Open Source Software and IPM Decision Tools:

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Open Source Software and IPM Decision
Tools Some history advantages vs. proprietary
closed source software, and how open source
software can be used for web-based
database/GIS/decision support systems
Leonard Coop, Research Associate Entomology Dept.
and Integrated Plant Protection Center Oregon
State University
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• Software development what tools should I use?

• - Performance features/power/learning
• curve, etc.
• - Cost
• - License restrictions
• - Interoperability/Extendability
• - Support

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Unix - the basis for open source software

• - The core Unix approach non-GUI, interoperable
  toolkit of single purpose applications
• - A hypothetical example
• Web user uploads a data file for GIS/plotting
• cat rawdata.txt datafix.pl GRASS gnuplot
  pbmtogif apache
• Web user sees a map plot of data

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Open vs non-open source options

• Internet/Infrastructure
• DNS MS DNS
• TCP/IP IPX/NetBEUI (archaic)
• HTTP/HTML none
• SunOne/Java J2EE MS .net
• Server programs
• Email Sendmail MS Exchange
• Web Apache MS IIS
• File sharing Samba MS Network
• Portal system Metadot/PHPnuke,etc

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Open vs non-open source options

• Client client/server programs
• OS Linux BSD 95/98/ME/NT/2000/XP
• Web/Email Mozilla MS Outlook
• Office Suite Star/Open/K MS 95/97/2000/XP
• Photo GIMP Photoshop
• Stats R S
• Database mySQL Oracle, DBII
• Web devel perl,php,python ASP, Coldfusion
• GIS GRASS ESRI ArcInfo, ArcView

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The future of Apple Corp OS X (BSD)
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Open source options GIMP
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Searching for anything on the internet Google
(runs on 2000 Linux boxes)
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Finding open source software Freshmeat.net
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Open source options GRASS
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Managing open source projects SourceForge.net
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Open source options R
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Open Source Software What is the idea behind it?

• - Open source computing emerged from academia
• - Software development is a science - knowledge
  is shared openly, enabling evolutionary progress
• - Publishing source code (methods), brings peer
  review and accountability to the process

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1983 Richard Stallman started the Free Software
Foundation/GNU software project
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Staroffice Virtual clone of MS office version
5.2 free for Linux/Windows
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How compatible/useful is openoffice? From
slashdot.org (Feb. 24, 2002)
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Where does LINUX get its name?

• - From OSU (sort of)
• LINUX is named after its inventor Linus Torvalds,
  first developed in 1991 while a student in
  Helsinki Finland.
• He was named after Linus Pauling,
• Because he was a famous chemist, and
• was trained at OSU

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• Project Support Provided by
• USDA Western Region IPM Grants Program (1996-98,
  1999-2002)
• USDA Pest Management Centers - W. Region
  (2002-2004)
• IPPC (OSU Integrated Plant Protection Center) -
  state level IPM
• Commodity grants (Oregon Vegetable Commission,
  Oregon Essential Oil Growers League, Oregon
  Cherry Commission)

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Weather data for pest management models free or
fee?

• Weather networks

• 650 sites in OR, WA, ID, MT, WY, AK,
  W. Canada
• Agrimet, Hydromet (Bur. Reclamation)
• METAR, COOP (national weather service)
• RAWS (US Forest Service, BLM)
• Grower networks (e. g. Adcon, Automata)
• Key website at NWS-Missoula

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Online IPM Decision tools using open source
software

• - Pest Alert Systems
• - Portal System
• - Phenology Models
• - Phenology Maps
• - GIS examples with GRASSLinks
• - Decision Support Systems

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TV Pest Alert System - OSU Malheur Exp. Station
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New IPPC Pest Alert System
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New IPPC Pest Alert System - example posting
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Online IPM Decision tools using open source
software

• - Pest Alert Systems
• - Portal System
• - Phenology Models
• - Phenology Maps
• - GIS examples with GRASSLinks
• - Decision Support Systems

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IPPC/PM Centers NW Coalition Portal System -
Prototype
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IPPC/PM Centers NW Coalition Portal System -
Prototype
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IPPC/PM Centers Portal - full portal under
development
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IPPC/PM Centers Portal - login required for full
features
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IPPC/PM Centers NW Portal - "My" Portal Page
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IPPC/PM Centers NW Portal - Custom Channels plus
email/pager/ICQ notification
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IPPC/PM Centers NW Portal - Customize Layout
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Online IPM Decision tools using open source
software

• - Pest Alert Systems
• - Portal System
• - Phenology Models
• - Phenology Maps
• - GIS examples with GRASSLinks
• - Decision Support Systems

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IPPC Weather Data Degree-Days Website - since
1996
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GRASS -free open source the "Linux" of GIS
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PRISM - Parameter-elevation Regression on
Independent Slopes Model located at Oregon State
University www.ocs.orst.edu/prism
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(No Transcript)
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DD maps downscaling algorithm from 4 to 0.5
km/cell (64-fold in 2 dimensions)

