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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.