an integrated web based 2d-gel database for streptomyces coelicolor david goodwin (dwg@aber.ac.uk)

An Integrated Web Based 2d-gel database for Streptomyces

coelicolor

David Goodwin (dwg@aber.ac.uk)

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 :dwg@aber.ac.uk

Website :http://qbab.aber.ac.uk/s_coeli or“Streptomyces IGF” in Google