an integrated web based 2d-gel database for streptomyces coelicolor david goodwin ([email protected])
TRANSCRIPT
An Integrated Web Based 2d-gel database for Streptomyces
coelicolor
David Goodwin ([email protected])
About Me....
• Software Engineer• Aberystwyth Computer Science
Graduate (2002)• Not a Biologist• Skills include Java, J2EE, PHP, Unix,
System Administration ....
The Existing Solution● http://qbab.aber.ac.uk/s_coeli/referencegel
● Not dynamic,● Supports one image,● Not database based (therefore no
searching),● No accountability,● Not easy to update,● Not yet seriously documented,● Future proof?
The Requirements ...
● Integrated with other Streptomyces resources online (e.g. ScoDb),
● “Future Proofed”,● Scalable (e.g. Support multiple gels),● Traceable,● Instant updates,● Cheap / low maintenance.
The Technical Design
● Database back end (Postgres),● Database Abstraction Layer (In PHP),● Web based presentation layer for
displaying the information (In PHP).
The Database
● Contains entries for :➢ Proteins,➢ Genes,➢ Image Gels,➢ Users of the system,➢ And various mapping tables.
The Database Abstraction Layer
● Aim – to decouple the database from the presentation layer.
● Objects used to encapsulate information from the database, which are returned to the caller.
● Removes SQL from the caller, and keeps it in one class (makes maintenance easier).
Presentation Layer
● Displays the information to the user,● Written in PHP (rapid development?),● Possibly customisable by the end user?
So ? What will it do for me?
● Search by protein name/information (pI, MW etc),
● Search through images,● Search by gene identification,● Search by Date/Who added it/ScoDb
number....● Linked to and from the ScoDb.● And more – just ask!
Some Screenshots
The Welcome Page.....
After selecting which image.. choose where on the gel you want to zoom in on ......
Zoomed in view of a 2d gel
Yellow plus signs show known proteins.These are “clickable” to give ......
Details on a fictional protein....
Note : This is still (obviously) work in progress, – therefore if there is a particular field or feature which anyone requires, please let me know.
The End.
Email :[email protected]
Website :http://qbab.aber.ac.uk/s_coeli or“Streptomyces IGF” in Google