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.

Official source

Moodle Page

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

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Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.

Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic" data (i.e., experimental data obtained with technologies that require the genome sequence, such as genomic DNA microarrays). These, in combination with computational and statistical approaches to understanding the function of the genes and statistical association analysis, this field is also often referred to as Computational and Statistical Genetics/genomics.

Data modeling in software engineering is the process of creating a data model for an information system by applying certain formal techniques. It may be applied as part of broader Model-driven engineering (MDD) concept. Data modeling is a process used to define and analyze data requirements needed to support the business processes within the scope of corresponding information systems in organizations. Therefore, the process of data modeling involves professional data modelers working closely with business stakeholders, as well as potential users of the information system.

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.

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.