Our first KBase API tutorial was held on the 14th and 15th of June 2012, at Argonne National Laboratory. The primary goal of the tutorial was to provide a guided tutorial through available KBase tools via the API (application programming interface). On the first day, the class entered an interactive tutorial using IRIS (interactive remote invocation service). After that, they performed an activity to annotate a mystery genome. In a matter of minutes, the group was able to examine the functional roles identified, construct a flux balance model for the newly annotated genome, and run a gap filling service on the new model.
After a review of the KBase CS (central store), the participants performed another exercise: they selected two closely related organisms, built a model for each, and looked for differences between the models that might explain known phenotypic differences.
On the second day, they conducted an activity to compute pangenomes from data in the CS. Participants downloaded a KBase DMG (disk image) with Perl libraries and executed simple Perl programs. The second half of the day was spent divided into small groups based on interest, and working closely with particular KBase team members.
The tutorial instructors included *Ross Overbeek, *Tom Brettin, *Robert Olson, *Terry Disz, and *Chris Henry. Participants included *Paramvir Dehal (LBNL), *Andreas Wilke (ANL), *FangFang Xia (UChicago), *Bruce Parrello (ANL), Gordon Pusch (ANL), Irene Ong (UW-Madison), Nick Thrower (Michigan State), Elena Vinay (UW-Madison), Matt DeJongh (Hope), Andrea Houg (Hope), Joshua Kammeraad (Hope), Shinnosuke Kondo (Hope), Nicholas Chia (Mayo), Matthew Benedict (ISB), Mike Sneddon (LBNL), Janaka Edirisinghe (ANL), and Gyorgy Babnigg (ANL).
*denotes KBase Team Member