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Circuitscape Capstone Presentation

Circuitscape Capstone Presentation. Team Circuitscape Katie Rankin Mike Schulte Carl Reniker Sean Collins. Sponsor: Dr. Brad McRae. Population genetics researcher in Forestry department Works on gene flow theory Study of how genetic information travels between animal populations

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Circuitscape Capstone Presentation

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  1. Circuitscape Capstone Presentation Team Circuitscape Katie Rankin Mike Schulte Carl Reniker Sean Collins

  2. Sponsor: Dr. Brad McRae • Population genetics researcher in Forestry department • Works on gene flow theory • Study of how genetic information travels between animal populations • Developed a new theory for gene flow • Used this theory for doctoral dissertation

  3. Population 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

  4. Gene Flow X Leopard Example • Effect of gene flow • Spots is desirable • Both populations will become spotted

  5. Dr. 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

  6. Population Genetics Example

  7. Example Continued Sneetch habitat Not sneetch habitat Sneetch samples

  8. A C B D Example Continued Could use a simple Geographic Distance Model

  9. E F Population Genetics Example

  10. A B 1 A B Nm = 1 1 1 C G = 1 B A Conceptual Basis for Dr. McRae’s Theory • Gene flow is increased by multiple connections and pathways • ….very much like conductance in a circuit 1 B A 1 1 C

  11. 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 Old v. New Implementation

  12. Our Solution

  13. Overview Of Process Resistance Matrix File Result Matrix Load into System Calculate

  14. Output

  15. Requirements • Basic • 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

  16. Architecture Overview GUI Reader Matrix Solver Writer

  17. Graphical User Interface Module • 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 Writer Reader Matrix Solver

  18. 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. GUI Writer Reader Matrix Solver

  19. Matrix Solver Module Calculate genetic conductivity • JMP library is used to solve the system of linear equation GUI Writer Reader Matrix Solver

  20. Writer Module • Writes the data generated by Matrix Solver module to ASCII text files GUI Writer Reader Matrix Solver

  21. Design Paradigm: Spiral • Four phases • Planning and risk analysis • Prototype creation • Client review • Redefinition of requirements for next phase

  22. Timeline 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 Phase 1

  23. Timeline Continued April 5 • Finding disconnected regions • Generating current maps 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 Phase 2

  24. Challenges & 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

  25. Future Work • Improving speed of effective resistance/ conductance calculations • Additional input formats • Visualization tool • Markov chain calculation • Shortest path calculation

  26. Conclusion • Gene 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.

  27. Questions? Please come to our demonstration at 1:45pm in the College of Engineering and Technology room 269.

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