Last week our paper on Panoptes was published in Bioinformatics. Panoptes is the software we use to power several web applications on the MalariaGEN site, including the Ag1000G browser. Although it’s taken us a while to get this paper in print, these web applications have been in production for a couple of years now. To celebrate, I thought I’d post links to some screencasts featuring the Ag1000G browser which we made around the time it was first launched back in 2014/2015. We’ve made some updates to the Ag1000G browser since these videos were made, but they’re still relevant, and hopefully provide a useful introduction to some of the capabilities of the Panoptes framework.

5 minute tour

Below is a screencast that Steve Pritchard made, giving a brief tour of the main features in the Ag1000G browser:

Extended tour

Below are 4 videos I made while giving a longer tour of the Ag1000G browser. These are much more rough-and-ready (apologies) but go into more depth on various features.

Part 1 - tables, queries, plots

The first video looks at the samples table and illustrates some basic features around querying the table and making interactive plots:

Part 2 - larger tables

The second video looks at the variants table and illustrates some features available for working with larger tables:

Part 3 - genome browser

The third video looks at the genome browser functionality, which has been fantastic for it’s ability to zoom in and out and summarise data at any genomic scale:

Part 4 - visual analytics

The fourth video looks at some of the visual analytics features, including how to select data items and see how items are related across different representations of the data:

Future work

We are working on a new (2.0) version of the Panoptes framework, which addresses some of the scalability limitations in the current (1.6) production release, as well as improving the data import process and providing new capabilities in the user interface. The new version is still in beta, but please feel free to get in touch if you are interested in trying it out.

I should add that although Panoptes has been deployed in production for a while, I still don’t think of it as a finished product by any stretch. Rather it is an exploration of some ideas about how to visualise, explore and interact with large genome variation datasets. Working with large and complex data is a major challenge, and I’m very conscious that there are many questions people might like to ask of the Ag1000G data that are very difficult or impossible to answer with the current Ag1000G browser. All of us involved in ongoing development of Panoptes would love to make connections with others working on similar problems, and to hear from anyone who has ideas, comments or frustrations about the software as it stands.