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 firstname.lastname@example.org for more information.
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.
|09:00||Resolve installation issues|
|11:30||Episode 4 (part 1)|
|13:00||Episode 4 (part 2)|
|10:00||Episode 8 (part 1)|
|10:45||Episode 8 (part 2)|
|14:00||Episode 11 (part 1)|
|14:45||Episode 11 (part 2)|
|15:30||PhD students discussion of projects|
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?|