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An Integrated Web Based 2d-gel database for Streptomyces coelicolor David Goodwin (firstname.lastname@example.org). Software Engineer Aberystwyth Computer Science Graduate (2002) Not a Biologist Skills include Java, J2EE, PHP, Unix, System Administration. About Me. The Existing Solution.
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An Integrated Web Based 2d-gel database for Streptomyces coelicolor David Goodwin (email@example.com)
Software Engineer Aberystwyth Computer Science Graduate (2002) Not a Biologist Skills include Java, J2EE, PHP, Unix, System Administration .... About Me....
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!
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 ......
Note : This is still (obviously) work in progress, – therefore if there is a particular field or feature which anyone requires, please let me know.
Email : firstname.lastname@example.org Website : http://qbab.aber.ac.uk/s_coeli or “Streptomyces IGF” in Google The End.