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Team:BU Wellesley Software/Notebook/HeidiNotebook
From 2011.igem.org
Heidi's Notebook
Contents |
Bootcamp with BU
Week of 5/30 Learned all the bio basics this week! Great lectures by Doug, Traci, Suma, and Swapnil. After getting a general idea of the wet lab side of our team, we have a much better idea of how to approach the rest of the summer. We outlined what each sub-team (computational team, wet lab team, and human computer interaction team) will work on and how they all fit together in our "iGEM Story."
Finishing up G-nome Surfer 2.0
Week of 6/13 Before work on G-nome Surfer Pro kicks into high gear, we're adding one more feature to G-nome Surfer 2.0--extended desktop! We'll most likely add it as a feature for G-nome Surfer Pro too, so it's good that we're getting the kinks worked out early.
Brainstorming G-nome Surfer Pro
Week of 6/13 We took what we learned at BU and started designing an effective and natural way to navigate through prokaryotic chromosomes. See your paper prototype [http://www.youtube.com/embed/PM8hbKfU5iI].
In the meantime, we're also discussing how to optimize publications to support many more publications (In G-nome Surfer 2.0, you can only see around 20 publications. We need about 200).
Wheel and Bar
Week of 6/13 Finished two versions of the functional prototype of the Chromosome wheel and hands. Discussing the advantages and disadvantages of each version. Gene visualizations using GView
Week of 6/20 Hooked up bar and wheel. Inserted faked gene data. Demonstration for BU
Publications
Week of 6/13 Research different possibilities on where to pull publications--PubMed? Geneious? Google Scholar? Talked to bio researchers about what they look for when searching for publications--Publication date? Journal?
Week of 6/20 Brainstorming new interaction/visualization for publications. After sketching several possibilities, we've decided on creating a drag and drop implementation. You will see a box with publication cards (like in a library card stack) that you can shuffle through and pull out or drag back in.
Started implementing the publications box, and successfully got shuffle interaction as well as pulling out cards that contain fake data (read from a text file). Code is starting to get sloppy...
Combined with Wheel and Bar to demo for BU
Week of 6/27 Completely scrapped the publications box we worked on last week. It was getting too hacky, and we were getting lost in the code. We're looking through MSDN's sample code for drag and drop. Worked through the PubMed html and wrote up a parser using HTMLAgilityPack.
Week of 7/4 Finished up drag and drop functionality. Finally moving on from publications!!
Extended Desktop
Week of 7/4 Started setting up the front-end for Extended Desktop. So much easier after completely restructuring the code. Data binding rocks!!
Week of 7/11 Finished up extended desktop. We had a minor glitch with collections, but now everything is standardized. All moveable items can be stored into the drawer. Also implemented backward interaction (move items back to the main after having thrown them into extended)
Sequences and Translations
Week of 7/11 Spruced up the front-end, adding labels to all components so you can always reference what gene it corresponds to. Basically we just data template-ed everything.
Week of 7/25 Added spacing to sequences and translations to chunk them and make them easier to read. Wrote up code to align them (top turns transparent so you can compare them side by side). Next thing on our to do list is to make them scroll together.
User Studies
Week of 7/25 No crashes!!! HOORAY! Took notes on a few minor fixes to implement. Very organized and successful overall :)
