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OpenTreeOfLife / hackathon

A repo for the 2014 OpenTree / Arbor / HIP hackathon
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Build OT access into Bio* toolboxes and other widely used platforms #3

Open arlin opened 10 years ago

arlin commented 10 years ago

An obvious step toward greater accessibility is to build access to OpenTree resources into toolboxes such as BioPerl, BioPython, BioJava, and R packages like ape. This could include some strategic prioritization of which OT services and which packages to target. It ought to include documentation and examples so that others can see how to get a Tree of Life (or parts of it, or source trees) into their favorite phylogeny analysis platform. In some cases this could be done by converting OT output from NeXson into another format, then importing using existing tools.

hlapp commented 10 years ago

:+1:

Niteloser commented 10 years ago

This idea sounds interesting. I have extended ape with some new functions back in 2011 for GSoC, so I am somewhat familiar with the package. I was thinking of maybe participating in the hackathon and helping interface OpenTree with ape. Would this be a matter of calling the OpenTree API and loading resulting trees in ape? What other functionalities might be feasible for the hackathon?

rvosa commented 10 years ago

This seems like a no-brainer, either as core to these Bio* toolkits or as plugins compatible with them (which might be publishable as simple application notes).