Adaptors for chado-DBI and/or chado-XML?. GFF? GTF? BED? GAME? BSML? TIGR add BSML adaptors to BioPerl? Sequence feature apps should read/write GenBank & EMBL formats (BioPerl and BioJava handle this). 
Support a few standard external reps of data:. Schema change coordination manners: notify gmod-schema list of all proposed changes. Minor releases / tagged versions as needed by development groups, no guarantee of installable tarball. Major (or "public") release is a coordinated release of all apps, with testing. Need to track which app versions work with which schema versions. Apps are encouraged to be backward compatible with older versions of schema. 
Schema changes need extensive coordination, versioning and testing across all affected apps. Different apps should share portions of schema wherever that makes sense. Use namespaces (using PostgreSQL "create schema" or table prefixes?) corresponding to Chado modules. Establish clear naming conventions for Chado extension to avoid intermodule conflicts:. Support chado schema for genome features. What if multiple DB instances running on same site?. name=human readable, possibly ambiguous string. db=short symbolic name of datasource (MOD), used to look up conf file. lib/ - appname or shared library, Perl plugins, jar files. data/ - inputs and outputs operator writable - appname. db.conf - one for each datasource at the installation server, port, DB, login, password, banner/site-specific page config info optionally source one of these after nf according to "db" URL param (Perl: use CPAN INI parser to load). nf always source this first global site params. conf/ - all configuration files (attr/value format). sbin/ - system binaries that may do dangerous things. Prefix all executables with 2-3 letter app prefix $GMOD_HOME= /usr/local/gmod/ (default - set before installing). 
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Minimum: 20GB disk, 512 MB ram, 1.8 GHz Pentium or equiv. Recommendations based on current MODs to be determined. TomCat 4.1 (auxiliary Web server to support server-side Java/JSP).Allen, Ken to investigate effort required to port their apps to ModPerl 2.0 or CGI.With Modperl 1.3, temporarily need to migrate to Modperl 2.0 (currently broken) or CGI soon.Windows: optional as cost/benefit less favorable. The following environment variables should be set:Īny of Linux/BSD, Solaris, OSX.
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