Transcript here - Bioanalytical Sciences Group

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
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http://qbab.aber.ac.uk/s_coeli/referencegel
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Not dynamic,
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Supports one image,
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Not database based (therefore no searching),
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No accountability,
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Not easy to update,
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Not yet seriously documented,
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Future proof?
The Requirements ...
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Integrated with other Streptomyces
resources online (e.g. ScoDb),
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“Future Proofed”,
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Scalable (e.g. Support multiple gels),
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Traceable,
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Instant updates,
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Cheap / low maintenance.
The Technical Design
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Database back end (Postgres),
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Database Abstraction Layer (In PHP),
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Web based presentation layer for displaying
the information (In PHP).
The Database
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Contains entries for :
➢
Proteins,
➢
Genes,
➢
Image Gels,
➢
Users of the system,
➢
And various mapping tables.
The Database Abstraction Layer
●
●
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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
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Displays the information to the user,
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Written in PHP (rapid development?),
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Possibly customisable by the end user?
So ? What will it do for me?
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Search by protein name/information (pI, MW
etc),
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Search through images,
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Search by gene identification,
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Search by Date/Who added it/ScoDb
number....
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Linked to and from the ScoDb.
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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