Progress 06/01/07 to 05/31/12
Outputs
OUTPUTS: During the period of the project 6/1/07 - 5/31/12, Purdue University has provided the infrastructure, maintenance, and enhancements to the NPDN National Repository which contains the diagnostic lab records from the land grant universities, state departments of agriculture, and a couple of industry sources. Combined, over 476,000 sample lab records have been entered which contain 7,841 unique pests/pathogens, 2,879 unique hosts, 3,070 unique counties, and 150 unique diagnostic labs. The pest and host lists over this 5 year period have had respectively, (2,056,838) additions, (7,454,921) modifications, and (659,14) deletions. Features or enhancements in 2011 have been made which allow for the entry of nematode data as well as modifications to identify and report on lab sample data which comes from the ipmPIPE plot source or the sentinel plant network public gardens. The NPDN portals are a means to communicate meeting minutes and documents to stakeholders and provide a public outreach via the national and regional portals. The original portal was a custom built system which became very resource intensive. The challenges for the NPDN IT staff were to reduce the resources required and provide the necessary functionality for the content managers. After gathering user and system requirements, an open source content management system was chosen and implemented with the first release in December 2009 for the national portal, the WPDN released in September 2010, the NCPDN, NEPDN and SPDN released in December 2010, and the GPDN released in May 2012. Two main reports, the pest category report, and the pest/host index report were released in 2010. The direct data entry upload form via website and the first submission by State E-Mail report features were released in 2009. In 2008, the Phase 2 fields were added and it system documentation was created. With all of these improvements 39 new user accounts with regional access privileges were added in 2012 as directed by the Executive Committee, resulting in more use of this robust collection of information. PARTICIPANTS: Eileen Luke, the PI of the project, is the director of the Center for Environmental and Regulatory information Systems (CERIS), a recognized center at Purdue University. Ms. Luke has managed the IT responsibilities of the NPDN at Purdue and all associated administrative efforts. Michael Hill is the NPDN Project Manager/Systems Analyst and the lead person on all software and web development for the NPDN National Repository and the portals. Mr. Hill received the CISSP (Certified Information Systems Security professional certification. Preston Wiley, also possessing the CISSP certification, provided the network and systems support. Dr. Virginia Russell, Ph.d in Biology, provided the subject matter expertise in the taxonomy of the pests and hosts while working with the NPDN database committee. The Purdue staff have attended and made presentations at the NPDN regional meetings in order to obtain feedback and build better communication and collaboration between the diagnosticians and IT staff. Collaborations and participations at other meetings such as the National Plant Board, APS, and ESA took place during the duration of this project. TARGET AUDIENCES: The diagnosticians of the LGU's and state departments of agriculture are the primary target audience. With the several years of data collection, a data sharing policy has been implemented, and non-sensitive data has been sent to researchers and epidemiologists. In addition key management staff of both NIFA and APHIS, receive the first in state alerts when a pest or pathogen is first reported to the NPDN National Repository. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
One very significant impact has been the efforts of the National program Area Committee in the review and standardization of the pest and host lists. The CAPS (Cooperative Agricultural Pest Survey) program uses the same standardized pest and host lists and these lists allow for potential linkages of information to other agencies and their systems. The Data Sharing Policy has put into practice for all diagnosticians as designated by the Executive Director in their region access to all regional data in the National Repository, as well as the associated first in state reports for their respective region. This helps to improve both the quality and validity of the data by adding additional review and the opportunity for the regional directors to verify critical data at the diagnostic lab level. In addition, key USDA Program leaders in NIFA and APHIS have received the first in state data notifications at the national level. These reports are pro-actively distributed not requiring the diagnosticians to take the initiative for access and provide a means to assist in earlier detection. The reports and features provided a pro-active means to better inform the diagnosticians and to then provide faster feedback in data quality and validity. The software and NPDN National Information Repository along with the IT/diagnosticians meeting in 2007, 2008, 2009, and 2010 have created a collaborative and engaging environment between the diagnosticians and the NPDN IT staff.
Publications
- Contributions on IT subjects related to the use of the repository, enhanced features, and IT security tips have been made to the NPDN monthly newsletter can be found on the url - http://www.npdn.org. - 2012, 2011, 2010, 2009, 2008, and 2007. IT Committee reports have been posted on the national web site indicating progress and significant decision and outcomes from the IT/Diagnosticians meeting. An IT Committee poster was presented at the NPDN National meeting December 2009.
