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DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries.
 

DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries.

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N Purswani, L. Tweedy, Z. Patel, C.Suriel-Melchor – DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries. ...

N Purswani, L. Tweedy, Z. Patel, C.Suriel-Melchor – DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries.
Biobricks are an important standard in the emerging field of synthetic biology. These standardised genetic parts are essentially lego for geneticists (or at least the ones who don’t play with actual lego). They allow for an easy, modular approach to genetic engineering and their component-like nature is a valuable starting point for the computer aided design of complete genetic systems.
Such tools rely on informatics tool and a well-kept database is vital. The current repository for biobrick information is at MIT, and has been around since the inception of the idea. As such, it contains parts of multiple standards, and the quality of their annotation is extremely variable. There is a need for alternative tools, and DASBrick, a client-server system employing the widely used Distributed Annotation System, aims to address this need.

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  • If you have a data source, you can act as a server and distribute your data to other people who might want to use it-the clients When serving DAS data you might be a client and a server at the same time, giving away data from your experiments and visualising data from other labs. A protocol is a common language/format in which annotations will be exchanged between labs.
  • -The alternative to a centralised database is a system that permits the integration of disparate data sources
  • Allignment: Can also be used to pass from two different coordinate systems, such as PDB and UniProt Types: A valid type could be codon Features: The information on features can contain size and description
  • Google allows the user to upload their apps to Google’s own servers. Whereas DAS is about distributed information, the GAE is about distributed computing power and space. By using the GAE, the user does not have to pay for or maintain their own server. GAE allocates space automatically, on the cloud, as the application grows

DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries. DASbrick: A cloud based Rich internet application for Synthetic Biology Parts Registries. Presentation Transcript

  • DASBrick The DAS Client-Server System for BioBricks
  • Background
    • Synthetic Biology
    • BioBricks
  • MIT Parts Registry
    • Main repository - 1000s of parts
  •  
  • MIT Parts Registry
    • Main repository - 1000s of parts
    • Inconsistent Annotations
      • Data entry
      • Data viewing
  •  
  •  
  • MIT Parts Registry
    • Main repository - 1000s of parts
    • Inconsistent Annotations
      • Data entry
      • Data viewing
    • Limited Search/Filter functions
    • Cannot Download Annotations
    • Centralised Database
    • Problems updating Composite BBs
  • DAS
    • Distributed Annotation System
    • Standardised format
    • Servers:
      • Reference (entry points & DNA)
      • Annotation (features)
      • URL request -> XML
    • Client
      • Multiple sources
      • Visualisation
  • What is DAS?
    • DAS is a server/client system that implements a standardised protocol for interchanging and visualising biological data
  • Why DAS?
    • Decentralisation: It eliminates the need of a central repository
      • Each lab can keep control over their own data, and can decide freely how to serve it.
      • Different data sources can be integrated without them being aware of each other
      • No need to know technicalities in order to visualise data
  • Aims
    • Server:
      • Extend DAS protocol to suit BioBrick info
      • Use cloud computing
    • Client
      • BioBrick Annotation Viewer
      • Improve on MIT Parts Registry
  •  
  • Our DAS Server
    • The server takes a request via html
    • It retrieves information from the attached database
    • It sends back this information in a standard format
    • The response can be visualised by any client
    • We wrote our own DAS client- DASBrick
  •  
  • DAS Server Requests: Entry Points Retrieves a list of genomic segments, from which annotation data will be served Sequence Returns the sequence of the segment specified Alignment Provides pairwise or multiple alignment of sequences. Features Gives a list of features contained in the segment. Types List of types of the features. Stylesheet Provides server advice on GFF on how to display the data.
  • The Google App Engine
  • How the DAS Server works in the GAE
  •  
  • DAS Client
    • Adobe Flex Builder 3
    • Flash-based vs. Javascript
    • Desktop or Web-based
    • Goals:
      • Request data – Part Loader
      • Filter – Search Function
      • Visualize – Annotation Viewer
      • Further annotate - NCBI BLAST component
  • Enter DAS Source URL Start Part List generated. Select part of interest Sequence & Feature annotations displayed. Part saved to Recently Viewed list. Blastn automatically performed on part sequence. BLAST results displayed upon return. Export Part Text file generated containing Sequence, Feature, and BLAST information. Bookmark Current Part Part saved in Bookmarked Parts list to allow for viewing in a later session. Continue to investigate more parts, enter a new DAS source, or close application to end session. User Workflow
  • Problems
  • Desktop vs Web-based
    • Problems with GAE
    • File API classes for writing files
  • Problems/Discussion
    • Server
      • Issues with GAE
      • Composite BioBrick
      • Limitations of DAS
      • (It did work!)
    • Client
      • Adobe Flex – Good choice
      • Only issue was with GAE -> Desktop
      • Primary objectives met
  • Future Work
    • Server
      • GAE developments
    • Client
      • Link GUI to Server extensions
      • Protein Annotations
      • Other Information Sources
    • Community
      • Registry & Standards