A flurry of deadlines: Grants, GSoC, workshops, and more…

We blogged in February commenting that we had a lot of events over the March / April period. Here’s a re-cap:

  • Attending conferences: Amongst the team we attended Bioschemas, the Elixir all-hands, and the Cambridge Scientific Computation Day.
  • InterMine training: We delivered a training workshop about using InterMine at the EBI, part of their Introduction to Omics data integration week-long course.
    • This went well despite a server-room meltdown which conveniently timed itself for the morning of the same day (the training session was in the afternoon, so we thankfully had time to get the servers back up!).
    • In contrast to previous years, every single hand went up when we asked if the participants wrote code as part of their job. Next time, we will try to allow for a longer session on using InterMine web services, rather than the 15 minute slot we allocated this time!
  • Developer Workshop and Hackathon: 5 days in sunny California, spending time with InterMiners from around the world. Longer blog posts to follow, but in the meantime you can browse the agenda for links to slides from each session, or the storify summary of tweets.
  • Google Summer of Code: We’re participating in Google Summer of Code (GSoC) this year (previously) as a mentoring organisation. We had over 50 interested students and 30 distinct applications, many of which were simply brilliant. The deadline for students applying, naturally, was the day after the hackathon, making finding time to provide student feedback a challenge. Maybe there’s a reason to be grateful for jet-lag induced wakefulness at odd hours!
  • Grants: A tale of two grants… :
    • New application: We had a grant application deadline that was, once again, the day after the hackathon. Uh-oh! Feverish figure fixes, tentative typo tweaks and word-count winnowing was squeezed in at every opportunity.
    • Good news about an old application: Meanwhile, we got the news that we’d been fortunate enough to have our hard work pay off: a grant we’d applied for last year as part of the BBSRC BBR 2016 call was agreed to! Hint: the future of InterMine is looking very FAIR, possibly even SPARQLing. More details in a later post.

Events coming up soon:

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BioJS Workshop Dec 2015

After the excitement around BiVi, I’d be remiss if I didn’t discuss all the work put into both a BioJS presentation at BiVi, and BioJS Workshop in the afternoon after BiVi.

We’re already avid BioJS fans at InterMine, because BioJS provides easy plug-in visualisations (for example, cytoscape). I’d expected that a Venn diagram depicting the BioJS crowd would intersect almost perfectly with the BiVi crowd, so I was surprised to find that they were actually completely separate groups.

The difference was explained to me by Manny Corpas as follows: While BioJS,  given the (mostly) browser nature of Javascript, is indeed about visualisations – not all of it is dedicated to visual things. BioJS modules can be related to data parsing, for example.

On the other side of things, BiVi is about visualisation – no matter the language. Indeed, quite a few of the demos we saw at BiVi were desktop or server based, and unrelated to Javascript at all.

The workshop covered the basics of Javascript development, and shown how to include/interact with BioJS components on a webpage – but the most interesting sessions for me (as someone who makes a living out of writing Javascript, among other things) was definitely the session at the end where we were talked through creating our very own BioJS component.

Dennis Schwartz bravely live-coded a pie chart using d3.js on a projector – not an easy task! We started by setting up the scaffolding of the project using the BioJS Slush generator. This created examples, set up a build process, and ensured the BioJS pre-requisites were present, like licence and tags (which allows the biojs registry sniffer to pick up biojs packages from the npm registry). Despite only having an hour or so to get it all done, by the end we had each coded a functioning basic component.

The workshop finished off nicely with group pizza to feed hungry biojshackers. Unfortunately I was unable to attend the hackathon the next day, but if its quality was anything like the workshop, I’m sure it must have been a fabulous success.

 

BiVi 2015

It’s the first year someone from InterMine has attended BiVi (Biology Visualisation), which is in its second year of a (currently) three-year plan to create a community around biology visualisation.

The atmosphere was pleasantly thriving, with probably 20 or 30 attendees from Cambridge, Edinburgh, London, Oxford, and even Institut Curie in France. I think it was safe to say that most of the attendees were people with a computer science background who worked in biology-related fields, although that wasn’t a strict rule.

Two themes were particularly popular this year:

  1. 3d molecule visualisation. Multiple different talks / groups of BiVians had exciting developments to show us, from Hapitimol, a visualisation with haptic feedback, to EZMol, with an easy-to-use wizard to produce visualisations, Foldsynth, a physics based engine from Goldsmiths, MARender, a Javascript-driven biomedical imaging library, and BioBlox, which gamifies protein docking to allow crowd-sourced research.
  2. Usability. Biology is a rich, complex field. Computer people making tools for biologists need to keeps things easy to use. EZMol, mentioned above, was created due to a notable lack of simple usable 3d visualisation tools. Our upcoming InterMine 2.0 release is another push towards creating a better user experience.

One of the most impressive tools demonstrated was Zegami, a tool to annotate, view, and filter images. It may have started as a biological tool, but it’s equally functional for your holiday snaps or for sorting and filtering Netflix movies. It’s a shame we don’t really have any image data in InterMine (well, in Fly or HumanMine at least) given how cool it looked.

zegami.png
Example from zegami.com: South Australian Museum invertebrates.

A few other tools / demos of note included:

  • Reactome pathway browser, which is fully embeddable into your own web app.
  • Jalview, ‘a free program for multiple sequence alignment editing, visualisation and analysis’. The main Jalview dev is also one of the organisers of the VizBi biology vis conference, next taking place in Germany.
  • Aequatus-vis uses Ensembl web services to visualise homologous gene families.

On day 2, I gave a short talk on the future of InterMine, focusing on why we want to revamp our UI, and what we think we’re doing better in InterMine 2.0. The slides are available on Google Drive (better format) or Slideshare.