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Progress 06/01/10 to 05/31/11
Outputs
OUTPUTS: During the period 6/1/10 - 5/31/11, Purdue University has continued to provide the infrastructure, operations, and enhancements to the NPDN National Repository. There were 128,496 diagnostic lab records processed as compared to 118,810 last year indicating a slight increase of data available. The 128,496 records had contributions from 130 labs representing the 50 states, District of Columbia, American Samoa, Northern Mariana Islands, and Puerto Rico. In addition, 11,959 records came from industry. Efforts continued with the review of the NPDN Master pest and host lists by the NPDN database committee. There were 409 additions, 1600 modifications, and 140 deletions to the NPDN Master Pest dictionary and 108 additions, 31 modifications, and 2 deletions to the NPDN master host dictionary. The Pest/Host Index Report was put into production in December 2010 providing confirmed pests/pathogens and the hosts they have been found on. Purdue has continued the expansion of the portal development with the implementation of the SPDN site in September 2010, and the NCPDN, the NEPDN, and the SPDN sites in December 2010. All four sites use Drupal the open source content management system. Purdue provides all backups, system and software upgrades, hardware and software operations, and enhancements for the national and 4 regional portals indicated. Under the direction of the NPDN Executive Committee, Purdue has set up a means to share requested non-sensitive information from the national Repository for research and epidemiological purposes. A secure section of the national web site is set up for the Executive team to review all requests that have been processed where exact data shared, with whom, and when are all listed. The degree day data, supplied by Oregon State University, has continued to be integrated with National Repository software, providing overlaid maps of occurrence and weather data. PARTICIPANTS: Eileen Luke, the PI of the project, is the director for the Center for Environmental and Regulatory Information Systems (CERIS) at Purdue University. Ms. Luke has managed the project allocating all IT resources and personnel, writing the work plans, serving as the database administrator, and handling all financial management. Michael Hill is the NPDN Project Manager/Systems Analyst and the lead person on all software and web development for the NPDN National Repository. Mr. Hill has received the CISSP (Certified Information Systems Security Professional) certification. Preston Wiley, the Network Security Manager at CERIS, provides network and systems support to the NPDN project. Mr. Wiley also earned the CISSP certification. Dr. Virginia Russell, NAPIS User Services Administrator, has a Ph.D. in biology and provides the subject matter expertise in the taxonomy of the pests and hosts. She has the lead role in reviewing and managing the pest and host lists. The pest and host lists are used by the CAPS(Cooperative Agricultural Pest Survey) program. In addition, Purdue University has utilized the expertise of graduate assistants in computer and electrical engineering with 1/2 time assistantships. Purdue has partnered with Oregon State University in the mapping and epidemiology effort with Dr. Len Coop as the lead scientist. Also, the nature of the NPDN requires contact and collaborations with the five other regional centers and their respective directors, diagnosticians, and associate directors as well as the major committees. The Purdue staff have made presentations at the regional meetings and obtained feedback from the diagnosticians to direct the national IT effort. Collaborations and participation at meetings with the NPDN regions, the CAPS program, the National Plant Board, and APS took place throughout the year. TARGET AUDIENCES: The NPDN National Repository is for the diagnosticians of the network and with the several years collection of the data being very robust is intended to expand to researchers and epidemiologists. Purdue University works closely with the diagnosticians hosting a collaborative IT/Diagnosticians meeting which was held in October 2010 to ensure that the IT goals are in sync with diagnostic objectives. Security awareness and education are a critical component to ensure a secure system and these topics are presented through the newsletter and regional NPDN meetings. A presentation was given at the National Plant Board indicating the security of the information of the National Repository and the desire to share the non-sensitive information for furthering research and epidemiological efforts. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The efforts of the NPDN National Repository have created a more robust collection of diagnostic lab data sparking interest by researchers and reporting data on a daily basis to the regional hubs of first occurrences of a pest/pathogen in a state. This delivers a data quality check as well as a pro-active alert to assist in earlier detection of pest/pathogen anomalies. The Pest/Host index report has become a very useful tool for all of those accessing the National Repository by providing a searchable feature of all confirmed pests/pathogens that have been reported in the National Repository allowing the diagnosticians a quick assessment of a 'new' pest/pathogen confirmed in their lab. Working to expand data collection, the direct upload feature is supported allowing labs another option to contribute to the National Repository. The continued standardization of the pest and host tables has created a useful working list for the diagnosticians and is used by the CAPS (Cooperative Agricultural Pest Survey) program demonstrating shared collaborations between USDA agencies. The NPDN National Web Portal is a significant tool for disseminating information to the diagnosticians and their associated partners and customers. Role based access allows for the sharing of 'sensitive information among those who need to know'. The average monthly hits for the National Web Site for January 1, 2010 - May 2010 was 48,440 and for January 1, 2011 - May 2011 was 120,287 indicating a 2.5 time increase in just a year's time. Overall, for June 1, 2010 - May 31, 2011 the average number of monthly hits was 78,638.
