User:Bstpeter07
Contents
- 1 Bridget St. Peter
- 2 Week of May 18th (1)
- 3 Week of May 25th (2)
- 4 Week of June 1st (3)
- 5 Week of June 8th (4)
- 6 Week of June 15th (5)
- 7 Week of June 22nd (6)
- 8 Week of June 29th (7)
- 9 Week of July 6th (8)
- 10 Week of July 13th (9)
- 11 Week of July 19th (10)
- 12 Week of July 27th (11)
- 13 Week of August 3rd (12)
Bridget St. Peter
participating in an Research Experience for Undergraduates at Marquette University in conjunction with Anna Mohr and Alex Heaton under the supervision and guidance of Dr. Kim Factor
The following log includes tasks that have been completed and other important reserach items
Any Italized text is suggested reading for the entire group
Week of May 18th (1)
May 18th
- began research on basic aspects of Sheboygan agriculture:
- started searching for lists of dairy farms
- found information for Sheboygan County Land and Water Conservation for possible future research
Information on Permits for Dairy Farms in Sheboygan Sheboygan County Land and Water Conservation Department, Administration Bldg. 3rd Floor, Rm. 319, 508 New York Ave. Sheboygan, WI 53081. Phone (920) 459-1370 or toll-free (800) 666-3440 extension 5746.
- Information of the spread of the disease. Defra will be a very important website in further research Basic Information on the Disease
Time: 2 hours
May 19th
- began a list of possible parameters
- found information on new FMD technologies including an infrared detective device
- furhtered search for list of farms in Sheboygan county
left voicemail for (920)459.5900 mike baldwig (spelling), told he has an updated list also have number for Sheboygan Agricultural Center :920.459.1370 Manager of the Agricultural committee in Sheboygan Patrick Miles Phone: 459-1372 Email: milespem@co.sheboygan.wi.us
- began reading a report on the 2007 UK Outbreak. This includes detailed anaylsis of the outbreak and links to sources pertaining to the methods of control used.Government response to the Foot and Mouth Disease 2007 Review
Time: 5 hours
May 20th
- contacted Mike Ballweg in order to acquire a list of dairy farms and sent a follow up email to obtain list
- read reports suggested by Alex Heaton and took notes on the reports
FAO and Economic Impacts
- started to list out parameters for our research
- made a list of potential variations we can make to our own model after reading several other models
- made a list of footnotes and related articles that would be beneficial to read
Time: 4 hours
Reading from Alex's page:
- read the Keeling report;Models of FMD
1. In order to make our model unique, we have to pick out parameters that effect Sheboygan county specifically. The Interspread model gives us hope: "replication of the interspread methodology by independent research groups is feasible" that's what we needed to hear
2. we need to find more about local knowledge, I am thinking interviews and fieldtrips, honestly, they continue to highlight the importance of local ideas. Besides, sometimes the models seem too intense for farmers so I think one of our goals should be to make the model user friendly.
3. When we pick our parameters we should create some sort of alogrithm and or method as to why we are choosing them so this can be emulated for different counties or countries. This can make our model more general even though it is specific.
- read EpiMan-FMD Abstract, the full article will be necessary
Time: 2 hours
Total for 20th: 6 hours
May 21st
- met with group and talked about project options
- ACQUIRED list of dairy farms in Sheboygan county and distributed to group members
- considered ways to plot farms
Time: 1.5 hours
May 22nd
- met with Dr. Factor
- met with group to talk about research options
Time: 2 hours
May 23rd
- searched for possible dairy farm tours Grow Wisconsin Dairy Team
- read articles posted on the DEFRA website: Logistics of Testing and Response Plan for Exotic Animal Diseases
- read Dairy Cattle Health and Management Practices in the United States
- note to group:pay special attention to table 1.
