e-Fungi: an e-Science infrastructure
for comparative functional
genomics in fungal species
Norman Paton
The University of Manchester
Who?
• Academics
• Academics
– Norman Paton
– Nick Talbot
– Steve Oliver
– David Hoyle
– Magnus Rattray
– Brian Lings
– Simon Hubbard
• Researchers
– Mike Cornell
– Intikhab Alam
– Nedim Alpdemir
• Researchers
– Darren Soanes
– Liming Chen
Why?
?
What?
• Bioinformatics:
– Develop a data warehouse that
combines sequence and
functional data from multiple
fungi.
– Develop libraries of
bioinformatics analyses for
studying cellular processes,
pathogenicity and evolution.
• Computer Science:
– Develop techniques for
maintaining the warehouse in a
systematic manner.
– Integrate distributed analyses
with centralised warehouse
using service-based
middleware.
• Biologically:
– Conduct studies that cast light
on the evolutionary and
functional relationships
between fungal species.
– Conduct studies that focus on
pathogenicity, in particular
refining understanding of
virulence factors.
• Community:
– Make available computational
and data resources, as well as
software for wider use.
Whence?
• GIMS: Genome Information
Management System:
– http://img.cs.man.ac.uk/gims
• Phytopathogenic Fungi and
Oomycete EST Database:
– http://cogeme.ex.ac.uk
• OGSA-DQP: Service-based
distributed query processor:
– http://www.ogsadai.org.uk/dqp
Whither?
When?
• Science:
– June 2005: First written-up
study from comparative
functional genomics in
fungal species.
– October 2005: Initial
analysis library publicly
available.
• Technology:
– April 2005: First public
release of e-Fungi data
warehouse; incremental
extensions to data and
queries thereafter.
– October 2005: First webbased interface to e-Fungi
data warehouse.
– December 2005: Servicebased access to e-Fungi
data warehouse through
OGSA-DAI.