Circuitscape Design Review Presentation Team Circuitscape l Mike

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

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

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

Population Genetics Example 4

Example Continued Sneetch habitat Not sneetch habitat Sneetch samples 5

Example Continued A C B D 6

Population Genetics Example E F 7

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

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

Solution Easily Accessible & User Friendly 10

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

Architecture Overview GUI File. Reader Matrix Solver File Writer 12

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

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

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

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

Starting Screen 17

GIS Node Value File 18

GIS Points of Interest 19

Example: GIS 20

Output Resistances 21

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

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

Challenges Completed, cont. l Challenge Finding effective conductance/ resistance between two points on a grid of resistors. l 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. 24

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

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

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

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

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