- possible contact: 970.494.7000
E-mail: NAHMS@aphis.usda.gov, National Animal Health Monitoring System
Time: 2 hours
Week of May 25th (2)
May 26th
- worked with group to create outline started by Alex Heaton
- research ways to calculate latitude and longitude and a method to convert two coordinates of lat. and long. into distance
- set up excel file for lat. and long. coordinates
- finalized a dairy farm tour with A-OK Farms
- sent an email to the UW-Madison Vet Department inquiring about a possible interview
- researched Wisconsin biosecurity procedures
- created a list of other contacts to consider for biosecurity issues
- research and read different texts on graph theory
Time: 7.5 hours
May 27th
- found latitude and longitude coordinates for 1/3 of the farms
- researched animal health procedures currently used
- Animal Health Procedures
- Biosecurity Information
- pay special attention to page 2 and 3
- found PowerPoint by the Wisconsin Biosecurity Workgroup describing the disease and certain measures, will share with group
- read more Biosecurity info
Time: 5 hours
May 28th
- clarified list of factors to consider by classifying them into groups
- discussed possible next steps with entire group
Time: 3 hours
May 29th
- toured A-OK Dairy Farm
Time: 4 hours
Week of June 1st (3)
June 2nd
- discussed next steps with group
- discussed Alex's methods to determine dominating sets
- detailed goals of further research
- re-read articles to find documentation for our choosing of factors and ways to quantify these factors
- obtained books on graph theory in order to research ways to find dominating sets
Time: 4.5 hours
June 3rd and 4th
- research ways to find dominating sets
Time: 3.5 hours
June 6th
- continued reserach on dominating sets
- discussed factors of transmission with Alex
- Reading:
Time: 5 hours
June 7th
- refined algorithm for dominating set using a method that elimates vertices from a possible dominating set
- came up with another test for 'goodness': a simple approximate size of the dominating set (equations found in research)
- researched and gathered articles footnoted in Keeling
Time: 3 hours
Week of June 8th (4)
June 8th and 9th
- researched dominating set ideas
- Dominating Sets in Planar Graph: Branch-Width and Exponential Speed-Up
- read Fundamentals of Domination in Graphs
- searched for ways to determine bounds on the cardinality of dominating sets
Time: 5 hours
June 11th
- came up with two methods to prove a minimum dominating set
- researched more ways to find minimum dominating sets
- Domination in Trees: Models and Algorithms (from: Graph Theory with Applications to Algorithms and Computer Science) pg.424
- created to do list and list of problems and issues the group needs to discuss and decide upon
- discussed plans for more next steps
Time: 6 hours
June 12th
- read "A Java Library of Graph Algorithms and Optimization" found by Anna
- This book offers Java scripts that related directly to graph theory. Algorithms are given in order to achieve specific outputs like a random graph or a random spanning tree.
Time: 3.5 hours
June 13th
- typed up previous ideas for dominating sets
- working out kinks with the project:
Approximations of dominating sets will be choosen for different reasons (minimum dominating set, cardinalitly of the set choosen for limits on resources, dominating sets that are considered 'close')
- brainstormed more ideas for approximating dominating sets
Time: 5.5 hours
Week of June 15th (5)
June 16th
- brainstormed ideas for approximating dominating sets
- discussed computer programming methods with Anna
- typed up new idea for dominating sets
- refined ideas for testing dominating sets
Time: 6 hours
June 17th
- researched Keeling references for ideas on what factors to include
- refined 'JUMP' a method for minimum dominating sets
Time: 3 hours
June 18th
- discussed state of the research with group
- met with Dr. Factor
- read research on former FMD models
Attention:'Two key observations were that FMD was out of control in the UK during mid-March and that in many cases the disease was spreading locally. The importance of local spread is illustrated by data collected during the preiod when the majority of contiguous premises were being removed as part of the control effort. Even then, over half of the new cases arose within 1.5 km of a previously reported case, or within 2.5 km of a case reported in the previous 7 days. Similarly, tracing studies indicated that at least 50% of transmission took place over distances <3 km. There is no evidence that this spread was caused by aerosol transmission and, in most cases, the actual mechanism of spread remains uncertain. However, it is clear that local spread was an important factor during this epidemic
