Difference between revisions of "Projects:ShortProjectIdeas"

Latest revision as of 21:21, 13 February 2014

Jalview and Archeopteryx

Rationale 

Jalview includes basic support for phylogeny, but it could do better. Archeopteryx is a powerful java based phylogeny visualization tool associated with the Forester package - but doesn't include any support for working with alignments or character matrices.

Approach 

This project would involve creating a prototype version of the Jalview Desktop that integrates Archeopteryx with Jalview's existiing alignment and PCA visualizations.

Challenges 

Understanding Jalview and Archeopteryx's datamodel and mapping them to allow data exchange. Understanding and adapting both application's GUI model to replace Jalview's existing tree viewer with an Archeopteryx window. Extending Jalview to take advantage of Archeopteryx's own analysis capabilities (e.g. taxon name analysis, etc,) and support for phylogenetic formats like phyloXML and NEXUS.

Involved toolkits or projects 

Java 1.7. Forester. Jalview.

Degree of difficulty and needed skills 

This is most likely a medium to difficult project. You will need to know how phylogenetic trees relate to multiple sequence alignments, and have the confidence to hack Java Swing Applications. There are lots of easy milestones in this project, but also some challenges - such as inferring taxon assignments with Archeopteryx's routined using the annotation Jalview retrieves from online databases.

Involved developer communities

Forester Jalview

What developer communities would be involved, and what are the primary communication channels (IRC, mailing lists, Twitter, etc)?

Mentors 

• [JimProcter|Jim Procter]
• [ChristianZmasek|Christian Zmasek]

Mind the Gaps

Rationale 

It is common practice to remove or ignore certain columns in an MSA when calculating phylogenies. However, these excluded regions are informative, since they give information about physical constraints need to support the evolving organisms, or the introduction of novel function.

This project is about exploring these 'phylogenetically uninformative' regions in the context of an inferred phylogenetic history, by creating interactive alignment/msa visualizations that allow the functional and structural variations to be explored and annotated in-depth.

Approach 

Create a prototype Jalview with a visualization mode that allows the functional and structural relationships between the evolutionarily diverse regions of sequences to be explored. At its simplest, this could be new view modes that hide or summarise the regions used to calculate robust trees, and allow the dissimilar or gapped regions to be analysed by realignment or comparison with known phenotype.

Challenges 

What are the anticipated challenges?

Involved toolkits or projects 

Java 1.7. Forester. Jalview.

Degree of difficulty and needed skills 

This is most likely a medium to difficult project. You will need to know how phylogenetic trees relate to multiple sequence alignments, and have the confidence to hack Java Swing Applications. There are lots of easy milestones in this project, but also some challenges - such as inferring taxon assignments with Archeopteryx's routines using the annotation Jalview retrieves from online databases.

Involved developer communities

Forester Jalview

What developer communities would be involved, and what are the primary communication channels (IRC, mailing lists, Twitter, etc)?

Mentors 

• [JimProcter|Jim Procter]
• Looking for a co-mentor