Team:BU Wellesley Software/Notebook/TailiNotebook

From 2011.igem.org

BU-Wellesley iGEM Team: Welcome


Taili's Notebook

Contents

Week of June 3 (Bootcamp!)

  • Overview of iGEM Competition
  • Introductory crash course on Biology and Synthetic Biology
    • Summary on Tuberculosis
  • Connection between Synthetic Bio and CAD concepts (super cool)
    • Existing tools developed for Synthetic Bio
    • Digital Logic


Week of June 10 (Brainstorming via [http://www.youtube.com/watch?v=Q8uXVq2yseI G-Nome Surfer])

  • Reconsider the application of G-nome Surfer towards Synthetic Bio
    • Provide support for prokaryotes (previously only focusing on eukaryotes)
    • New visualizations for displaying circular chromosomes
    • New visualizations for BLAST results
  • Improve existing [http://www.ncbi.nlm.nih.gov/pubmed/ PubMed] access function on G-nome Surfer
    • Ability to support over 200 publication results
    • Debug HTTP request bug in code
    • Optimize method for pulling data via internet
    • Design new ways for visualizing large quantities of text-based data
  • Brainstorm Extended Desktop feature
    • co-existence of multiple layers in a way that does not hinder interaction
    • smooth animation for data transfer between layers
    • Expand existing code on feature implementation


Week of June 17 (Implementation of initial prototype)

  • Explored interactions of a wheel-like feature for navigating circular chromosome based on [http://www.youtube.com/watch?v=PM8hbKfU5iI&feature=channel_video_title paper prototype]
  • Construct functional prototype of chromosome wheel and base pair navigation using [http://www.microsoft.com/surface/softwareplatform.aspx Surface SDK]
    • Adopted interaction approach via custom user control and Affine2DManipulationProcessor events (versus the alternative of using ScatterViewItems and preexisting contact events)
    • Dynamically generated tick marks and labels on wheel according to base pair information
    • Overlay of actual gene visualization by porting GView into WPF environment
  • Continued brainstorming concepts for new publications (PubMed feature) interaction
    • Studied [http://www.geneious.com/ Geneious] software's approach to handling publications
    • Pros and cons between PubMed and Google Scholar
    • Common methods for sorting and filtering publications during research


Week of June 24 (Prep for first demo)

  • Worked out GView adaptation into G-Nome Surfer
    • Created live access to GView through terminal access and .jar execution
  • Implemented publications feature on G-Nome Surfer
    • Shuffling interaction
    • Adopted cards-in-a-box metaphor for interaction
  • Added animations to Chromosome Wheel feature
  • Integration of Chromosome Wheel and publication feature with rest of project (zooming, search menu, individual gene exploration, sequences, ontology, back-end data management, etc)


Week of July 1 (Refined direction for competition)

  • Adapted implementation of new codes using [http://msdn.microsoft.com/en-us/library/ms752347.aspx data binding] and unit testing techniques (WAY more organized code!)
  • Refractored publication feature code using new techniques
    • Implemented real-time result retrieval
    • Optimized HTML parsing code using [http://htmlagilitypack.codeplex.com/ HTML Agility Pack]
    • Reduced lag time to less than 2 seconds for over 200 results


Week of July 8 (Adopting [http://msdn.microsoft.com/en-us/magazine/dd419663.aspx Model-View-ViewModel] concept)

  • Restructured entire G-nome Surfer Pro application by using the Model-View-ViewModel concept
    • Separated all previously existing classes into Models, Views, ViewModels, and auxiliary classes
    • Merged all resource dictionaries into a common dictionary
    • Cleaned up and removed unnecessary code
  • Replaced all components of the application from various different controls into SurfaceUserControls
  • Re-wrote Publications feature using new MVVM concept
    • Applied articles-in-a-box metaphor to Publications feature
    • Implemented drag and drop interaction using the [http://msdn.microsoft.com/en-us/library/ee804812(v=surface.10).aspx DragandDropFramework]
    • Improved color scheme for Publications feature


Week of July 15 (Adding Extended Desktop feature)

  • To support better information organization and workflow efficiency, we designed an extended desktop feature, similar to a drawer/file cabinet metaphor
    • Implemented additional layer on G-nome Surfer Pro as extended desktop
    • Filtered horizontal touch manipulation for layer
    • Implemented object transferring between layer mechanism

Week of July 22 (Sequence templates, real data, error testing on system)

  • Created new style templates for Sequences and Translations
    • Text formatting, labels, color schemes
  • Enabled real data process for all features in application
  • Debugged and prepared system for first wave of usability studies

Week of July 29 (Usability Studies)

  • Modifications to system based on user input
    • Adopted white text on black background style to allow text be read in low light environments
    • Increased size of publication articles for easier manipulation
    • Fixed full abstract bug
  • Maintained system stability (no crashes during studies at all)

Week of August 5 (User Studies, sequence alignment)

  • Implemented real-time sequence snapping alignment and detachment
  • Brought G-nome Surfer Pro to Boston University's CIDAR lab for user studies
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