Video Tip of the Week: G-nome Surfer for table-top genome browsing
The other day a tweet came over my “genome” search column that intrigued me:
Tabletop interface? Wha? Ok–I had to check this out. And, in fact, this group has software that will let you explore eukaryotic genomes (G-nome Surfer) and lately prokaryotic genomes (G-nome Surfer Pro) on a coffee-table-ish device. They have evaluated the utility of this for educational settings, and in this paper they report on the whole project: design, validation, evaluation, and feasibility in educational settings.
First, though, let me just say that the name is doomed to mis-reading and mis-typing, I’m sure. Already people joke in my twitter feeds all the time about Garden Gnome Browsers….
But as to the work: I am a bit confused on why this is called a “reality-based interface” as opposed to the vertical genome viewers. Is my laptop’s browser really less reality-based than a coffee-table version? Hmm.
The paper goes on to describe a number of new interfaces and strategies that are getting biology out of the traditional deskbound strategy–many of which were new to me and interesting. There’s a section that talks about integrating tabletop interfaces into lab benches–but the feasibility of this is not addressed in those proposals reportedly. But it was fun to imagine.
The rest of the paper focuses mostly on the development and deployment of a table-top interface in an academic setting, for both educational and research support.
This included an assessment of the current state of genome browsers–which I have to say I agree with:
We observed that bioinformatics tools in general and genome browsers in particular have a high threshold: they are powerful, but in order for a researcher to take advantage of their power, they must have both broad domain knowledge and extensive training.
Why yes, they do need training. But I am having a hard time imagining how to run our workshops with everyone bent over a coffee table. Totally changes the dynamic of that…
I don’t dispute their analysis of how users are currently interacting with bioinformatics tools. I guess I’m just not clear on how making them horizontal really lowers the barriers. One of the things they claim to want to solve is “Alleviating Data Explosion” and the problems of so much information that we are all facing. But I’m not convinced this gets us closer to that. I really really really still want something that lets me hold several tools at the same time in my view–and my favorite way I’ve seen to do that would be a modified Caleydo-style interface where I could put UCSC Genome Browser on one panel, Reactome in another, PubMed or a specific paper on another pane, and so on…
That said, I think it’s time to open a bar in Kendall Square with these–a few beers with the genome geeks and a few of these tables would be fun for after work gatherings.
So here you can have a look at how G-nome is implemented. There’s no verbal track, and I’d have to recommend turning off the music…
So is this the future of your genome browsing and teaching? They paper includes details of their evaluation for usability, utility and impact in a course. I’m not convinced it really did improve student attitudes, and the numbers were pretty small in the bioinformatics lab course.
I’m not sure this takes us significantly further towards managing big data and improving workflows. But I am glad someone has attempted to look at usability and effectiveness of interfaces–that has been really lacking in this field for a long time, and it’s not easy to do. Nor is it well supported. And the folks who do genome analysis aren’t often in close contact with folks who are doing visualization and human-computer interaction studies. There’s a lot of opportunity and need for new strategies to interact with huge volumes of data and visualize them. I’m thinking that whether they are horizontal or vertical in space is not the biggest issue with that, though.
Shaer, O., Strait, M., Valdes, C., Wang, H., Feng, T., Lintz, M., Ferreirae, M., Grote, C., Tempel, K. & Liu, S. (2012). The design, development, and deployment of a tabletop interface for collaborative exploration of genomic data, International Journal of Human-Computer Studies, 70 (10) 764. DOI: 10.1016/j.ijhcs.2012.05.003