Chymeric Tutorials

Do awesome stuff - awesomely.

Free and Open Science for Your Thesis

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Topics such as open peer review, open data, and open notebook science are of increasing interest to the scientific community. Many of the concepts behind this new spin on science are rooted in the FOSS (Free and Open Source Software) world and draw credibility from its staggering success. As such, we would refer to the aforementioned set of trends in science as FOS (Free and Open Science).

With so much talk about FOS going on - and even spilling over into high-profile editorials about publication review - it is distressing how little FOS is actually taking place. Talking about the next big thing is indeed quickening, but we would rather show you how to become a part of it. And what better place to start your voyage into both academia and the FOS world than your thesis or dissertation?

Bash Cheat Sheet

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This is a collection of bash scripts solving a series of eclectic use cases which we have encountered in the past. These instructions use linux commands and directory structures.

Portage Cheat Sheet

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This is a small sample of commands dealing with a series of simple use cases involving Portage. For all the code examples please note that emerge needs to be run as root. Other commands such as equery can be run as user. The Gentoo Wiki hosts a longer (though different) Portage/Gentoo cheat sheet on this page.

Miscellaneous Cheat Sheet

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This is a collection of workflows, commands, or bash scripts solving a series of common use cases. These instructions use linux commands and directory structures.

Write Octopress Themes

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Octopress is a fast and clean blogging platform which advertises itself as “a blogging framework for hackers”. Here we provide the first comprehensive documentation on how to best create new Octopress themes by hacking the default theme (or any theme based on it). We base our instructions both on general tools which you can use for better hacking and on solutions to popular use cases.

Btsync With Systemd (on Gentoo)

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What is Btsync?

Btsync is a peer-to-peer (p2p) file sharing client. Btsync uses the BitTorrent protocol, and is formally named “BitTorrent Sync”. The p2p file sharing protocol allows users to keep folders in sync without actually having to upload data into the cloud (meaning without having to depend on servers - which may not be theirs - for storage). This is highly beneficial as it allows for better security, more privacy (should you care), and - possibly most importantly - very fast sync over local networks.

Some users have voiced concerns over the fact that Btsync is closed source. While this is regrettable, we have not come across any actual instances of negative repercussions.

Btsync and Gentoo

Here we present an ebuild and associated files which enables you to easily get Btsync up and running on your Gentoo system. (Please pay attention to the einfo message printed after emerge). Our ebuild is currently mainly optimized to run with systemd, though we provide some (untested) initd and confd scripts We are currently trying to get it Btsync into the portage main tree (see our feature request), but need udev/init.d testers.

How-To: NeuroGentoo

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Gentoo linux is a modern, extremely flexible, and very transparent linux distribution. Among many other things it provides:

  • Rolling releases (continuous versioning, in brief: no tedious “OS version updates” for you - ever)
  • Building from source (custom geared for every machine - from ancient laptop to data-analysis power-box)
  • Seamless support for live source packages (get that very latest version with that one new function that solves all your problems - directly from the source code upstream wrote 5 minutes ago!)

Cutting the Gentoo publicity short, and getting to the point: Gentoo is awesome for science.


Already In!

Sadly, until July 2013 Gentoo provided almost no neuroscience software. In response, we started writing up some ebuilds for popular neuroscience (mainly neuropsychology, to be precise) software packages. With the help of a handful of enthusiastic Gentoo-Science overlay maintainers we have managed to help Portage bring you up-to-date and development versions of the following software packages (in order of ebuild pull):

  • sci-biology/psychopy
  • sci-biology/pybrain
  • sci-libs/nipy
  • sci-libs/nipype
  • sci-libs/nibabel
  • sci-libs/pydicom
  • sci-biology/mne-python
  • sci-biology/pysurfer