[IPython-dev] Announcement: Galaxy IPython Integration - interactive programming in Galaxy

Kyle Kelley rgbkrk at gmail.com
Sat Aug 2 11:23:16 EDT 2014


Thanks for sharing. I went ahead and created a Galaxy account. What's the
simplest path for trying out the IPython notebook integration within Galaxy?

-- Kyle

On Sat, Aug 2, 2014 at 1:03 AM, Björn Grüning <bjoern.gruening at gmail.com>

> Hi all,
> we proudly present the first release of the Galaxy IPython project.
> Galaxy IPython is a visualization plugin which should enable Galaxy
> users with coding skills to easily process their data in the most
> flexible way. With this plugin, it is possible to analyse and
> post-process data without downloading datasets or entire histories. One
> of our aims was to make Galaxy more attractive and accessible to
> bioinformaticians and programmers, and we hope that this project will
> build some bridges.
> More information about Galaxy: http://galaxyproject.org/
> Screencast: http://www.youtube.com/watch?v=jQDyTuYnn1k
> Disclaimer: Even though the Ipython notebooks can be stored and reused,
> this plugin will break the Galaxy philosophy of reproducibility, I feel
> personally bad about that, but I also think it is a great opportunity to
> get more bioinformaticians into Galaxy, and to get Galaxy used more
> often as a teaching resource. By being able to teach not only about
> workflows but also about data analysis tasks often necessary with
> Bioinformatics, Galaxy will be significantly more useful in teaching
> environments.
> A few features we have up and running:
> * Use IPython directly in the main window or in the Scratchbook
> * Completely encapsulated IPython environment with matplotlib,
> biopython, pandas and friends already installed.
> * IPython runs completely self-contained within a docker container,
> separate from your Galaxy data
> * Easy access to datasets from your current history via pre-defined
> IPython functions
> * Manipulate and plot data as you like and export your new files back
> into your Galaxy history
> * Save IPython Notebooks across analysis sessions in your Galaxy history
> with the click of a button.
> * View saved IPython Notebooks directly in HTML format, or re-open them
> to continue your analysis.
> * Self-closing and self-cleaning IPython docker container
> Notebooks are secure, only accessible to the intended user
> Please follow the installation instruction on our project page under:
> https://github.com/bgruening/galaxy-ipython
> The underlying IPython Notebook (+Galaxy sugar) is stored under:
> https://github.com/bgruening/docker-ipython-notebook
> https://registry.hub.docker.com/u/bgruening/docker-ipython-notebook/
> You can also install a ipynb datatype:
> https://github.com/bgruening/galaxytools/tree/master/datatypes/json
> https://testtoolshed.g2.bx.psu.edu/view/iuc/datatyp_ipynb
> Comments welcome!
> Happy research!
> Eric & Björn
> _______________________________________________
> IPython-dev mailing list
> IPython-dev at scipy.org
> http://mail.scipy.org/mailman/listinfo/ipython-dev

Kyle Kelley (@rgbkrk <https://twitter.com/rgbkrk>; http://lambdaops.com)
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/ipython-dev/attachments/20140802/47a28873/attachment.html>

More information about the IPython-dev mailing list