Plasmidb 0.6 review
DownloadPlasmidb project is a interface to a simple MySQL database, which itself contains information about projects in molecular biology.
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Plasmidb project is a interface to a simple MySQL database, which itself contains information about projects in molecular biology.
The focus is the data pertaining to bacterial plasmids, but also the protein sequences which are being worked on for a particular project, DNA sequences of target genes.
The database is designed to be extensible, so after learning about how the interface works, a user could add data types in SQL tables and write an interface to be able to edit it easily.
Here are some key features of "Plasmidb":
Standard cloning or expression plasmids (e.g. their antibiotic selection markers, any RNA polymerase promoters).
Database sequences you may be currently working on (their accession numbers, sequences, coding sequences).
Products you may wish to express or purify from them. e.g. His-tagged protein or RNA run-off transcripts etc.
Primers you have ordered.
Restriction enzymes.
DNA sequencing data.
Protein prep yields and data about purity.
Despite this being a work-in-progress, I have found the database to be very useful.
The database contains user and session information, so only upon logging-in, can one view and edit the database information.
What's New in This Release:
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.
Plasmidb 0.6 keywords