Stoichiometric models creation and analysis procedures for metabolic engineering = Stehiometrisko modeļu izveides un analīzes procedūras metaboliskajai inženierijai
Authors:   ,   Latvia University of Agriculture, Pentjuss Agris 
Published: June 2021

Doctoral thesis had been developed in the period from September 2011 until February 2016 in department of Computer Control of Faculty of Information Technologies, Latvia University of Agriculture. The PhD thesis consists of 145 pages, which include 15 tables, 44 figures, and 12 annexes, which are summarised in separate volume. For the development of this thesis 196 sources were used including 194 in foreign language. Promotion thesis hypothesis: It is possible to upgrade stoichiometric model creation and validation procedures, to decrease calculation time, manual work and manually processed data amount. The aim of PhD thesis: The aim of thesis is to develop stoichiometric computer models based procedures of metabolic engineering task solving procedures to reduce computation and manual work. In order to achieve the aim of the PhD thesis several tasks were completed: 1. To analyse the mathematical regularities between the stoichiometric modelling and molecular processes of metabolism; 2. To research operating principles of stoichiometric model analysis methods;3. To improve stoichiometric model development and validation procedure to reduce time consumption, number of operations and manual processing of data. 4. To develop stoichiometric model analysis methods visualization tool for metabolic engineering tasks. 5. To create stoichiometric model analysis methods sets of procedures for reduction time consumption number of operations and number of analysed solutions.The content of the PhD thesis: it is structured according to the aim and the tasks of PhD thesis consisting of 5 chapters: First chapter includes general description about biological parameters, basic information and metabolism processes, which is used in stoichiometric model as creation, validation, improvement and analysis. Also includes description about systems biology modelling methods, where main text is dedicated for stoichiometric modelling, using linear algebra, matrixes, and mathematical vectors properties for stoichiometric model analysis problems research. Second chapter includes description about 6 different stoichiometric modelling analysis methods. For Each method specific functionality is described, necessary analysis methods input and output data is researched and analyzed how the modelling aim should be combined with analysis methods properties. Third chapter includes existing stoichiometric model creation procedure and using this information and promotion thesis author gain experience creating and upgrading several stoichiometric models, was upgraded. It consists from 5 subclasses, where using procedure in cyclic development process new author made procedure decreases stoichiometric model development time. Are described and classified sthoichiometric model constraints. Fourth chapter includes author developed visualization method for stoichiometric model analysis methods in user friendly interface. In chapter are researched different systems biology used computational tools, vector graphic creation tools, which are used to create first time a visual metabolic network for automatic flux visualization. Fifth chapter includes 12 different type and dificulty procedures or stoichiometric model analysis. These procedure allow improving metabolic engineering purposed task decreasing model analysis computational time, user manual work and solution set amount. The main results, conclusions and future development prospects are described in the conclusions of the PhD thesis.