IC Bioinfs/Project1/Timeline

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For Monday First of Feb!!

Discuss steps in database design. Make sure we upload resources we need to start working on the project next week. Possible tasks:

  • Info on biobricks and the registry- Theories on how it's organized and what kind of features do we need- Requires user input (will need to re-evaluate after talking to PhD students)
    • Use the flaws of the Registry to design our entries. Focus on the implementation of the DAS server on our database. Admit that we have no idea on how to use DAS.
  • Info on existing solutions that others have come up with. Include-
    • Websites
    • Summary and features of programs
  • Info on the knowledge that we need to understand the project, upload in OWW:
    • Databases and BioSQL knowledge
    • DAS knowledge
  • Sketch of timeline- First set of aims and "deadlines":
  • Design database entries:
    • On which parts are they compatible? WHY? UNDERSTAND COMPATIBILITY
    • Composite parts: Can build one entry from others.
    • Entries in registry- pick a model- F2620? Def not imperial college igem 09!!
  • Possible parameters to include (based on F2620):
    • Name of part
    • Description
    • Performance
    • Compatibility
    • Parameters
    • Review score/No. of reviews- fix problem
    • Twins?/Similar parts!
  • DAS- Where does it come in?
    • Consider current annotation viewers- No information of the source of the genes.
    • Need to improve the viewing by adding the info fromo all the other external sources
    • Need to improve ontologies
  • TASKS:
    • Aurora- DAS
    • Luke- Things others have done. Put up link to that review.
    • Zabeen- How would BioSQL fit?/Contribute to DAS
    • Nuri- Parts registry.- Compile some more info about it.
    • ALL: Try and design possible biobrick entries and schema.
  • OTHER: