WormBase | Toronto Open Science Code Sprint

Join us in Toronto this March at our first ever Mozilla Toronto Open Science Code Sprint on Sat/Sun March 07-08 2015. At this 2-day event we will be bringing together researchers working on open science projects with developers, designers and other scientists from the community to collaborate on tools helping further science on the web. Every day this week, we’ll feature a guest post on one of the projects we’ll be sprinting on: Contributorship Badges, Cytoscape.js, Matplotdash, Pathogens & Disease Immunity, WormBase.

Today’s guest post is from Sibyl Gao, web developer for WormBase.org. Don’t forget to register to collaborate with us on open science!


WormBase: explore worm biology

Some organisms are used by scientific researchers as models for studying biology and disease. A lot of research studies have been done and a lot of knowledge accumulated about these organisms, making these organisms even more valuable tools for research. The knowledge obtained needs organizing and a channel to reach other researchers, who may benefit from it. WormBase is among those that try to help with this.

We focus on the model organism Caenorhabditis elegans, a tiny transparent free-living worm species. WormBase (http://www.wormbase.org/) is a project dedicated to supporting C. elegans research community with curated data and open source tools for accessing them. Our curators have developed a rich set of schemas for different data types. Some types are about biological entities (e.g. genes, constructs, molecules), and some are about biological events (e.g. interactions, expression, phenotype). Different types of data describe associations with each other. Snippets of data are also associated with references that identify the source, such as a paper. Following association links, as well as using our custom search, to find data objects of interest is an important use case of WormBase website.

WormBase website is developed using Catalyst, a Perl based web framework. A RESTful API exposes data searching and data fetching functionalities that allow development of a site front-end without setting up the full dependencies. This approach is what has been used for developing our mobile site, a lightweight front-end developed with Backbone.js that consumes JSON objects obtained from the API.

I’d like to take the opportunity of this code sprint to explore data visualization tools and enhance user interface, using our mobile site as a testing ground. So far WormBase has an individual page for each data object/instance, describing it in great detail and presenting its relations in lists and tables. But we haven’t offered any visualization or analysis tools to make better sense of all the information available. Maybe our users would like to select several data objects and visualize how they relate to each other. Maybe they’d like to compare some sequences or compare lists that each object has. Another area to explore is our user interface: navigating sites with many links can make people feel lost. How quickly help them reorient themselves and keep track of where they’ve been maybe something useful.

Learn more about us:
Website: http://www.wormbase.org/
Mobile: http://m.wormbase.org/
Publication: WormBase 2014: new views of curated biology

How to contribute:
Github (for WormBase mobile): https://github.com/WormBase/website-mobile
Issue tracker: https://github.com/WormBase/website/issues

Looking for help in:
(Developer) Data visualization tools
(Designer) Interface design
(Developer) Complex query search
(Biologist) Insight on use cases that need better support