[IPython-dev] [GSoC 2015]: BioJS components pluggable into IPython

Sebastian Wilzbach seb at wilzba.ch
Fri Feb 6 08:48:33 EST 2015

Dear IPython developers,

(I don't know whether this mailing list is the correct place for this question - I am happy to proceed with this discussion on the appropriate place)

I am one of the developers of BioJS.
If you never heard about BioJS: It is a very young project that aims to build reusable JavaScript components for life sciences.
One of the coolest projects that we have built lately is the BioJS registry at biojs.io

So why do I write you? 

Python and IPython are very popular among Bioinformaticians (e.g. BioPython) and we would like to make our visualizations components easily accessible for IPython users.
One example is that instead of showing raw sequences in JSON or a "pre"-block, we could use an interactive multiple sequence alignment viewer.

We have started to work on a similar project for Galaxy [1] and some time ago I opened a Github issue about the IPython inclusion on the BioJS github repo [2].
Unfortunately we currently lack the resources to concentrate fully on shipping widgets to IPython.
Hence we consider to propose a GSoC project which at least partially will be about this integration.
(As 3 months even with a learning period is a long time we could wrap some other widget-related issues from IPython into this project)

So here is my question:

Is there anyone on this list interested in this project and maybe even in providing guidance as a GSoC mentor from the IPython team?
(I imagine that we would have one BioJS & one IPython mentor)

If you have a spontaneous idea or remark(s) related to this project, don't hesitate to let me know.



[1] https://github.com/biojs/biojs2galaxy
[2] https://github.com/biojs/biojs/issues/111

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