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Course

ChE-411: Principles and applications of systems biology

Summary

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.

Lectures

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

Moodle Page

http://go.epfl.ch/ChE-411

Summary

Lectures

Instructor

Vassily Hatzimanikatis

Official source

Moodle Page

http://go.epfl.ch/ChE-411

Lectures in this course (18)

Introduction to MATLAB Log in to Mediaspace to watch this video

Covers the basics of MATLAB and includes an exercise session on metabolic modeling.

Systems Biology: Metabolism Modeling and Analysis Log in to Mediaspace to watch this video

Covers systems biology fundamentals, metabolism modeling, and analysis techniques, emphasizing metabolic flux distributions and omics integration.

Introduction to MATLAB Tools and Installation Log in to Mediaspace to watch this video

Covers the introduction to MATLAB tools and provides installation instructions for Thermodynamics-based Flux Analysis, including pre-requirements like GIT and CPLEX.

Metabolic Modeling: FBA and TFA Log in to Mediaspace to watch this video

Introduces Flux Balance Analysis (FBA) and Total Flux Analysis (TFA) in metabolic modeling using MATLAB.

Metabolic Modeling: TFA and Kinetic Models Log in to Mediaspace to watch this video

Explores metabolic modeling using TFA and kinetic models, covering growth simulation, nutrient trade-offs, phenotypic analysis, and metabolomics integration.

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