Beyond the Genome: taking GigaScience into the Clouds

cloudsWith the summers conference season over, GigaScience are still keeping mobile, and this week Laurie is taking in “Beyond the Genome”, our BioMed Central stablemates Genome Biology and Genome Medicine meeting in Washington  DC.  Now in its second year, and its great line-up voted by Genome Web as one of the top-3 genomics meetings, by covering key parts of our “big-data” scope and having our editorial board members Mike Schatz and Karen Nelson on the scientific committee, it was obvious we had to attend.

Monday kicked off proceedings with the Genome Informatics pre-Meeting, excellently chaired by Mike who put together a great line-up of talks on Cloud Computing (Matt Wood from AWS, and Ben Langmead plugging his Myrna and  Crossbow tools) Lincoln Stein giving interesting and extremely “big-data” insights into the handling of the enormous ICGC datasets, reproducible workflows and Galaxy from James Taylor (a subject close to our hearts, his slides here) and a BGI perspective from our very own Yingrui Li (slides here) amongst others.

Technical Notes – call for Cloud computing tools

With Cloud computing becoming such a key tool in data-intensive science, and coming from the BGI being in the the unique position of being journal with it’s own Cloud (BGI-Cloud), today was a good opportunity to announce our call for submissions and volunteers to work with us on a new type of Cloud computing article – Technical Notes. By using BGI-Cloud as a test environment, GigaScience would like to particularly highlight tools, methods or procedures for the analysis or handling of large-scale data that are optimized to run in a cloud environment. Whilst there are already several hubs and platforms for useful cloud-based tools and workflows (CloudBioLinux being an excellent example), our series/hub hopes to combine some of the advantages of these with the visibility and quality assessment of the more traditional journal article.

By offering reviewers and editors access and free time to review and test these articles and tools in a standard environment, we hope to increase reproducibility and ease-of-testing of research, and take a first step towards what many hope will be a future of “executable articles“. To trial this we are offering initial volunteers with tools of interest the opportunity of some free time in the BGI cloud (on top of BGI’s already generous covering of the open-access article-processing charges for the journals first year), so please contact us at if you you would like to talk to us about submitting a Technical Note and associated application.

With days on Cancer, Exomes (nicely tied in with the Genome Biology special issue) and Microbiomes still to come, Beyond the Genome has already been interesting and insightful, and it will be hard to top the first day. For those not fortunate enough to attend you can follow the action on twitter with the hashtag #BtG11 or from Oliver Hofmann’s fantastic notes.

We’d like to thank Mike, Yingrui and Lincoln for the nice GigaScience mentions and plugs in their talks, and our colleagues at BMC for letting us attend.