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

Matthias Bussonnier bussonniermatthias at gmail.com
Fri Feb 6 13:45:19 EST 2015

Hi Sebastian

Le 6 févr. 2015 à 05:48, Sebastian Wilzbach <seb at wilzba.ch> a écrit :

> 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)

Yes this is a really good place to ask, I'll have more comment about that bellow though.

> 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.

From what I can tell, your component are mostly javascript, though I guess they could be use with non-python kernels. Hence I would suggest reaching wider like on the jupyter mailing list/google group (though it's still young) 
an directly with other kernels. 


> 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)

I think we are more or less in the same state, with a limited resource. 
We will be splitting the widget repository as a standalone project in the next few month, 
which should make contributing easier. 

> 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)

We wil be happy to help, I can't definitively  say wether or not we can have a mentor, 
but the situation have not changed a lot since the last requests we had, so I would expect a no. 

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

I'll add that to our regular meeting, to see if we think of something.


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