Universität Wien

270193 VU (Introduction to) Network analysis with Python (2024S)

3.00 ECTS (2.00 SWS), SPL 27 - Chemie
Prüfungsimmanente Lehrveranstaltung
VOR-ORT
Moodle
Fr 03.05. 10:00-16:00 Seminarraum 4 Institut Physikalische Chemie HP Währinger Straße 42

An/Abmeldung

Hinweis: Ihr Anmeldezeitpunkt innerhalb der Frist hat keine Auswirkungen auf die Platzvergabe (kein "first come, first served").

Details

max. 12 Teilnehmer*innen
Sprache: Deutsch, Englisch

Lehrende

Termine (iCal) - nächster Termin ist mit N markiert

Freitag 17.05. 10:00 - 16:00 Seminarraum 4 Institut Physikalische Chemie HP Währinger Straße 42
Freitag 24.05. 10:00 - 16:00 Seminarraum 4 Institut Physikalische Chemie HP Währinger Straße 42
Freitag 31.05. 10:00 - 16:00 Seminarraum 4 Institut Physikalische Chemie HP Währinger Straße 42
Freitag 07.06. 10:00 - 16:00 Seminarraum 4 Institut Physikalische Chemie HP Währinger Straße 42

Information

Ziele, Inhalte und Methode der Lehrveranstaltung

Learning Outcomes

Students will gain an understanding of network science and learn various examples of where networks science can be applied in biochemistry and beyond. Students will get a feel for the type of networks that can be constructed to represent various (chemical) interactions and the network properties and modelling techniques that can be used to answer scientific research questions about those interactions. Furthermore, students will gain a gentle introduction to programming in Python in order to learn how to use the Networkx package for generating and analysing networks.

Course Content

• Introduction to graph theory and the calculation of structural network properties
• Discussion of different network types and examples of real networks
• Introduction to analysing networks in Python using the networkx package
• Discussion of functionalising code, good coding practices and writing pseudo code
• Genome-scale modelling of metabolic networks

Method

The course will be divided into lectures and programming practicals. Each set of theory will be followed by examples on how to implement the theory in Python and a set of programming tasks. A combination of course participation, presentations and a programming assignment will be used to assess the material covered in the lectures and practicals.

To complete the practical tasks of this course, students will require access to a computer or laptop with a web browser. Programming tasks are designed to be hosted on a server which has the required software pre-installed and to which students enrolled in the course will be granted access.

The course will be instructed in English.

Art der Leistungskontrolle und erlaubte Hilfsmittel

Assessments

• Participation in lectures and practicals
• Oral presentation of a research paper
• Python programming assignment
• Oral presentation of the programming assignment

Mindestanforderungen und Beurteilungsmaßstab

The course is designed to be an introduction to network science and to programming. Students are not expected to have prior programming experience. Course attendance is mandatory. Students may be excused for one day unless otherwise agreed upon. 50% of the maximal points, as outlined below, must be attained to pass the course.

Marking Scheme

A maximum of 100 points can be achieved in the course. The 100 points are divided into:
• Participation in lectures and practicals: 15 points
• Research paper presentation: 20 points
• Programming assignment: 45 points
• Programming presentation: 20 points

Grades will be assigned as follows:
• 1 (excellent): 100-89 points
• 2 (good): 88-76 points
• 3 (satisfactory): 75-63 points
• 4 (sufficient): 62-50 points
• 5 (insufficient): 49-0 points

Prüfungsstoff

There are no restrictions with regards to the resources that students can use to complete their assignment(s), provided that all work submitted/ presented for assessment is original and has not been plagiarised. All assessments are based on the materials provided during the course.
The additional reading materials may be used to gain a deeper understanding of the content provided in the lectures and practicals. Student may be expected to read some of the additional material(s) in order to gain full marks.

Literatur

Reading Materials

A majority of the course material is based on the following textbook and chapters:

Barabasi, A.-L. & Marton, P. (2016) Network Science. Cambridge University Press. [available online at http://networksciencebook.com/]
• Chapter 1 -5, 8-9

The course is supplemented with examples from the following research papers and others:

Barabási, A., Oltvai, Z. (2004) Network biology: understanding the cell’s functional organization. Nature Reviews Genetics. 5, 101–113.

Barabási, A.-L., Gulbahce, N. & Loscalzo, J. (2011) Network Medicine: A Network-based Approach to Human Disease. Nature Review Genetics. 12,56-68.

Compeau, P.E.C., Pevzner, P.A. & Tesler, G. (2011) Why are de Bruijn graphs useful for genome assembly? Nature Biotechnology. 29, 987-991.

Firth, J.A., Hellewell, J., Klepac, P., Kissler, S., CMMID COVID-19 Working Group, Kurcharski, A.J., Spurgin, L.G. (2020) Using a real-world network to model localized COVID-19 control strategies. Nature Medicine. 26, 1616-1622.

Motter, A.E., Gulbahce, N., Almaas, E. & Barabási, A.-L. (2008) Predicting synthetic rescues in metabolic networks. Molecular Systems Biology. 4, 168.

Orth, J., Thiele, I. & Palsson, B. (2010) What is flux balance analysis? Nature Biotechnology. 28, 245–248.

Jeong, H., Mason, S.P., Barabási, A.-L. & Oltvai, Z.N. (2001) Lethality and centrality in protein networks. Nature, 411: 41-42.

Watts, D.J. & Strogatz, S.H. (1998) Collective dynamics of ‘small-world’ networks. Nature. 393, 440-442.

Zuordnung im Vorlesungsverzeichnis

AN-2, BC-1, CHE II-1, BC-CHE II-8, CH-CBS-05, Design

Letzte Änderung: Do 29.02.2024 10:26