Lecture

Metabolic Modeling Exercises

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In course

ChE-411: Principles and applications of systems biology

The course introduces and develops the key concepts from systems biology and systems engineering in the context of complex biological networks. The lectures elaborate on techniques and methods to model and analyze complex biological problems. ...

Description

This lecture covers exercises on genome-scale metabolic models, including FBA and TFA analysis, as well as modeling kinetics with ordinary differential equations. Students will simulate E. coli growth under different conditions, investigate nutrient uptake vs. growth rate trade-offs, and analyze phenotypes based on oxygen and glucose uptakes.

Instructor

Vassily Hatzimanikatis

Dr. Vassily Hatzimanikatis is currently Associate Professor of Chemical Engineering and Bioengineering at Ecole Polytechnique Federale de Lausanne (EPFL), in Lausanne, Switzerland. Vassily received a PhD and an MS in Chemical Engineering from the California Institute of Technology, and his Diploma in Chemical Engineering from the University of Patras, in Greece. After the completion of his doctoral studies, he held a research group leader position at the Swiss Federal Institute of Technology in Zurich (ETHZ), Switzerland. Prior to joining EPFL, Vassily worked for three years in DuPont, Cargill, and Cargill Dow, and he has been assistant professor at Northwestern University, at Illinois, USA. Vassilys research interests are in the areas of computational systems biology, biotechnology, and complexity. He is associate editor of the journals Biotechnology & Bioengineering, Metabolic Engineering and Integrative Biology, and he serves on the editorial advisory board of the journals Bioprocess and Biosystems Engineering, Journal of Chemical Technology and Biotechnology, and Industrial Biotechnology. He has written over 70 technical publications and he is co-inventor in three patents and patent applications. Vassily is a fellow of the American Institute for Medical and Biological Engineering (2010), he was a DuPont Young Professor (2001-2004), and he has also received the Jay Bailey Young Investigator Award in Metabolic Engineering (2000), and the ACS Elmar Gaden Award (2011).

Official source

Ontological neighbourhood

Computer engineering

Computer data storage: File systems

Theoretical computer science

Programming language theory: High-level programming languages

Related concepts (32)

Metabolic pathway

In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reactions catalyzed by enzymes. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell. These enzymes often require dietary minerals, vitamins, and other cofactors to function.

Metabolic network

A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions. With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human.

CLS (command)

In computing, CLS (for clear screen) is a command used by the command-line interpreters COMMAND.COM and cmd.exe on DOS, Digital Research FlexOS, IBM OS/2, Microsoft Windows and ReactOS operating systems to clear the screen or console window of commands and any output generated by them. It does not clear the user's history of commands, however. The command is also available in the DEC RT-11 operating system, in the open-source MS-DOS emulator DOSBox and in the EFI shell.

MATLAB

MATLAB (an abbreviation of "MATrix LABoratory") is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages. Although MATLAB is intended primarily for numeric computing, an optional toolbox uses the MuPAD symbolic engine allowing access to symbolic computing abilities.

Command-line interface

A command-line interface (CLI) is a means of interacting with a device or computer program with commands from a user or client, and responses from the device or program, in the form of lines of text. Such access was first provided by computer terminals starting in the mid-1960s. This provided an interactive environment not available with punched cards or other input methods. Operating system command-line interfaces are often implemented with command-line interpreters or command-line processors.

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