View source for Projects:ShortProjectIdeas


===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]

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===Project title===
; Rationale :
A brief motivation of the project

; Approach :
This project would involve extending the PartitionFinder using Python to make a fully-functioning cross-platform app and GUI.

; Challenges :
What are the anticipated challenges?

; Involved toolkits or projects :
What programming languages, toolkits, libraries, etc?

; Degree of difficulty and needed skills :
An easy project might not need any previous programming skill; a difficult project needs related technical skill and likely some domain knowledge

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

; Mentors :
List the mentors, along with your preferred contact information

* [mailto:mentor1@domain.org mentor1 name]

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===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