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Circuitscape Design Review Circuitscape Design Review PresentationPresentation

Team CircuitscapeMike SchulteSean CollinsKatie RankinCarl Reniker

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Client: Dr. Brad McRaeClient: Dr. Brad McRae

Researcher in Forestry departmentWorks on gene flow theory

– Study of how genetic information travels between animal populations

Developed resistor theory for gene flowUsed resistor theory for doctoral

dissertation

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Population GeneticsPopulation 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

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Population Genetics Example

5Sneetch samples

Example Continued

Sneetch habitat

Not sneetch habitat

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C

D

A

B

Example Continued

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E F

Population Genetics Example

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….very much like conductance in a circuit

A B

C

1 1

1

A BG = 1

Nm = 1A B

1 1

1A B

C

Conceptual Basis for Resistor TheoryGene flow is increased by multiple connections and pathways

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ProblemProblem

Currently Coded in Matlab– Limited Distribution

Expensive Not user friendly Most people cannot run the program

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SolutionSolution

Easily Accessible & User Friendly

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Spiral Model Methodology & Spiral Model Methodology & RationaleRationale

4 steps– Planning– Create prototype– Submit prototype to sponsor– Redefine prototype and requirements

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Architecture OverviewArchitecture Overview

GUI

FileReader Matrix SolverFile

Writer

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GUI ModuleGUI 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.

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Reader ModuleReader Module

reads in ACSII text filesThe module translates the data contained in

the text files and passes it to the Matrix Solver module.

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Matrix Solver ModuleMatrix Solver Module

calculate genetic conductivitymaintains 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

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Writer ModuleWriter Module

writes the data generated by Matrix Solver module to ASCII text files

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Starting ScreenStarting Screen

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GIS Node Value FileGIS Node Value File

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GIS Points of InterestGIS Points of Interest

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Example: GISExample: GIS

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Output ResistancesOutput Resistances

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Error HandlingError Handling

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

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Challenges CompletedChallenges Completed

Challenge

Understanding how the simulation is supposed to model gene flow

Solution

Meetings and e-mail correspondence with sponsor

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Challenges Completed, cont.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.

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Challenges RemainingChallenges 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.

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Challenges Remaining, cont.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.

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Completed TasksCompleted TasksMarch 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 connectionsApril 5 Finding disconnected regions Generating current maps

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Remaining TasksRemaining TasksApril 12 Handling nonadjacent nodes defined by a

functionApril 19 Stress testing and optimization for memory

usage Usability TestingApril 30 Code Documentation User Documentation

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ConclusionConclusion

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.