Universität Wien

300095 VU Metabolic network reconstruction and analysis (2024S)

5.00 ECTS (3.00 SWS), SPL 30 - Biologie
Continuous assessment of course work
Moodle

Registration/Deregistration

Note: The time of your registration within the registration period has no effect on the allocation of places (no first come, first served).

Details

max. 25 participants
Language: English

Lecturers

Classes (iCal) - next class is marked with N

  • Thursday 07.03. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 14.03. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 21.03. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 11.04. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 18.04. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Wednesday 24.04. 13:15 - 16:30 Seminarraum 1.1 PC, Biologie Djerassiplatz 1, 1.003, Ebene 1
  • Thursday 25.04. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 02.05. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Wednesday 08.05. 13:15 - 16:30 Seminarraum 1.1 PC, Biologie Djerassiplatz 1, 1.003, Ebene 1
  • Thursday 16.05. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 23.05. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Wednesday 29.05. 13:15 - 16:30 Seminarraum 1.1 PC, Biologie Djerassiplatz 1, 1.003, Ebene 1
  • Thursday 06.06. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 13.06. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Wednesday 19.06. 13:15 - 16:30 Seminarraum 1.1 PC, Biologie Djerassiplatz 1, 1.003, Ebene 1
  • Thursday 20.06. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1
  • Thursday 27.06. 09:45 - 11:15 Seminarraum 1.3, Biologie Djerassiplatz 1, 1.005, Ebene 1

Information

Aims, contents and method of the course

The course introduces students to the construction and analysis of metabolic network models for predicting metabolic fluxes from gene sequence data. Such models can be used to predict substrate uptake and secretion rates as well as biomass growth rates for many organisms using simple gene-reaction mappings.

Learning objectives

The students will know which information is contained in metabolic network models and what they can be used for.
They will be able to perform a basic computational analysis of such models, and will be able to use them for the prediction of metabolic fluxes with constraint- and optimization-based methods.
They can construct metabolic network models from genetic sequence data and suitable enzyme/reaction databases with suitable software tools.

Contents

Structure and properties of metabolic network models
Working with metabolic network models: flux balance analysis, flux variability analysis
Genome-scale models
Reconstruction of models from genetic data

Assessment and permitted materials

- Written exam (50%)
- Solutions of computer exercises (50%)

Minimum requirements and assessment criteria

All partial evaluations must be positive to pass the course. Minimum score to pass is 50% in total.

Examination topics

In the exam, students need to show that they are able to constructively apply and discuss the methods taught in the course.

Reading list

Bernhard O. Palsson: Systems Biology. Constraint-based Reconstruction and Analysis. Cambridge University Press, 2015
Costas D. Maranas, Ali R. Zomorrodi: Optimization Methods in Metabolic Networks. John Wiley & Sons, 2016
The Economic Cell Collective: Economic Principles in Cell Biology. No commercial publisher | Authors open access book, 2024. doi: 10.5281/zenodo.8156386.

Association in the course directory

MES3, M-WZB, MEC-9, MBO 7

Last modified: We 31.07.2024 12:06