Circuitscape Design Review Presentation

1. Circuitscape Design Review Presentation Team Circuitscape Mike Schulte Sean Collins Katie Rankin Carl Reniker

2. Client: Dr. Brad McRae • Researcher in Forestry department • Works on gene flow theory • Study of how genetic information travels between animal populations • Developed resistor theory for gene flow • Used resistor theory for doctoral dissertation

3. Population Genetics • Study of flow of genetic information between demes • Demes are groups of animals • Gene flow theory • Concerned with amount of genetic flow and difference • Not concerned with the spread of specific traits

4. Population Genetics Example

5. Example Continued Sneetch habitat Not sneetch habitat Sneetch samples

6. A C B D Example Continued

7. E F Population Genetics Example

8. A B 1 A B Nm = 1 1 1 C G = 1 B A Conceptual Basis for Resistor Theory • Gene flow is increased by multiple connections and pathways • ….very much like conductance in a circuit 1 B A 1 1 C

9. Problem • Currently Coded in Matlab • Limited Distribution • Expensive • Not user friendly • Most people cannot run the program

10. Solution Easily Accessible & User Friendly

11. Spiral Model Methodology & Rationale • 4 steps • Planning • Create prototype • Submit prototype to sponsor • Redefine prototype and requirements

12. Architecture Overview GUI FileReader Matrix Solver File Writer

13. GUI Module • GUI module provides a convenient interface for the users to select options. • These options are parameters for the calculations and the names and locations of data files.

14. Reader Module • reads in ACSII text files • The module translates the data contained in the text files and passes it to the Matrix Solver module.

15. Matrix Solver Module • calculate genetic conductivity • maintains a uniform representation of the habitat generated from data from the Reader module. • the JMP library is used to solve the system of linear equations

16. Writer Module • writes the data generated by Matrix Solver module to ASCII text files

17. Starting Screen

18. GIS Node Value File

19. GIS Points of Interest

20. Example: GIS

21. Output Resistances

22. Error Handling • The GUI displays a pop-up for errors, such as: • File not found • Invalid input files • Warnings about possibly unwanted effects

23. Challenges Completed • Challenge Understanding how the simulation is supposed to model gene flow • Solution Meetings and e-mail correspondence with sponsor

24. Challenges Completed, cont. • Challenge Finding effective conductance/ resistance between two points on a grid of resistors. • Solution • Nodal analysis is applied to the grid to generate a system of linear equations. • The JMP library is used to solve this system as a sparse matrix equation.

25. Challenges Remaining • Challenge Handling very large data sets (at least 100,000 data points) without running out of memory. • Plan • Experiment with different algorithms for solving matrix. • Use and discard input values and calculated data rather than storing it in memory.

26. Challenges Remaining, cont. • Challenge Allowing the user to define the relationship between distance and conductance with an equation at runtime. • Plan Find and incorporate a free library which parses a string into an equation.

27. Completed Tasks March 10 • Find effective conductance/resistance • Find distance • Merge nodes with zero resistance March 31 • GUI • Reading from Excel and GIS files • Writing data to text files • Handling diagonal connections April 5 • Finding disconnected regions • Generating current maps

28. Remaining Tasks April 12 • Handling nonadjacent nodes defined by a function April 19 • Stress testing and optimization for memory usage • Usability Testing April 30 • Code Documentation • User Documentation

29. Conclusion • Gene flow simulations are an important tool for conservation planning and wildlife research. • There are definite areas for expansion that cannot be implemented because of time constraints.