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.
Where:
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 niso@biosustain.dtu.dk 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.
https://pad.carpentries.org/2018-09-10-dtu
| 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 |
| 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 |
Prerequisites
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 |