Team:BU Wellesley Software/Notebook/TailiNotebook

From 2011.igem.org

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==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 [https://www.gview.ca/ 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

Revision as of 13:37, 5 July 2011

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
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