• Use the GIS to calculate local 5x5 weighted
  regression equations for each cell at the coarse
  resolution (4 km), model is cumulative DD a
  b(elevation)
• Save model parameters a b as maplayers
• At the high resolution (0.5km), use model
  parameters to estimate cumulative DDs and use
  distance-weighted averages to smooth edges
• Display new downscaled maps

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Original map - 4 km resolution
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Gaussian smoothed map (based on 4 km resolution)
Middle Mountain not apparent
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Downscaled map - 0.5 km resolution
Middle Mountain apparent
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Preliminary validation of downscale
algorithmmap-predicted vs actual DDs
------------------------------------------- Data
sources correlation coefficient vs. actual
DD orig (4km) gaussian downscaled --------
----------------------------------- verification
sites (included in mapmaking) (5
locations) 0.99 0.97 0.99 validation sites
(excluded from mapmaking) (7 locations) 0.67 0
.76 0.81 ----------------------------------------
---
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IPPC Weather Data Degree-Days Website - since
1996
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IPPC Weather Data Degree-Days Website daily DD
maps
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DD maps now with downscaling - Medford region
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DD maps - Grower run network in Medford
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DD Maps - deviations from normal (up this year
150 DDs)
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Targeted DD maps Downy Brome in Hermiston,
Lygus bug in Ontario (Treasure Valley)
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IPPC Weather Data Degree-Days Website
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Online/interactive DD Mapping Calculator for
custom maps
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Online/interactive DD Mapping Calculator for
custom maps
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IPPC Weather Data Degree-Days Website
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DD difference maps Locate off-kilter weather
stations
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Single site selection for DD calculations/review
data Table mode
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Online IPM Decision tools using open source
software

• - Pest Alert Systems
• - Portal System
• - Phenology Models
• - Phenology Maps
• - GIS examples with GRASSLinks
• - Decision Support Systems

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IPPC Weather Data Degree-Days Website - since
1996
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DD calculator site selection - from GRASSLinks
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Example output - DD Calculator (checking weather
station data)
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Example output - DD Calculator (checking weather
station data)
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Selection of nearest weather station - Medford
growing region
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Other GRASSLinks options - zoom, query, advanced
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But wait, GRASSLinks license is NOT compatible
w/GRASS!
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Better to CHANGE GRASSLinks license than to
redevelop
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Result GRASSLinks license is now GRASS/GPL
compatible (uses a BSD-style do whatever you want
license)
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GRASS and many open source projects use the GPL
license
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GRASS and many open source projects use the GPL
license 1. Include free access to source code 2.
No one can deny you these rights
1.
2.
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Once again to freely develop GRASSLinks itself,
and GRASSLinks applications - IPPC page
http//ippc2.orst.edu/glinks
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Crofts Apple Mite Survey/Database
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Crofts Apple Mites - Query results and database
form
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Crofts Apple Mites - Database query results
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Crofts Apple Mites - Database query results
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GRASSLinks display request form - select
maplayers, options
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GRASSLinks display request form - select
maplayers, options
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GRASSLinks resulting map of avg. ann. daily max
temperatures
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GRASSLinks resulting map - zoom in to local
region for query
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GRASSLinks - EPA Ecoregions (under development)
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GRASSLinks - EPA Level III IV Ecoregions - PNW
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GRASSLinks - EPA Level III IV Ecoregions - NW OR
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GRASSLinks - EPA Level III IV Ecoregions - NW OR
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GRASSLinks - EPA Level III IV Ecoregions - NW OR
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GRASSLinks - EPA Level III IV Ecoregions - NW OR
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GRASSLinks Degree-Day Models
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GRASSLinks Codling moth model in Hood River
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GRASSLinks Codling moth model in Hood River
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GRASSLinks - Willamette Valley Land Use
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GRASSLinks 30 meter land use - Willamette
Valley (version developed by OSU FSL)
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GRASSLinks 30 meter land use - Willamette
Valley (zoom to Albany SE corner, query near
Hyslop farm)
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GRASSLinks 30 meter land use - Willamette
Valley (follow link to STATSGO database)
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GRASSLinks Example usage with current daily DD
maps
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GRASSLinks Example usage with current daily DD
maps
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GRASSLinks Example usage with current daily DD
maps
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GRASSLinks Example usage with current daily DD
maps
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GRASSLinks Example usage with current daily DD
maps
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Online IPM Decision tools using open source
software

• - Pest Alert Systems
• - Portal System
• - Phenology Models
• - Phenology Maps
• - GIS examples with GRASSLinks
• - Decision Support Systems

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IPM Integration via Decision Support Systems
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IPM Integration via Decision Support Systems
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IPM Integration via Decision Support Systems
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Summary of some advantages to using open source
software

• - Usually free (especially important for
  computers as commodities and embedded devices)
• - Source code included
• - Online support communities
• - Bugs and security holes promptly fixed
• - Evolutionary upgrades
• - Evolved from Unix not Dos better security
• - Interoperability

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Future Directions

• Improve GRASSLinks, host community development
• via SourceForge.net
• Continue GRASSLinks projects
• Expand sub-hourly based models and mapping
  (plant disease risk models)
• Web server/computer/networking improvements
• INTEGRATION of all online decision support
  system components Portals and dynamic information