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

Björn Grüning bjoern.gruening at gmail.com
Sat Aug 2 02:03:38 EDT 2014

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 

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:

The underlying IPython Notebook (+Galaxy sugar) is stored under:
You can also install a ipynb datatype:

Comments welcome!
Happy research!
Eric & Björn

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