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IDEA 12: Phylogenetic Tree plugin ¶

Most of the software for visualization of phylogenetic tree is command line driven. Cytoscape's enhanced graphical abilities can be used to layout a phylogenetic tree, zoom a region, assign colors to groups of nodes and edges, generates publication-quality images. A Cytoscape plugin (PhyloTreePlugin) could become very useful tool for scientists studying phylogenetic trees. A student (GSoC 2009) already implemented some algorithms to visualize the rooted trees, this year we want to extend the plugin to support the visualization of un-rooted tree to make the plugin complete. The task includes the support of more format of phylogenetic tree and implements more algorithms for visualization of phylogenetic tree.

Language and skills: Java

Idea by: Peng Liang Wang

Potential Mentors: Peng Liang Wang, Scooter Morris, sign up here

Phylomovies: interactive animations of gene tree evolution

This project would produce a tool useful for both science and outreach, and which could ultimately become linked with the Ensembl database and be used by thousands of biologists worldwide every day.

Rationale
Evolving DNA is usually represented by static pictures, like trees, that are sometimes difficult to decipher. A movie is a more natural medium for presenting the evolutionary processes that shape the genomes of all living species. Comparative genomics databases such as Ensembl, Pfam, and HomoloGene use large amounts of data and powerful inference methods to construct highly-resolved evolutionary histories of individual gene families, including the characteristic patterns of duplication and speciation leading to the gene content observed today. However, the static nature of image-based visualizations can make the interpretation of such "gene family trees" a bit difficult.

In the same way that the Google-acquired Trendalyzer technology uses animation to clarify and expose trends in economic data, an evolutionary movie would help scientists and the public better understand the meaning and importance of evolutionary data.
Approach
The goal of this project would be to create an online widget that loads gene tree data in standard formats (XML / NHX format trees) and generates an interactive movie, allowing users to temporally navigate through the evolution of a given gene family. This would involve the design, implementation and exhibition of a novel visualization interface.

In terms of implementation, one option would be to use the PhyloWidget codebase as a starting point, although other options (such as Flash) should be considered, depending on the student's expertise. A mock-up animation of the evolution of the Tropomyosin gene can be found here. Animations relating a gene tree can also be found here [1].

Possible extensions to the tool would include the incorporation / correlation of species tree information and divergence time estimates, and exporting animations to non-interactive movie formats.
Challenges

* (medium) Identify the most appropriate libraries and tools to work with
* (hard) Define and implement a system for converting static phylogenetic trees (and associated metadata) into animations
* (medium-to-hard) Create an interface for visualizing / exploring / exporting the animations

Involved toolkits or projects

* Possible languages: Java, Flash, Javascript
* Possible toolkits / libraries: PhyloWidget, Archaeopteryx, ScripTree

Degree of difficulty and needed skills
Medium. Will require creative thinking, interface design, and solid background in a client-side browser language (Java, JavaScript or Flash).
Other topics
Any alternative proposals aimed towards improving the "accessibility" of phylogenetic trees to non-specialist audiences are encouraged. Also, alternative proposals would include implementing new methods for visualizing biological data on trees: e.g., bootstrap values / tree uncertainty, population size estimates, or uncertainty in divergence times.
Mentors
Gregory Jordan (PhyloWidget), Albert Vilella (Ensembl Compara)

Google maps-like multi-genome browsing in Jalview

Rationale
The amount of genomic data is increasing exponentially since the advent of the next generation sequencing techniques. New visualizations tools are needed to be able to compare genomic data at multiple resolutions in a natural way. One way to do this would be to adopt user interaction principles from successful multi-resolution interfaces, such as Google Maps.
Approach
Most problems with Jalview's interface become obvious when working with large alignments. An initial examination of the UI issues should first be made, and some solutions proposed to improve the user's experience when working with large alignments (and trees). These solutions should then be prototyped using a snapshot of the current Jalview 2.X codebase so their effectiveness can be assessed by expert users.
Challenges

* (easy/medium) adapting Jalview's existing multi-window visualizations implemented in AWT and Swing
* (hard) efficient multiscale rendering of very large multiple sequence alignments
* (medium/hard) solving the memory and rendering issues that arise when interactively visualizing and editing very large alignments.

Degree of difficulty and needed skills
Medium to hard. Java. Experience with either or both AWT and Swing. Some familiarity with low level file handling, or alternately, experience with handling datasets with many thousands of sequences (e.g. with Picard).
Other Topics
There are plenty of other areas to work on in Jalview - topics include AJAX and DAS (extending the JalviewLite for working with DAS annotation servers), Phylogenetic visualization (wider tree format support and better interactive visualization) and extending support for RNA (linked secondary structure visualization, alignment and analysis services). Please contact the Mentors for further information.
Mentors
Jim Procter and Albert Vilella