Publications
- Contributions on IT subjects to the NPDN monthly newsletter particularly on security tips can be found on the url - http://www.npdn.org. The dates include all months from June 2010 - May 2011 with the exception of November 2010. Also, training schedules and usefull tips on the use of the reports and queries are covered in the newsletter. The IT Committee reports have been posted on the national web site as well indicating progress and significant decisions and outcomes from the IT/Diagnostcians meeting.
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Progress 06/01/09 to 05/31/10
Outputs
OUTPUTS: During the period 6/1/09 - 5/31/10, Purdue University has continued to provide the infrastructure, maintenance, and enhancements to the NPDN National Repository. The First Submission by State Report feature was added which indicates the first time a pest/pathogen has been reported to NPDN for a particular state. Mailing lists were created for the regional directors and National Program Leaders so that they are receiving this report on a daily basis providing a pro-active effort. A new access level was developed and implemented for all data in a state that allows access for the SPRO's or their designee. Also, the Pest Category Report has been added to make it easier for the diagnosticians to complete their accomplishment summary reports. There were 118,810 diagnostic lab records processed as compared to 106,250 last year indicating an increased volume of diagnostic lab data available. Efforts have continued with the review of the NPDN Master pest and host lists by the NPDN database committee. There were 397 additions, 2,322 modifications, and 318 deletions to the NPDN Master Pest dictionary and 168 additions, 783 modifications and 1 deletion to the NPDN Master Host dictionary. Other highlights of the software changes included - 1.Version 3.0 of Phase 2 XML Schema implementation 2. enhancement of the keyword search feature for the Diagnostic Lab dictionary 3. upgrade of NPDN mapping server 4. update of Diagnostic lab Report for 2010 and 5. update of Regional Report by Enter Date and Sample Date for 2010. Purdue University assumed the responsibility for the development of the national and regional web portals. This included but was not limited to the use of Drupal, an open source content management system, joint conference calls with the IT and Web committees, webinar training for new editors, and security audits on portal development conducted by CERIAS staff. The new NPDN National Web Portal was successfully moved into production on November 30, 2009. PARTICIPANTS: Eileen Luke, the PI of the project, is the director for the Center for Environmental and Regulatory Information Systems (CERIS) at Purdue University. Ms. Luke has managed the project allocating all IT resources and personnel, writing the work plans, serving as the database administrator, and handling all financial management. Michael Hill is the NPDN Project Manager/Systems Analyst and the lead person on all software and web development for the NPDN Natioanl Repository. Mr. Hill has received the CISSP (Certified Information Systems Security Professional) certification. Preston Wiley, the Network Security Manager at CERIS, provides network and systems support to the NPDN project. Mr. Wiley also earned the CISSP certification. Dr. Virginia Russell, NAPIS User Services Administraotr, has a Ph.D. in biology and provides the subject matter expertise in the taxonomy of the pests and hosts. She has the lead role in reviewing and managing the pest and host lists. The pest and host lists are used by the CAPS(Cooperative Agrucultural Pest Survey) program. Keith Watson, CERIAS (Center for Education and Resesarch in Information and Assurance Security) research engineer, has provided guidance and expertise in the security assessment of the entire NPDN network. In additon, Purdue University has utilized the expertise of graduate assistants in computer and electrical engineering with 1/2 time assistantships. Purdue has partnered with Oregon State University in the mapping and epidemiology effort with Dr. Len Coop as the lead scientist. Also, the nature of the NPDN requires contact and collaborations with the five other regional centers and their respective directors, diagnosticians, and associate directors as well as the major committees. The Purdue staff have made presentations and posters at the various regional and national NPDN meetings. TARGET AUDIENCES: The NPDN National Repository is for the diagnosticians of the network and thus Purdue University works closely with them hosting a collaborative IT/Diagnosticians meeting once a year to ensure that the IT goals are in sync with diagnostic objectives. Security awareness and education are a critical component to ensure a secure system. Security issues are often presented at the regional NPDN meetings. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The NPDN National Web Portal is a significant tool for disseminating information to the diagnosticians and their associated partners and customers. Use of a content management system allows for more efficient and less resource intensive management. The efforts in the NPDN National Repository have created a more robust collection of diagnostic lab data sparking interest and providing data on a daily basis to the regional hubs. The continued standardization of the Pest and Host tables has created a useful working list for the diagnosticians and will allow for potential linkages of information to other agencies and their systems provided the effort is in compliance with the NPDN Data Sharing policy. In addition, the CAPS (Cooperative Agricultural Pest Survey) program uses the same standardized pest and host lists.
