PhyloSoC:Biodiversity Conservation Algorithms and GUI

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This project is part of the 2007 Phyloinformatics Summer of Code which is part of the Google Summer of Code project. This web page will serve as the central resource for information relation to the project "Biodiversity conservation algorithms and GUI" that is being developed by Klaas Hartmann.


News

  • This page started --[Hartmann] 09:53, 8 May 2007 (EDT)

Project Overview

Klaas will implement various algorithms that utilise phylogenetic information to prioritise species for biodiversity conservation. A GUI will also be developed allowing these algorithms to be utilised by conservation managers. The overall goal is to provide a package that brings together as many existing algorithms and methods as possible and provides an interface between mathematical results and their intended final audience.

More detail at: SoC Application

Timeline of Goals

I will spend the first half of my time on the project implementing the various algorithms that have been developed in the literature. The second half of the project will be spent developing a GUI, documenting the project and developing a test suite.

Weeks < 1

  • Prior to project start an appropriate GUI development package and cross platform compilation system should have been determined

Weeks 1

  • Determine how to integrate the project with BioPerl and Bio::Phylo
  • Determine how the GUI will be developed and where this fits in with BioPerl
  • Evaluate the data structure currently used to represent trees, a more efficient data structure may be required for some algorithms

Week 2

  • Implement any species specific indices not already included in the package (eg. Quadratic Entropy -> although I think there is Perl code for this somewhere)

Week 2,3,4,5

  • Implement algorithms for solving the NAP (various greedy and dynamic programming algorithms)

Week 6

  • Finalise implementation of algorithms and check their validity.
  • Plan the GUI and do a mock up

End week 6: Mid term evaluation

  • Most of the algorithms should be completed and a plan for the GUI should be available

Weeks 7,8,9

  • Implement the GUI
  • Distribute a preliminary version to peers for comment

Week 10

  • Act on comments from peers
  • Document the project

Week 11-12

  • Develop a set of test cases and test routines for the project
  • Tie up loose ends

Beyond SoC

This work is of great interest to me and I would continue adding to this project as results become available.

Literature References

The following papers contain most of the current results regarding the NAP that this project would seek to implement:

My work:

http://www.kavenga.com/klaas/papers/HartmannSteel2006_NAP.pdf http://www.kavenga.com/klaas/papers/HartmannSteel_Chapter.pdf

Other work:

Moulton, V., Semple, C., Steel, M. Optimizing phylogenetic diversity under constraints. Journal of Theoretical Biology.

Minh, B. Q., S. Klaere, and A. von Haesler. 2006. Phylogenetic diversity within seconds. Systematic Biology in press.

Pardi, F. and N. Goldman. 2007. Resource aware taxon selection for maximising phylogenetic diversity. Systematic Biology in press.

Pardi, F. and N. Goldman. 2005. Species choice for comparative genomics: no need for cooperation. PLoS Genetics 1:e71.

Simianer, H., S.~Marti, J.~Gibson, O.~Hanotte, and J.~Rege. 2003. An approach to the optimal allocation of conservation funds to minimize loss of genetic diversity between livestock breeds. Ecological Economics 45:377--392.

Steel, M. 2005. Phylogenetic diversity and the greedy algorithm. Systematic Biology 54:527--529.

External Links

Original Proposal

Project blog

Source code