- Maybe the transmission range can be scaled down in some methods to account for this
Time: 2.5 hours
June 19th and 20th
- read through more books on graph theory to search for new possible methods
- brainstormed and created new method
Time: 4 hours
Week of June 22nd (6)
June 22nd
- typed up new method
Time: 1.5 hours
June 23rd
- revised method
- thought of ways to compare methods
- met with Alex to discuss methods
need to make powerpoint for next Thursday
Time: 6 hours
June 25th
- worked on powerpoint presentation for July 2nd
Time: 2 hours
June 26th
- came up with terms for glossary
Time: 2 hours
June 28th
- discussed methods and computer programming with group
- talked about the presentation on Thursday
- discussed the next steps for project
(Anna will continue to program our methods and debug them while Alex and I will work on comparing them)
Time: 2 hours
Week of June 29th (7)
June 29th
- met with group to continue work on presentation
- research different findings on FMD airborne transmission in order to possible create a new model graph
- Read: http://www.atmos-chem-phys-discuss.net/3/677/2003/acpd-3-677-2003-print.pdf Investigation of airborne foot-and-mouth
disease virus transmission
- started to work with Anna's program
- revised JUMP
Time: 3.5 hours
June 30th
- worked on presentation and revised methods
Time: 2 hours
July 1st
- met with group
- started to define glossary of terms
- set up computer for handling programs
- worked out some bugs on programs
Time: 5.5 hours
July 2nd
- prepared for presentation
- group presentation
- updated main REU page
- worked on comparision/output chart for JUMP
Time: 5 hours
July 3rd
- revised comparison test
- did iterations of programs to compare variables of JUMP
Time: 4 hours
Week of July 6th (8)
July 6th
- worked on comparing variables of JUMP
- iterations with all sorts of changes in variables
Time: 3 hours
July 7th
- typed up observations of JUMP variables
- suggested strengths and weaknessess of the method
Time: 3.5 hours
July 8th
- revised observations
- checked for specific variables within program
- need to check method on different types of graphs
- need to check method against different tests
- need to quantify results of variable effects"
Time: 3 hours
July 9th
- ran more JUMP programs
**seems to be no sort of regression, may point to error in program
- need more tests to quantify results, pathlength test?
Time: 2 hours
July 10th
- built adj. matrices and run test runs to test program
- discussed next steps with Anna
Time: 3.5 hours
Week of July 13th (9)
July 13th
- continued to compare jump
- looked at Anna's new programs
- brainstormed more ideas for testing methods
Time: 1.5 hours
July 14th
- searching for best possible outputs in JUMP
- still waiting on program to run JUMP thousands of times (7380)
- talked with Anna about the benefit of programming other methods
Time: 5.5
July 15th
- ran Bulk Run for OWN and created optimal graph
Time: 2 hours
July 16th
- discussed programs and methods with Alex
- ran more Bulk Runs for OWN
- provided update for Dr. Factor
- anaylzed JUMP data
Time: 6 hours
July 17th
- anaylzed JUMP data
Time: 6 hours
Week of July 19th (10)
July 19th
- jump data: fixed: CLOSENESS AND STARTING POINT (G)
- anaylzed outputs
- need to do (L)
- different fixed points
- want outputs of actual size of dominating set
- create graph of results
Time: 6.5 hours
July 20th
- anaylzed jump data
Time: 1.5 hours
July 23rd
- anaylzed jump data
- finding optimal results for inputs of dominating sets\
Time: 2.5 hours
July 24th
- found optimal results for JUMP for MinDist
- need to find for MinRandPaths
- need to compare to other methods
Time: 5 hours
July 25th JUMP MIN RANDPATH
- created graphs for JUMP results
- working on finding optimal jump lengths, don't think it has a significant difference
Time: 3 hours
Week of July 27th (11)
July 27th
- compared JUMP to OWN
Time: 3 hours
July 28th and July 29th
- write up on the JUMP method, all complete except for the RandPath results and conclusion
- compared JUMP to OWN
Time: 9.5 hours
July 30th
- edited JUMP method, edited evaluation of jump method
- typed up comparison for JUMP to OWN
Time: 6 hours
July 31st
- finished comparison for JUMP v. OWN
Time: 2 hours
Week of August 3rd (12)
August 3rd
- editted JUMP sections of paper
- wrote introduction to paper
- discussed paper with group
Time: 6 hours
August 4th
- worked on poster
- revised all portions of paper
- organized paper
Time: 8 hours
August 5th August 6th
