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GMOD Architecture Working Group

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?.

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GMOD Architecture Working Group

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  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 • Chado::AutoDBI • 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: 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

  5. 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

  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!!!!!!

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