Biology is a living thing

For about a month now, I have been working on my bachelor thesis to "extend WikiPathways to improve educational capabilities", that's the proposal title anyway. I'm doing this under the supervision of chem/bio-informatician Egon Willighagen at BiGCat (thanks to him for the title of this post) and data engineer Anders Riutta at the Gladstone Institutes.

TLDR: In short, I'm making the pathway diagrams in WikiPathways more "story based" in hope to make understanding them easier. Check out a demo here.

What's this WikiPathways then?

WikiPathways is a community-driven, open-source platform and database for biological pathways. But first, what are pathways? They are (hopefully) simple representations of the interactions between genes, metabolites, or proteins that drive a particular cellular process (there's one of cancer metabolism below). Thanks to "omics" technologies we now have a huge amount of data for these interactions. Hopefully, this means we can find out more about our bodies, possibly even curing diseases (yes Trump, it's true). All of this data is often hard to understand or even find. Think of trying to find a book on Vincent van Gogh in the New York Public Library, only to find the books are listed by the author's mother's maiden name (okay, it's not quite like that but you get the picture). That's where WikiPathways comes in. Through its search tool, researchers can easily find what they're looking for and then gain an understanding through the interactive diagrams. When you click on a pathway element, a box pops up leading you to further information. The pathways are also accompanied with up-to-date descriptions to further help researchers understand.

Cancer cell metabolism in Humans

Interactive descriptions

To help further improve the ability for researchers to understand information in WikiPathways, I am integrating interactive descriptions. By clicking links within the description, the rendering of the pathway diagram changes. It can zoom in on sections, highlight metabolites, or open the pop-ups. The idea is that this will improve the "story-telling" of the pathway and it's a tactic very successfully adopted by Proteopedia. You can see a GIF of it in the tweet below or check out the online demo.

Sounds cool but... what's the point?

It's incredibly important for scientists to be able to easily access and understand relevant information so that their research can progress. Biology is extremely complex and any effort to make it easier to understand can lead to great breakthroughs in both medicine and academia. This is especially true for diseases such as cancer, where a deep understanding of the many aspects of tumour metabolism is required for the development of effective treatments. The interactive descriptions will help researchers explore pathways in an intuitive manner so that they can easily build an understanding of the pathway they're looking at.

Interested in more?

I've written a proposal for this project and have made it openly available on Figshare here. In it, you can read about the methods I'm using and how I'll be testing the efficacy of the interactive descriptions.

I'm hoping to extend this research through the Google summer of code (GSoC) by developing "story-based" pathway presentations. If you'd like to hear about that you can read my ideas here.

Please let me know your thoughts in the comments! Special thanks to Egon and Anders for supervising me and answering my questions.

Jacob Windsor

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

Maastricht, Netherlands