorithm subsequently attempts to extract the specific process variables and their particular attributes that uniquely characterize a class of process outcomes such as high- or low-yield fermentations.The basic components of our pattern recognition methodology are described along with applications to the analysis of two sets of data from industrial fermentations. Results indicate that truly discriminating variables do exist in typical fermentation data and they can be useful in identifying the causes or symptoms of different process outcomes. The methodology has been implemented in a user-friendly software, named db-miner, which facilitates the application of the methodology for efficient and speedy analysis of fermentation process data. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 443-452, 1997.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
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