GMOD Architecture Working Group

1
GMOD Architecture Working Group

• GMOD Summer 2006
• Prepared for Scott Cain
• By
• Eric Just

2
Common Elements

• ALL of the following have been immensely
  successful in getting us to work together
• Chado
• GBrowse
• Apollo
• GMOD applications
• Loader
• ChadoAutoDBI
• GFF3

3
Common Middleware Layer?

• Would give us a common framework for development
• Speed up development
• Learn one middleware, use on many projects
• More efficient use of time
• Adds a do-it-yourself aspect to GMOD
• Makes extending/customizing easier

4
Middlware Approaches

• Object-Relational Mapping
• Perl ChadoAutoDBI
• Java Tim Carver et al.
• XML Dumping/Reading/Loading (XORT)
• Object Oriented Perl/BioPerl (Modware)
• Each different approach has its strengths and
  weaknesses

5
But..

• Its hard for people to evaluate the different
  approaches
• Learning curve associated with different
  languages/platforms
• Who has the time?
• Installation can be tricky
• We need to decide on a development platform for
  GMOD apps
• However, AMPAP must understand the basic idea
  behind each approach

6
How To Evaluate

• Gather requirements for a toy application
• Middleware proponents could code solution using
  their middleware of choice
• Next meeting, talk us through it
• Common problem will help compare different
  approaches

7
What are the requirements for this toy
application?

• Simple web page showing position, peptide
  sequence, and description of a gene transcript
• Simple curation page to edit some information
  about a gene?
• Console script to output fasta sequences of all
  protein coding transcripts?

8
Volunteers

• Make static mock ups of any web page or curation
  form
• Post on Drupal site
• After its posted, middleware to crank out code
• Thanks!!!!!!