TechBlog: Jupyter powers bioinformatics, again

GenePattern Notebook screenshot

Bioinformatics isn’t easy for newbies. It’s typically done on the Linux command line, where users direct the computer using text-based instructions rather than clicking a mouse.

But there are alternatives. One popular choice is Galaxy; another is GenePattern. Both allow researchers to execute complex bioinformatics tools via open-source, point-and-click, web-based interfaces, freeing them from the burdens of the command line, programming, and software installation. As such, they make bioinformatics workflows relatively user-friendly. And that trend is continuing.

Continue reading

TechBlog: Jupyter Joins the Galaxy

journal.pcbi.1005425.g001

{credit}PLoS Comput Biol 13(5):e1005425{/credit}

There’s a galaxy of tools in the Galaxy bioinformatics environment — 4,807 at last count. With them, researchers can do just about anything, computationally speaking. One thing they couldn’t do was work with their data programmatically. Now, thanks to a recent software update, that gap has been filled.

In a paper published on 25 May in PLoS Computational Biology, the Galaxy team describes a plug-in that provides access to both Jupyter (neé IPython notebook) and RStudio.

Continue reading