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.
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
Keep in mind to write a nice Tool Shed Tool if you catch yourself using
IPython in Galaxy to often for the same task.
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
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:
Eric & Björn