Team:BU Wellesley Software/Notebook/MikeyNotebook

From 2011.igem.org

BU-Wellesley iGEM Team: Welcome


Mikey's Notebook

I recently graduated from Olin College with a degree in electrical and computer engineering. I'm excited to work with Wellesley and BU this summer before starting work at Google in September.

Contents

June 3

  • Learned basics of synthetic biology
  • Learned about parallels between automated design tools in IC design and tools used in synthetic biology
  • Played around with Clotho platform

June 10

  • Worked on design for prokaryotic chromosome navigator
  • Made a short video with a [http://www.youtube.com/watch?v=PM8hbKfU5iI paper prototype]

June 17

  • Started work on implementing G-nome surfer for prokaryotes (G-nome Surfer Pro)
  • Learned about Microsoft's WPF framework
  • Read about data [http://msdn.microsoft.com/en-us/library/ms752347.aspx binding] and [http://msdn.microsoft.com/en-us/library/ms742521.aspx templating]

June 24

  • Implemented an "infinite scrolling" listbox
  • Read about model view view-model design pattern for WPF
  • Worked with Heidi, Taili, Casey, Megan, and Consuelo to implement G-nome Surfer Pro demo

July 1

  • Designed a publications view with Heidi, Taili, and Casey
  • Planned out a refactoring of the code base

July 8

  • Worked with Michelle to design an interface for Trumpet
  • Began development work on Trumpet for the microsoft surface

July 15

  • Added drag functionality for Trumpet
  • Added sequence and translation view to G-nome Surfer

July 22

We started our final push before the usability study. By this point we had refactored our code using the model view view-model (MVVM) pattern and had a couple pieces of functionality left to add. I worked on speeding up the initial rendering of the chromosome bar. The chromosome bar may contain tens of thousands of gene objects. As a result, it was important to get the rendering of the individual gene objects as fast as possible. By analyzing different methods for rendering the genes, I was able to reduce the total rendering time from fifteen minutes to thirty seconds.

We also hooked up the backend data source. This step went off without a hitch. We had previously agreed upon an interface that the data store had to follow and we used a mocked version while waiting for development to finish. When Megan finished the backend, we swapped the mock version and the real version and the application worked!

July 29

The usability study was completed without the app crashing! After the study, the lab met to discuss changes to be made to the application in preparation for testing the application at BU. Most of the changes focused around consistency. All the sequence/publication/translation views needed to look the same. There were also a couple of performance issues. Some of the longer operations, such as running BLAST, were tying up the main UI thread. We ran these operations in a separate thread and showed some sort of loading message to the users.

August 3

I've been working on writing a C# API to the registry of standard parts. I've found a couple of candidates for RESTful APIs:

  • Registry API page http://partsregistry.org/Registry_API
  • Registry DAS system http://partsregistry.org/DAS_-_Distributed_Annotation_System
  • TU Delft Parts Registry Mirror http://igempartview.appspot.com/api.jsp
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