GMOD Architecture Working Group GMOD Summer 2006 Prepared for Scott Cain By Eric Just.

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Presentation transcript:

GMOD Architecture Working Group GMOD Summer 2006 Prepared for Scott Cain By Eric Just

Common Elements ► ALL of the following have been immensely successful in getting us to work together  Chado  GBrowse  Apollo  GMOD applications ► Loader ► Chado::AutoDBI ► GFF3

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

Middlware Approaches ► Object-Relational Mapping  Perl: Chado::AutoDBI  Java: Tim Carver et al. ► XML Dumping/Reading/Loading (XORT) ► Object Oriented Perl/BioPerl (Modware) ► Each different approach has its strengths and weaknesses

But….. ► It’s 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

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

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?

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!!!!!!