Team:BU Wellesley Software/Notebook/TailiNotebook

From 2011.igem.org

Revision as of 18:44, 3 August 2011

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