GMOD Architecture GMOD Architecture Working GroupWorking Group

GMOD Summer 2006GMOD Summer 2006Prepared for Scott CainPrepared for Scott Cain

ByByEric JustEric Just

Common ElementsCommon Elements

►ALL of the following have been ALL of the following have been immensely successful in getting us to immensely successful in getting us to work togetherwork together ChadoChado GBrowseGBrowse ApolloApollo GMOD applicationsGMOD applications

►LoaderLoader►Chado::AutoDBIChado::AutoDBI►GFF3GFF3

Common Middleware Layer?Common Middleware Layer?

►Would give us a common framework Would give us a common framework for developmentfor development

►Speed up developmentSpeed up development Learn one middleware, use on many Learn one middleware, use on many

projectsprojects More efficient use of timeMore efficient use of time

►Adds a do-it-yourself aspect to GMODAdds a do-it-yourself aspect to GMOD Makes extending/customizing easierMakes extending/customizing easier

Middlware ApproachesMiddlware Approaches

►Object-Relational Mapping Object-Relational Mapping Perl: Chado::AutoDBIPerl: Chado::AutoDBI Java: Tim Carver et al.Java: Tim Carver et al.

► XML Dumping/Reading/Loading (XORT)XML Dumping/Reading/Loading (XORT)►Object Oriented Perl/BioPerl (Modware)Object Oriented Perl/BioPerl (Modware)

► Each different approach has its Each different approach has its strengthsstrengths and weaknessesand weaknesses

But…..But…..

► It’s hard for people to evaluate the different It’s hard for people to evaluate the different approaches… approaches… Learning curve associated with different Learning curve associated with different

languages/platformslanguages/platforms Who has the time?Who has the time? Installation can be trickyInstallation can be tricky

►We need to decide on a development We need to decide on a development platform for GMOD appsplatform for GMOD apps

►However, AMPAP must understand the basic However, AMPAP must understand the basic idea behind each approachidea behind each approach

How To EvaluateHow To Evaluate

►Gather requirements for a ‘toy’ Gather requirements for a ‘toy’ application application

►Middleware proponents could code Middleware proponents could code solution using their middleware of solution using their middleware of choicechoice

►Next meeting, talk us through itNext meeting, talk us through it►Common problem will help compare Common problem will help compare

different approachesdifferent approaches

What are the requirements for What are the requirements for this ‘toy’ application?this ‘toy’ application?

►Simple web page showing position, Simple web page showing position, peptide sequence, and description of a peptide sequence, and description of a gene transcript gene transcript

►Simple curation page to edit some Simple curation page to edit some information about a gene?information about a gene?

►Console script to output fasta Console script to output fasta sequences of all protein coding sequences of all protein coding transcripts?transcripts?

VolunteersVolunteers

►Make static mock ups of any web page Make static mock ups of any web page or curation formor curation form

►Post on Drupal sitePost on Drupal site►After its posted, middleware to crank After its posted, middleware to crank

out codeout code

►Thanks!!!!!!Thanks!!!!!!