Educators:
Steffen Klamt (de.NBI-SysBio)
Date:
7 February 2024
Location:
Lisbon
Contents:
This 1-day course introduces principles of constraint-based modeling and computational design of metabolic networks coupled with a live demonstration and hands-on exercises with the MATLAB package CellNetAnalyzer (CNA) and its Python-variant CNApy. The lecture will overview the key methods of constraint-based modeling and metabolic network design:
– Fundamentals of constraint-based modeling of metabolic networks
– Metabolic flux (balance) analysis
– Flux Variability analysis
– Phase planes and Yield spaces
– Metabolic pathway analysis
– Minimal cut sets and computational design of metabolic networks.
In the Hands-on Session the participants will have a guided tour through key features of CellNetAnalyzer (CNA) and its Python-variant CNApy (live demonstration) and will practice the use of CNA or/and CNApy by exercises with small example networks as well as with realistic metabolic models.
Learning goals:
The workshop introduces principles of stoichiometric and constraint-based modeling coupled with hands on exercises using CellNetAnalyzer and a demonstration of CNApy. The hands on exercises throughout the workshop will ensure that attendees become familiar with the software tools and with analyzing, creating, editing, importing, simulating and storing biochemical networks.
Prerequisites:
- Some knowledge of mathematical modeling will be advantageous.
Please install/download CNA or/and CNApy prior to the course and test whether it runs on your system (you should have installed at least one of the two toolboxes). You can download the latest version of CNA from the following website:
https://www2.mpi-magdeburg.mpg.de/projects/cna/cnadownload.html
For using CNA you need MATLAB. If you do not have access to MATLAB you may download a 30 day trial version here:
https://www.mathworks.com/campaigns/products/trials.html
For installation of CNApy please follow the instructions on:
https://github.com/cnapy-org/CNApy
Please download also the CNApy example projects from:
https://github.com/cnapy-org/CNApy-projects
Finally, for the hands-on exercises please aslo download the following two files:
https://www2.mpi-magdeburg.mpg.de/projects/cna/exercise.pcx
https://www2.mpi-magdeburg.mpg.de/projects/cna/exercise.svg
Keywords:
CellNetAnalyzer (CNA), CNApy
Tools:
CellNetAnalyzer, CNApy
Contact:
Steffen Klamt (
Registration:
https://forms.gle/HBVK9vpLoEEjxJ7V8
For more information see:
https://olissipo.inesc-id.pt/olissipo-school-on-mathematical-modelling/