This course will introduce computational modeling of large (genome-scale) metabolic reaction networks through a scalable framework known as constraint-based modeling. Emphasis will be on the usage in both biotechnology and systems biomedicine. Main topics will be fundamental constraint-based modeling methods, omics data integration, multi-scale modeling and microbial community modeling. The course will combine theoretical lectures with tutorial exercises and computational exercises in Python.
Course coordinators
- dr. Maria Suarez Diez, Wageningen University
- dr. Marian Breuer, Maastricht University
Course credits
1.5 ECTS for following the course. An additional 1.5 ECTS when successfully completing a final assignment.
Course description
Constraint-based modeling is a powerful modeling framework that allows to model reaction fluxes in genome-scale metabolic network models, with uses in fundamental and applied questions relevant to biotechnology, microbiology and biomedicine. These genome-scale metabolic models encompass all metabolic reactions encoded in an organism, possibly contextualized to a particular cell type and condition. Constraint-based modeling provides a scalable framework to analyze these large-scale models, whether they describe microbes, human cells in health and disease or multi-cellular systems like microbiota and the whole body. In this course, you will be introduced to:
- the principles of constraint-based reconstruction and analysis (COBRA)
- the underlying mathematical foundations of constraint-based modeling
- content, structure and reconstruction of genome-scale metabolic models
- basic and advanced methods for interrogating models and interpreting results
- methods for integration of omics data with genome-scale metabolic models
- multi-scale applications, in particular dynamic Flux Balance Analysis
- constraint-based modeling of microbial communities
- open source COBRA software, with a focus on the Python package COBRApy
- standards for reconstruction and model sharing
- example applications to biomedicine and biotechnology
The course is structured into both lectures and practical sessions so that theory can be illustrated with biologically motivated computational examples.
Learning objectives
- Introduction to COBRA
- Proficiency with the COBRApy package in Python
- Familiarity with typical applications of constraint-based modeling in biomedicine and biotechnology
Target audience
Constraint-based modeling is a rapidly growing field that is being used in both fundamental and applied research and biotechnology. It sits at the intersection between quantitative modeling, bioinformatics and cellular physiology, and as such, is an example of systems biology at work.
While participants would benefit from some knowledge of either quantitative modeling, bioinformatics or metabolism this is not required. This includes, for example, scientists working in a laboratory and wanting to learn more about building or using genome-scale metabolic models, as well as those who have used some basic COBRA methodologies, but want to know how else it can be applied to their research.
Lecturers
- Maria Suarez Diez (WUR)
- Marian Breuer (Maastricht University)
- Efsun Duman (WUR)
- Claudia de Buck (WUR)
- Jelle Bonthuis (Maastricht University)
Course program
Monday (Feb 10)
9:30 – 17:30 Basics of constraint-based modeling
Tuesday (Feb 11)
9:30 – 18:00 Structure and reconstruction of genome-scale metabolic models
Social evening
Wednesday (Feb 12)
9:30 – 17:30 Methods for constraint-based modeling and modeling applications
Thursday (Feb 13)
9:30 – 17:30 Data integration and dynamic modeling
Friday (Feb 14)
9:30 – 15:15 Multi-cell modeling
Course location
The course will be given in the Orion Building:
Monday: room B4014
Tuesday-: room B3032
Wednesday: room B3031
Thursday: room B3042
Friday: room B5015
Coming by car: see the map in this link
Public transport: Travel by train to the train station Ede-Wageningen. From there you can take either the bus to the Campus or a taxi. A taxi ride is around € 25 one way. The bus station is next to the train station. You can use the app OV9292 for the schedule. You can find the different bus stops on the map. Hermes Bus 303 goes to the bus stop on Campus/Forum, that is the bus stop at the crossing of Bronland and Bornsesteeg. The bus leaves from Platform A at the train station. Bus 303 leaves 4 times in an hour.
Additional information
For practical sessions, participants require their own laptop with Python and the package COBRApy pre-installed (see https://github.com/opencobra/cobrapy/blob/stable/INSTALL.rst for instructions).
For more information about the course you can contact Maria Suarez Diez or Marian Breuer.
Wildcards
If you would like to join this course using a wildcard, please contact the community manager, Petra Aarnoutse.
Until the maximum number of wildcard spots is reached, you can register with a wildcard until December 30, 2024.
Always mention in your application from which academic group the wildcard comes. Your registration is only valid after confirmation by the community manager.
Registration
- € 480 (excl. VAT) for PhD/MSc students
- € 720 (excl. VAT) for academic researchers (non-profit)
- € 1080 (excl. VAT) industry participants (for profit)
Course fees includes course materials and catering (coffee, tea and lunch)
You can register for the course by filling out this registration form
There is room for max. 25 participants.
Find general enrollment information here.