Publications
- Contributions on IT subjects to the NPDN monthly newsletter which can be found on the url - http://www.npdn.org. The dates include July 2009, September 2009, November 2009, March 2010, April 2010, and May 2010. IT Committee poster for the NPDN National meeting in December 2009.
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Progress 06/01/08 to 05/31/09
Outputs
OUTPUTS: During the period 6/1/08 - 5/31/09, Purdue University has continued to provide current maps and reports as requested by the SPDN in support of the online training system developed at the University of Florida. Training maps were provided indicating the states and counties where first detector training was provided as well as categories indicating the amount of training. IT Security has been a continuous maintenance activity requiring daily review of security and audit logs. The servers for scanning network vulnerabilities have been reviewed to prevent problems by addressing issues in a proactive manner. Purdue hosted a secure programming course conducted by CERIAS (Center for Education and Research in Information Assurance Security) on July 1-2, 2008. Major items covered in the class included: applied secure software engineering, secure coding,technologies and subsystems, and attacks. There were 106,520 diagnostic lab records processed. Phase 2 was implemented in production at Purdue on May 5, 2008 for the national level. The changes to support Phase 2 required adding 24 additional fields to the National Database. In Phase 2, six of the fields also allow multiple values to be sent. Overall, this represents a significant amount of changes to the current databases at both the national and regional levels. A new online data entry form that allows users to directly upload a sample to the National Repository website was developed. The concept of the form was demonstrated at the IT/Diagnostician's meeting in November and has been updated to fully support all Phase 1 and Phase 2 fields. An XML schema was created for the Phase 2 upload. A group of beta testers were formed and the software was released in March 2009. With over 16,000 pests or pathogens in the NPDN Master Pest list, naming conventions have consumed a great deal of effort. The list has continued to be a 'work in progress' with the National Database Committee doing significant reviews of groups of pests. During the period, there were 494 additions, 141 deletions, and 1,718 modifications to the NPDN Master Pest dictionary. There were 224 additions, 7 deletions, and 39 modifications to the NPDN Master Host dictionary. The NPDN data maps can be overlaid with degree day data that is available from OSU on a realtime basis. At present, there are four thresholds (32, 41, 45, and 50) for each degree day available. The maps are now in production and the Epidemiology Committee members and those who have received the 45 minute training session can dynamically search data they have permission to view and create the various layered maps. PARTICIPANTS: Eileen Luke, the PI of the project, is the director for the Center for Environmental and Regulatory Information Systems (CERIS)at Purdue University. Ms. Luke has managed the project allocating all IT resources and personnel, writing the work plans, serving as the database administrator, and responsible for all financial management. Michael Hill is the programmer/analyst and the lead person on all software and web development for the NPDN National Repository. Mr. Hill has received the CISSP (Certified Information Systems Security Professional) certification. Preston Wiley, the Network Services Specialist at CERIS, provides network and systems support to the NDPN project. Mr. wiley also also earned the CISSP certification. Virginia Russell, NAPIS User Services Administrator, has a Ph.D in biology and provides the subject matter expertise in the taxonomy of the pests and hosts. She has the lead role in reviewing and managing the pest and host lists. Ketih Watson, CERIAS (Center for Education and Research in Information and assurance Security) research engineer, has provided guidance and expertise in the security asessment of the entire NPDN network. In addition, Purdue University has utilized the expertise of graduate assistants in computer and electrical engineering with 1/2 time assistantships. Purdue has partnered with Oregon State University in the mapping and epidemiology effort with Len Coop as the lead scientist. Also, the nature of the NPDN requires contact and collaborations with the other 5 regional centers and their respective directors, diagnosticians, and associate directors as well as the major committees. The Purdue staff have made presentations and posters at the various regional and national NPDN meetings. TARGET AUDIENCES: The NPDN National repository is for the diagnosticians and so Purdue University works closely with them hosting a collaborative IT/Diagnosticians meeting once a year to ensure that the IT goals are in sync with the diagnostic objectives. Security awareness and education are a critical component to ensure a secure system. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The addition of the Phase 2 fields adds more symptomatic data to the national repository which will aid in better epidemiological studies. The direct upload software allows participation from other labs, not necessarily funded by NPDN, and builds a more robust collection of diagnostic lab data. The XML schema that was developed for PHASE 2 provides easy transfer of data across multiple platforms. The standardization of the Pest and Host tables has created a useful working list for the diagnosticians and generated other interest from such groups as the USFS. The mapping tools and software developed at Purdue provide the capability to link NPDN data with weather data and pest risk models developed at Oregon State University which can help detect anomalies of potential bio-security threats and aid extension agents in pest management decisions.
