Endy:Notebook/BioBrick Studio Mobile

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(→Requirements: rough interface ideas)
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**Ability to request for the long description of a part
**Ability to request for the long description of a part
**Provide the contact information of the part engineers
**Provide the contact information of the part engineers
 +
* 12:13, 8 April 2009 (EDT): some rough] interface ideas.  The goal is to have two-levels - at the bottom is a simple, traditional strain database that considers metadata associated with organisms frozen in a freezer, possibly with plasmids in them.  The second level considers the physical implementation of 'parts' in these plasmids.  Level 1 would be fully functional (and immediately useful) without level 2.
 +
<pre>
 +
import registries
 +
 +
registry = registries.fetch('MIT')
 +
 +
recents = registry.recents() # grab recent entries, etc.
 +
 +
strain = registry.fetch('MIT_001') # the lowest level organization is in terms of strains - organisms in a freezer somewher
 +
base_genotype = strain.base_genotype  # they have genotypes, resistance markers, etc.
 +
comments = strain.usage_notes
 +
resistance_markers = strain.markers
 +
...
 +
 +
plasmids = strain.plasmids  # strains can have plasmids which also have resistance markers, origins, etc.
 +
for plasmid in plasmids:
 +
    plasmid.markers
 +
    plasmid.origin
 +
    part_BBa = plasmid.part('BBa')  # get a part embedded in the plasmid using shortcut notation
 +
    part_BBb = plasmid.part('BBb')
 +
    part_Eco_Bam = plasmid.part(('EcoRI','BamHI')) # get a specific cut of the part by specifying pairs of sites
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 +
    part = part_BBa
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    part.description  # parts have metadata associated with them
 +
    ...
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 +
...
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part1 = plasmid1.part('BBa','left') # left and right cuts of parts
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part2 = plasmid2.part('BBa','right')
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composite_part = part1.compose(part2) # create part composition
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...
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 +
</pre>
== Design ==
== Design ==

Revision as of 12:13, 8 April 2009

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Project Description/Abstract

BioBrick Studio is a software application on a mobile computing platform that:

  • Facilitates review, annotatation, design, and implemention of standard biological parts
  • Supports communication between members of the synthetic biology community and industry affiliates
  • Is a component of the BioBuilder Educational Toolset which are tools for an education and outreach project underway

Review

Synthetic Biology Software Tools

Requirements

  • Overall Application
    • Create models of the flow of the views
  • BioBrick Studio Library
    • List the "Recent" BioBrick parts
    • List the BioBrick parts by category
    • Provide a means to study the details of the features in a BioBrick Part
    • Fetch the long description
    • Support keyword search
    • In the sequence viewer, increase the size of the label based on the size of the sequence
    • Present the DNA sequence as a graphical object that can be "flicked" left and right
    • Allow for the sequences to be viewed in the portrait and landscape orientations
    • Provide a means for easily emailing the developer of the part
    • Once you select a part offer suggestions for similar parts
  • BioBrick Studio Canvas
    • Allow for changes of the individual nucleic acids
    • Pinch/Spread through the levels of abstraction
      • Levels of Abstraction
        • BioBrick Part Features (eg. Promoter, RBS, etc...)
        • Secondary Structures
        • Primary Sequence
  • Standard Biological Parts Web Service
    • Include the short description for all parts returned by the service
    • Ability to query for the number of parts in a subset (i.e. Favorites, Recents, By Type)
    • Ability to request for parts n to m in a subset (eg. Favorite parts 1 to 20)
    • Ability to request for the long description of a part
    • Provide the contact information of the part engineers
  • 12:13, 8 April 2009 (EDT): some rough] interface ideas. The goal is to have two-levels - at the bottom is a simple, traditional strain database that considers metadata associated with organisms frozen in a freezer, possibly with plasmids in them. The second level considers the physical implementation of 'parts' in these plasmids. Level 1 would be fully functional (and immediately useful) without level 2. 
import registries

registry = registries.fetch('MIT')

recents = registry.recents() # grab recent entries, etc.

strain = registry.fetch('MIT_001') # the lowest level organization is in terms of strains - organisms in a freezer somewher
base_genotype = strain.base_genotype  # they have genotypes, resistance markers, etc.
comments = strain.usage_notes
resistance_markers = strain.markers
...

plasmids = strain.plasmids   # strains can have plasmids which also have resistance markers, origins, etc.
for plasmid in plasmids:
    plasmid.markers
    plasmid.origin
    part_BBa = plasmid.part('BBa')  # get a part embedded in the plasmid using shortcut notation
    part_BBb = plasmid.part('BBb')
    part_Eco_Bam = plasmid.part(('EcoRI','BamHI')) # get a specific cut of the part by specifying pairs of sites

    part = part_BBa
    part.description  # parts have metadata associated with them
    ...

...
part1 = plasmid1.part('BBa','left') # left and right cuts of parts
part2 = plasmid2.part('BBa','right')
composite_part = part1.compose(part2) # create part composition
...

Design

  • Use a studio motif
    • Foyer - Entry point for the application
    • Library - Area to study and comment on existing BioBrick parts
      • Should also facilitate the study of non-standard DNA sequences
    • Palette - Users personal collection of BioBrick parts
    • Canvas - Design environment for the composition of new BioBrick parts
    • Services - Area to explore the availability and cost of implementation services

Implementation

  • BBa_Studio, Version 0.9.0.3 (Released on 3-17-2009)
    • Lists the "Recent" BioBrick parts (Under Construction)
    • Lists the "Favorites" BioBrick parts (Under Construction)
    • Lists the "Features" in a BioBrick Part (Under Construction)
  • BBa_Studio, Version 0.9.0.2
    • Fetches the sequence from the Registry
    • Shows the short description of a part
    • Foyer Ad Button redirects to the Safari Browser
    • "About BioBrick Studio" view under construction. It includes:
      • Version Number
      • Developers
      • Notice about the BioBrick trademark
      • License

Maintenance

Notes


Recent changes



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