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Circuitscape Capstone PresentationCircuitscape Capstone Presentation

Team CircuitscapeKatie RankinMike SchulteCarl RenikerSean Collins

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Sponsor: Dr. Brad McRaeSponsor: Dr. Brad McRae

Population genetics researcher in Forestry department

Works on gene flow theory– Study of how genetic information travels

between animal populationsDeveloped a new theory for gene flowUsed this theory for doctoral dissertation

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Population GeneticsPopulation Genetics

Study of flow of genetic information between populations

Gene flow– The movement of genetic material between

populations of plants or animals via migration Example

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Leopard ExampleLeopard Example

•Effect of gene flow

•Spots is desirable

•Both populations will become spotted

XGene Flow

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Dr. McRae’s Theory AdvantagesDr. McRae’s Theory Advantages

Competing Models– Markov Chain Theory

Is not accurate for handle large data sets Dr. McRae’s Theory

Accurate when handling large data sets– Geographic Distance Model

Doesn’t take multiple paths into account Dr. McRae’s Theory

Multiple paths Lack of paths

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Population Genetics Example

7Sneetch samples

Example Continued

Sneetch habitat

Not sneetch habitat

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C

D

A

B

Example Continued

Could use a simple Geographic Distance Model

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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 Dr. McRae’s TheoryGene flow is increased by multiple connections and pathways

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Old v. New ImplementationOld v. New Implementation

Matlab– Expensive– Most people do not have

Matlab– Difficult to use

Java Implementation– Runs as a stand alone product– Easy to download– Rapid GUI development– Many free available libraries– Platform independent

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Our SolutionOur Solution

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Overview Of ProcessOverview Of Process

Resistance Matrix File

Load into System

Calculate

Result Matrix

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OutputOutput

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RequirementsRequirementsBasic

– Does not need special software to use– Graphical user interface– User help documentation– Calculate effective resistance / conductance – Calculate geographic distance – Input and output data with ASCII files

Advanced– Allow connections between nonadjacent nodes – Detecting disconnected nodes on the grid– Generate current maps

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Architecture OverviewArchitecture Overview

GUI

Reader Matrix Solver Writer

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Graphical User Interface Graphical User Interface ModuleModule

Graphical User Interface 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.

GUI

Reader Matrix Solver Writer

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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.

GUI

Reader Matrix Solver Writer

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Matrix Solver ModuleMatrix Solver Module

Calculate genetic conductivityJMP library is used to solve the system of

linear equation

GUI

Reader Matrix Solver Writer

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Writer ModuleWriter Module

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

GUI

Reader Matrix Solver Writer

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Design Paradigm: SpiralDesign Paradigm: Spiral

Four phases– Planning and risk

analysis– Prototype creation– Client review– Redefinition of

requirements for next phase

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TimelineTimelineMarch 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

Phase 1

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Timeline ContinuedTimeline ContinuedApril 5 Finding disconnected regions Generating current mapsApril 12 Handling nonadjacent nodes defined by a functionApril 19 Stress testing and optimization for memory usage Usability TestingApril 30 Code Documentation User Documentation

Phase 2

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Challenges & SolutionsChallenges & Solutions

Understanding how the simulation is supposed to model gene flow

Solving large system of, at least, 100,000 linear equations required for nodal analysis

Parsing equations to define non-adjacent connections

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Future WorkFuture Work

Improving speed of effective resistance/ conductance calculations

Additional input formatsVisualization toolMarkov chain calculationShortest path calculation

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ConclusionConclusionGene flow simulations are an important tool

for conservation planning and wildlife research.

Our sponsor is pleased with the useful product we have created.

There are definite areas for expansion that could not be implemented because of time constraints.

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Questions?Questions?

Please come to our demonstration at 1:45pm in the College of Engineering and

Technology room 269.