Garki Online:
E‐Science Cyberinfrastructure for Research Data on Malaria Transmission
Timothy Wright, David Cieslak,
Greg Madey, S M Niaz Arifin, Neil F Lobo, Ying Zhou, Frank H Collins
IWPLS – September 15, 2009
The Garki Project
• Study of epidemiology and control of malaria in Nigeria’s Garki district (1969 – 1976)
• Data obtained
– Entomological, parasitological, and seroimmunological
– Metrics regarding using of insecticide and mass drug administration
– About 40 MB (22 tables) of non‐normalized data
– Missing pieces: data sleuthing required!
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The Garki Portal
• Effort to make Garki Project data easily accessible
– Raw data
– Dynamic queries
– Explanatory content
• Basic Requirements
–
–
–
–
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Workflow/content management (CMS)
User management/collaboration
Scalability (small database/large user base)
Rapid deployment
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The Recipe
• Web Service and CMS
– Apache2
• Load balancing
• URL rewriting
– Plone
• Load balancing (ZEO [Zope Enterprise Objects] configuration)
• Workflow with revision control
– Scales well: no issues until ≈512 simultaneous users
• Web Application Framework: Django
– Agile development; enables MVC
– Object‐relational mapping
• Database: MySQL
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The Garki Portal Architecture
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Providing Information
We use the data base to answer a biologist’s question, such as:
“How do mosquito catches (NBC, PSC etc) (mosquito numbers) relate to Propoxur
spraying? Is there a fall in PSC numbers with Propoxur spraying?”
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Group pertinent
village clusters and
spray regions
Set group time period
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Garki DB Sample Query
“How do mosquito catches (NBC, PSC etc)…“
Mosquito
E‐Station
Method
…
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Garki DB Sample Query
“…relate to Propoxur spraying?”
Mosquito
Spray
E‐Station
village
Method
compound
…
…
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Garki DB Sample Query
Need to use “E‐Station” to bridge the gap
Mosquito
E‐Station
Spray
E‐Station
id
village
Method
village
…
compound
compound
…
…
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Garki DB Sample Query
E‐Station
Spray
E‐Station
id
village
Method
village
…
compound
compound
…
Mosquito
Join
…
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Garki DB Sample Query
If the collection station was exposed to spray,
we assume that the mosquito was as well.
Mosquito
Join
E‐Station
Join
Spray
E‐Station
id
village
Method
village
…
compound
compound
…
…
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Sample Web Portal Report
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Conclusions
• Project intended as first foray into portals
• Future projects
– Data Privacy
– Streaming Data
– Computation
– Community Building
• Looking for (and found at IWPLS!)
– Expertise
– Portal Technologies
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