Projects / Plasmidb / Releases

All releases of Plasmidb

  •  20 Dec 2008 16:45
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    Release Notes: 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.

    •  29 Jun 2007 09:15
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      Release Notes: 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.

      •  07 May 2007 01:36
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        Release Notes: 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.

        •  16 Oct 2006 01:09
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          Release Notes: 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.

          •  27 Jul 2006 17:36
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            Release Notes: 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.

            •  23 May 2006 21:41
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              Release Notes: This release has more integration of DNA to protein sequences; DNAs are automatically translated to give protein sequences, and ProtParam-type information is generated from it. It has a simplified data model, more auto-calculated statistics, and improved BioPHP.

              •  23 Jan 2006 23:04
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                Release Notes: Plasmidb was meant to make interaction between biological sequences stored in the database with bioinformatics tools seamless. This release provides an idea of what the DB can and should do. In this release, molecular weights are calculated from DB protein and RNA sequences. On the Primer page, selecting each oligonucleotide produces output of the protein for which it encodes. More analyses of this type will follow.

                •  21 Oct 2005 21:46
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                  Release Notes: This release has been extended to include translation of DNA sequences, calculation of primer melting temperatures, whitespace stripping, and formatting. Other utilities include molecular weight calculation of products and a primer designer for automated cloning of multiple genes in a systematic fashion.

                  •  08 Apr 2005 06:49
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                    Release Notes: Session handling now works more reliably, but can be turned off in the configuration file. Bio::PHP support for translation of DNA->protein sequences has been started and is included in the distribution.

                    •  03 Mar 2005 12:58
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                      Release Notes: Improvements were made to the library, session management, and HTML display of links. The interface files were updated to work with the new classes.

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