Metabolic modeling for cell factory engineering

3. Pathway visualization

Overview

Teaching: 15 min
Exercises: 30 min
Questions

  • How can I draw a metabolic pathway map?

  • How do I visualize omics data in the context of pathways?

Objectives

  • Learn how to draw a metabolic pathway in Escher.

  • Learn how to visualize gene, reaction or metabolite centric data.

Using the standalone web application

Head over to escher.github.io/. Learn the basic features of Escher by watching the following video.

Adding a missing pathway

In the E. coli central carbon metabolism map, add the biosynthetic pathway for L-serine. Tip: Look up the biosynthetic steps on KEGG or EcoCyc if you can’t recall them.

Highlight gene expression changes

Using the E. coli central carbon metabolism map, visualize the gene expression data covered in the R lesson of the software carpentry course (data/expression_data_e_coli.csv). Play with the settings until you’re satisfied with the representation

Using Escher maps inside Jupyter notebooks

Furthermore, it is possible to embed Escher pathway visualizations inside Jupyter notebooks. This is very practical for visualizing simulation results.

Key Points