Publications
- Contributions on IT subjects to the NPDN monthly newsletter which can be found on the url - http://www.npdn.org.. The dates include May 2009, april 2009, January 2009, November 2008, and September 2008.
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Progress 06/01/07 to 05/31/08
Outputs
OUTPUTS: Since June 1, 2007, the NPDN National Repository has been in operation with a continued increase in sample data from the diagnostic labs. Of the fifty states, with the exception of Alaska, a diagnostic lab from each state has reported data to the NPDN, as well as Guam and Puerto Rico. In 2007, there was a 50% increase in sample data reported overall as compared to 2006. (84,399 reported in 2006, 125,025 in 2007) Although not noticed by the users, security and INFOSEC matters have continued to be addressed and reviewed with the assistance of CERIAS (Center for Education and Research in Information Assurance and Security) under the leadership of Keith Watson, senior research engineer. In addition to the overall improvement in data reported, there have been significant accomplishments in the development of both the reporting and epidemiology tools. Phase 2 efforts have been a major effort with the other regions and the software has been implemented in production for the National Repository. Phase 2 data contains additional symptomatic data which can aid in determining anomalies for epidemiology studies. Over 44 diagnosticians have been trained on the use of the mapping tools available for use in viewing their own lab data. Work has continued with the standardization of the NPDN Master Pest list and it is to be noted that this same list is shared and used by the NAPIS (National Agricultural Pest Information System) project. The major governance activities for the NPDN have been the participation at various regional meetings, operations meetings, and the management of the IT/Diagnosticians/Epidemiologists meeting held in November 2007 in St. Louis with Dr. Mark Stillwell as the facilitator. PARTICIPANTS: The main staff who worked on this project at Purdue University included Mike Hill, Eileen Luke, Virginia Russell, Preston Wiley, and Keith Watson. CERIAS (Center for Education and Research in Information and Assurance Security)has provided significant leadership and consultation in the NPDN project. TARGET AUDIENCES: The target audience of the NPDN National Repository are the NPDN National Program Leaders, the NPDN Regional Directors, and the Diagnosticians associated with the NPDN who have a user account. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
During this past year working cooperatively with the SPDN, Purdue was able to select data from the SPDN training system to generate the requested maps. This was part of the general national database support that Purdue provides. Examples of maps which were generated included 'First Detector Training by county for August 2003 - April 2008' and 'All Types of NPDN training by state for August 2003 - April 2008'. Summary tables and reports can be generated dynamically by the regional diagnosticians to review and report their region's findings and efforts. The new released information security and awareness web site was made available to the NPDN users. It covers the general categories of operational, system, and physical security and is specifically designed to make the diagnosticians more aware of IT security and how to respond should something appear out of the ordinary. The Pest dictionary was enhanced by capturing more details related to updates so that a complete history of modifications is archived. This effort was motivated by the efforts of the National Database Committee in their review and revisions of this list. The regional centers and national database have concentrated very heavily on Phase 2 developments since the beginning of 2008 and the main focus was the development of a standardized schema. The software for the upload to the National Repository was recently put into production on May 5, 2008. To improve communication and manage the complexity of the Phase 2 fields, the IT committee decided to create one overall common schema that the regions and national database could share for data uploading. Many additional reference lists were created for supporting Phase 2. The advantage in using published lists is the assurance of data quality for the Phase 2 fields being uploaded. Maintenance of these data lists will be managed by CERIS and will be available for download at where the current published lists are kept. The process for adding items to these lists will include sending an e-mail request to npdncodes@ceris.purdue.edu. A new method for downloading these files was created at CERIS that allows these xml lists to be generated dynamically on demand. The capability to save reports or dictionary outputs in Excel format was added. Previous reports could only be saved in a comma delimited format which did not provide formatting. By being able to save in Excel format the user can save a report to their local computer which reflects similar formatting to the web page they are viewing. The software to transfer NPDN legume virus data to ipmPIPE was developed and implemented in June 2007. The software changes included adding three new fields to handle the recording of diagnostic incidence. After receiving the formal approval to share legume virus date with ipmPIPE the data transfer software went into production on July 18, 2007 during the regularly scheduled 10:00am data transfer. Epidemiology maps with degree days were released to users who had the brief online training session. This has allowed the diagnosticians now to view their own lab data with the mapping and epidemiology tools provided.
Publications
- No publications reported this period
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