Plasmidb

More data can now be inserted with this release.
The interface has been tidied up in parts.
JavaScript functionality has been added for
tidying up DNA sequences. A logger was added to
catch errors. More pages were added. The requested
feature of adding directories to the path was
added. (This can now be set in app.conf). More
PDFs can be linked to data. Excel files can be
linked to ceertain data.

This version provides interface improvements, a
CSS restyle, and many framework improvements. PDF
maps can now be added easily to the list of
standard plasmids and many commercial plasmids are
included in the standard database. This is the
last major release before migrating to Ruby on
Rails.

Additional improvements to the UI have been incorporated into this release, with further linking of DB tables. Icons now allow the user to select the item of interest from one table, which selects a page on a different page. A basic SOAP interface has been written to allow the user to align sequencing data with the vector desired sequence for verification.

This release is a major redesign, simplifying some of the components released earlier, and using an Object Relational Mapper (ORM) from PHP/PEAR. Database queries are now as simple as $sequence->name = "Rpp1"; $sequence->save; Improvements in the data model allow complex components to be added or deleted, with an 'overview' page, to show which subunits are in each multi-protein complex.

Improvements in the directory hierarchy, as well as model view controller separation. More data is produced automatically from DNA coding sequences, for example protein molecular weights and extinction coefficients. Biophp has better object orientation, and now uses PHPUnit2 for automatic unit testing.