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 Sneetch samples Example Continued Sneetch habitat Not sneetch habitat

6 C D A B Example Continued

7 EF Population Genetics Example

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

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 FileReaderMatrix 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 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.