Jalview in 2012 and 2013

2012 was quite a year here at jalview.org. A number of long running projects finally bore fruit with the launch of our new website and logo, and the release of Jalview Version 2.8. The November release of Jalview was the first to support JABAWS 2, which was launched in December 2011, and to include RNA visualization features developed by our 2010 and 2011 Google Summer of Code students: Lauren Lui and Jan Engelhart. In July, we described these new features in a Jalview technology track talk at ISMB 2012, and also presented posters at ISMB and later on in Basel at ECCB 2012 and the Uniprot 10 symposium. We also ran a workshop in Heidelberg at VIZBI 2012 with Yann Ponty, in Tunis, at the Institut Pasteur during the LEISHDRUG Proteomics and Drug Design course, and also a two day hands-on course at the University of Edinburgh’s Wellcome Trust Centre for Cell Biology.

New people in the Jalview development community

In addition to Lauren Lui and Jan Engelhart, Jalview’s author list gained another member: Paolo di Tomasso, who added support for T-COFFEE scores. This year, we also welcomed a summer student, Anne Ménard (currently studying at Université Paris Sud), who added support for extended RNA secondary structure visualization. We also had the help of a training assistant, Saif Shehata (now a PhD student at École Polytechnique Fédérale de Lausanne), who helped update the Jalview manual for the Edinburgh 2012 training course, and tested all the training exercises with Jalview 2.7. In the last quarter of 2012, commits also started arriving from our latest community developer, Natasha Sherstnev, who’s been learning about Jalview development by adding a Stockholm format writer which allows Jalview to create alignment files that include secondary structure annotation that can be read by tools like HMMER and Infernal. Watch out for Anne and Natasha’s contributions in the Jalview development build.

Jalview’s Summer of Code in 2013

If you are a student and would like to work on Jalview as part of a summer project this year, then we’d like to hear from you. We can’t promise funding, but if you need to find a paid internship, then watch for announcements on the NESCent Phyloinformatics Summer of Code wiki page and the jalview website. Jalview has had a Google Summer of Code student every year since 2010, and we hope to participate again if the Google Summer of Code runs in 2013.

Summer of Code schemes are not just for students - it is also important to have mentors who can spare the time to come up with great projects and help students achieve their goals. If you are interested in mentoring (not just for Jalview!), then remember to keep an eye out for calls in the next few months on Twitter, Google+, and on sites like the NESCent Phyloinformatics Summer of Code wiki page and the Open Bioinformatics Foundation.

Upcoming Jalview Workshops in 2013

The Jalview EBI Tutorial and Hackathon takes place on the 21st and 22nd of January at the EMBL-EBI in Cambridge, UK. This two day event is for anyone interested in learning to use or extend Jalview, and will include talks from groups at the EMBL-EBI who use Jalview for research or on bioinformatics web sites. The two-day format means that beginners can explore Jalview at their own pace, and advanced Jalviewers have plenty of time to get together with Jalview developers to solve problems, and improve Jalview for their own needs.

Best wishes for 2013 from all at jalview.org!

UPDATE: Saif was missed out on the first version of this post, and we just closed registration for the 2013 EMBL-EBI Jalview workshop. Subscribe to the Desktop RSS feed for updates and workshop announcements!