Metabolic modeling for cell factory engineering: General information

General information

This two-day hands-on workshop covers the basics of constraint-based modeling of metabolism with a focus on cell factory engineering. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students and other researchers. You do need a basic working knowledge of Python in order to follow the course.


Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (the setup instruction can be found here). They are also required to abide by Software Carpentry’s Code of Conduct.

Contact: Please mail for more information.

Course materials

The course materials are available under the Episodes menu item (see the top of the page). Furthermore, all course notebooks can be downloaded at once here.



Day 1

09:00 Resolve installation issues
09:30 Episode 1
10:00 Episode 2
10:30 Coffee
10:45 Episode 3
11:30 Episode 4 (part 1)
12:00 Lunch break
13:00 Episode 4 (part 2)
13:30 Episode 5
14:30 Coffee
14:45 Episode 6
15:45 Wrap-up
16:00 End

Day 2

09:00 Episode 7
10:00 Episode 8 (part 1)
10:30 Coffee
10:45 Episode 8 (part 2)
11:00 Episode 9
12:00 Lunch break
13:00 Episode 10
14:00 Episode 11 (part 1)
14:30 Coffee
14:45 Episode 11 (part 2)
15:15 Wrap-up
15:30 PhD students discussion of projects
16:00 End



Must have attended software carpentry course or have significant programming experience with Python. Learners must install cameo and dependencies before class: please see the setup instructions instructions.


00:00 1. Getting started How can I get started with metabolic models?
00:30 2. Genome-scale metabolic models How do I explore the content (metabolites, reactions, genes, …) in a model?
How can I search by name and other attributes?
01:00 3. Pathway visualization How can I draw a metabolic pathway map?
How do I visualize omics data in the context of pathways?
01:45 4. Analyzing metabolic models How uniquely determined is the flux distribution returned by flux balance analysis?
What is the optimal oxygen uptake rate at maximum growth?
02:45 5. Manipulating models How can I add missing reactions to a model?
How can I delete a gene from a model?
03:45 6. Gene essentiality Medium-dependent essential genes?
04:45 7. Calculating yields How can I calculate the maximum possible yield for a desired product?
How does product yield vary with growth?
05:45 8. Heterologous pathways How can I find heterologous pathways ?
06:30 9. Gene deletion strategies How does one reroute flux towards production using gene deletions?
07:30 10. Gene expression modulation How can I predict over-expression and down-regulation targets?
08:30 11. Data-driven design of cell factories using the DD-DeCaF platform Can computational strain design algorithms outperform humans in enumerating promising strategies using metabolic models?
09:15 Finish