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An Integrated Web Based 2d-gel database for Streptomyces coelicolor

An Integrated Web Based 2d-gel database for Streptomyces coelicolor David Goodwin (dwg@aber.ac.uk). 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

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  1. An Integrated Web Based 2d-gel database for Streptomyces coelicolor David Goodwin (dwg@aber.ac.uk)

  2. Software Engineer Aberystwyth Computer Science Graduate (2002) Not a Biologist Skills include Java, J2EE, PHP, Unix, System Administration .... About Me....

  3. 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?

  4. 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.

  5. The Technical Design • Database back end (Postgres), • Database Abstraction Layer (In PHP), • Web based presentation layer for displaying the information (In PHP).

  6. The Database • Contains entries for : • Proteins, • Genes, • Image Gels, • Users of the system, • And various mapping tables.

  7. 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).

  8. Presentation Layer • Displays the information to the user, • Written in PHP (rapid development?), • Possibly customisable by the end user?

  9. 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!

  10. Some Screenshots

  11. The Welcome Page.....

  12. After selecting which image.. choose where on the gel you want to zoom in on ......

  13. Zoomed in view of a 2d gel Yellow plus signs show known proteins. These are “clickable” to give ......

  14. Details on a fictional protein....

  15. Note : This is still (obviously) work in progress, – therefore if there is a particular field or feature which anyone requires, please let me know.

  16. Email : dwg@aber.ac.uk Website : http://qbab.aber.ac.uk/s_coeli or “Streptomyces IGF” in Google The End.

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