Frequently Asked Questions

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Why NeuroDebian?
In the course of our own research endeavors we have joined forces to develop PyMVPA – a Python framework for multivariate pattern analysis of neural data. To conveniently deploy PyMVPA for anyone using Debian-derived distributions this package repository was created initially. Besides the PyMVPA project we collaborate with the NiPy team on various projects, such as NiBabel and NiPype. Quickly NeuroDebian became the ultimate integrated environment for all these projects – and we are constantly working on enriching this environment with as many additional relevant software as possible.
Debian, Debian, Debian – What about Ubuntu?
NeuroDebian offers backported binary packages for recent Ubuntu releases whenever possible. However, since Ubuntu (like many other derivatives) uses Debian as its foundation, it is more efficient to spend time maintaining packages in Debian, instead of having to directly contribute to countless child-distributions. After the appearance of new packages in Debian, Ubuntu typically synchronizes them quickly and they become available in the Ubuntu universe – a repository of Debian packages rebuilt for a particular Ubuntu release. We are not constantly rebuilding of all available NeuroDebian packages for new Ubuntu releases. Therefore, you might find some packages temporarily being available for older Ubuntu releases only – until the point when a new package version is made and gets built for all currently supported releases.
How do I get a new neuroscience-related FOSS into (Neuro)Debian?

The goal of NeuroDebian is to package neuroscience software for Debian. Hence getting software into NeuroDebian means trying to get it into Debian. There are at least two possibilities to achieve that:

  • You can approach packaging it yourself. Start by filing an ITP (Intent to Package) bugreport and, if you are not a Debian developer, ask us to mentor your upload to Debian.
  • Contact us and we’ll do the work for you, but then it might take a little longer, depending on our current workload and interest in a particular software.
I have heard that some packages are non-free. Will you charge me for them?
No. The term non-free refers to an archive section. NeuroDebian uses exactly the same archive sections as Debian proper. The non-free section contains packages that have certain restrictions regarding your freedom to employ them for a particular purpose. In contrast, for packages in the main section your are completely free to do whatever and in whatever context you like. Regardless of the actual license or archive section, all packages in NeuroDebian are provided free of charge and under the licensing terms of the original developers.
When does a package migrate from NeuroDebian into Debian proper?

In short: When it is ready. The longer answer is that there is nothing special to packages in NeuroDebian in comparison to packages conducted elsewhere. Packaging efforts are announced to Debian via ITPs and the packaging itself is available in some version control system – typically in the Git repositories of the pkg-exppsy group on Debian’s Alioth server, or another VCS, or on http://mentors.debian.net.

The only difference is that a particular package becomes available through the NeuroDebian repository before it has passed all checks for compliance with Debian’s standards. But even after a package becomes part of Debian, the NeuroDebian repository continues to provide binary packages of new versions for a recent set of Debian and Ubuntu releases (aka backports).

How to create a mirror of the repository?
The NeuroDebian repository can be mirrored with rsync. If you are interested in sponsoring storage space and bandwidth for another mirror, please contact us.
What means “The following signatures couldn’t be verified...”?

When you start using this repository, you probably get warning messages like this:

The following signatures couldn't be verified because
the public key is not available.

Or you will be asked questions like this over and over:

WARNING: The following packages cannot be authenticated!
...
Install these packages without verification [y/N]?

This is because your APT installation initially does not know the GPG key that is used to sign the release files of this repository. It is easy to make APT happy again. The simplest way is to install the neurodebian-keyring package that is available from the NeuroDebian repository. Alternatively:

  1. Get the key. Either download the repository key from here or fetch it from http://wwwkeys.pgp.net (2649A5A9).

  2. Now feed the key into APT by invoking:

    apt-key add #file#

    Where #file# has to be replaced with the location of the key file you just downloaded. You need to have superuser-privileges to do this (either do it as root or use sudo).

Why is NeuroDebian not a Pure Blend?

This is in the works, but...

There is no need for it to become one, as the existing Debian Pure Blends already offer the desired functionality within Debian. Similar to Pure Blends, NeuroDebian’s goal is to provide software for neuroscientists using the Debian operating system, and therefore the ultimate goal is to get all relevant software into Debian.

However, various reasons exist that prevent a particular software from entering Debian. Some are temporary, i.e. a package is already useable, but some technical bits do not meet Debian’s standards (yet) or a licensing issue needs to be resolved first. For some software the licensing is so restrictive that it cannot be distributed by Debian, and hence cannot even go into its non-free branch. Unfortunately, sometimes these issues cannot be solved to a degree that is acceptable for Debian. For some other packages Debian itself is not ready yet, e.g. huge data packages with neuroscience data (with sometimes over 1GB).

NeuroDebian aims to be a platform that provides a staging area for neuroscience software packages on their way into Debian. All packages are properly registered in the relevant Debian Pure Blends, e.g. Debian Science Cognitive Neuroscience or Debian Med Imaging. Inside Debian these efforts already provide a suitable framework for this purpose, and hence there is no need to establish yet another one.

I want to help. How do I get involved?

We always need people to help maintaining existing packages. If you need some additional software packaged and you want to try it on your own, we would be happy to mentor you. We also have a list of ongoing and planned projects, each listing a number of tasks that need to be done.

If you found something you are interested in, please email the neurodebian-devel mailing list and let us know about it. Thanks!

How can I cite NeuroDebian?

Please cite the following paper:

Halchenko, Y. O. & Hanke, M. (2012). Open is not enough. Let’s take the next step: An integrated, community-driven computing platform for neuroscience. Frontiers in Neuroinformatics, 6:22.

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