Today is the official start of coding! I have already started coding to make up time that I'll lose at the RNA Society Conference. I've added the .sto option as readable extensions into Jalview. There is already a Stockholm file parser in Jalview, but it wasn't obvious in the dialog box for opening alignment files.
I'm not quite as far as I want to be for coding, partly due to the time I spent on looking at RNA secondary structure viewers, but I think that the rest of the summer will be better for it. I am also still getting some requests from my thesis advisor for work, and I need to remind him that I have this other project going! He was very supportive of me doing GSoC, so I think he has just forgotten that coding has started.
I've talked to two other RNA biologists about the features they would like in an RNA secondary structure viewer. VARNA doesn't have all of the visualization that scientists might want, but perhaps I can add these if I have time. Thinking about how other scientists might use the secondary structure viewer has been a lesson in software development. How will the user launch VARNA? What kind of interaction will they have with it? What kind of interaction will Jalview and VARNA have?
I'm glad that most of the planning is over and I can really get into coding!