Matlab-based IPython notebooks

21 February 2018, update: the new JupyterLab was just released, and according to this tweet is really easy to integrate with Matlab. Probably worth checking out instead of the reasonably outdated instructions below!

I really like Python’s philosophy, but over the last years I haven’t been able to switch the code for my research from Matlab. At this point, the transition costs are too high for me, but it’s a move I have planned for some point in the future.

Now, Python has the awesome Jupyter (formerly IPyton notebook) feature, that allows for comments, code, and most importantly graphical output (i.e. figures you’ve just generated) to be shown in one document. This is a great way to share and explain the code you’re writing, since the reader immediately sees how output is generated without having to run all the analyses themselves.

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Software for (neuro)science

Since I started my PhD a few months ago, I have been thinking about the various bits of software I use for my research. I spend most of my days behind a computer – searching and reading papers, programming and analysing data. Although some pieces of software are widespread and easy to use when collaborating, there are a great many personal choices to make in computer languages and interfaces. So as a re-start to my new blog, here are some personal considerations and bits of computer goodness I tend to use. Continue reading