MetabMaster - Learn from "Pathway Stories"

This is a continuation from my previous post about my thesis project.

Pathway Stories

It's coming to the end of my thesis and time in Maastricht now ( :( or :) I don't know!). For the past three months, I have been working with WikiPathways to create "pathway stories". We know pathways on WikiPathways can be complicated and, at first glance, pretty god damn scary. Pathway stories make a pathway easier to read and understand in a "show don't tell" manner. I won't go into much detail on them here you can read this post for that.

Lung fibrosis pathway on WikiPathways. Scary!Lung fibrosis pathway on WikiPathways. Scary!


MetabMaster is an application I created to demonstrate pathway stories. It has a fair few pathway stories in it now and more will come soon. When you click the links in the description, the accompanying diagram will change visualisation state - zooming in, highlighting and stuff.

Pathway story in MetabMaster A pathway story in MetabMaster.

Creating pathway stories is enabled by a "Kaavio Flavoured" Markdown syntax (Kaavio is the diagram rendering library). With this syntax, you can do all of the usual Markdown magic plus create interactive links like a true wizard. Once you've written your description, the live preview panel lets you make sure everything's all funkin' before saving.

Pathway story creation page in MetabMaster The pathway story creation page

What's next?

Right now, I'm working on animating everything so that the diagram changes visualisation smoothly. This will help the reader see the context of where pathway parts are, especially when it comes down to zooming. Hopefully, these pathway stories will be integrated into WikiPathways soon :)

Upcoming post

Soon I'll write some more technological posts about how all of this was created. I actually used React and Angular at the same time in this thesis project so I hope I can give some nice insights into their differences.

Thanks for reading & please get in touch if you have any questions/suggestions!

Jacob Windsor

Likes creative computer-based stuff. Web, Science, Typography, Graphics... Trying to combine too many interests into something coherent.

Maastricht, Netherlands