Welcome to the Ultimate Platform for Neuroscience¶
[...] NeuroDebian will undoubtedly have a large impact on the quality of neuroscience research, both directly and indirectly, by making almost every known software package related to neuroscience work available in a stable and secure environment and broadening the standard set of techniques researchers can employ.
—– [2010-09-16] Department of Psychology, Ohio State University, Columbus, Ohio, USA
The NeuroDebian project provides a turnkey platform for neuroscience through integrating of related software within the Debian operating system. If you are using neuroscience-related software which comes with you installation of Debian or its derivative, such as Ubuntu, good chance is that you are already using NeuroDebian.
This website provides an additional repository with both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt newest versions of packages. Please see the Frequently Asked Questions for more information about the goals of this project, and read what people say about it. Take a look at the list of our current and planned projects if you want to get involved. If you appreciate this service, please spread the word about NeuroDebian. This service is provided “as is”. There is no guarantee that a package works as expected, so use them at your own risk. If you encounter problems, please report them.
News¶
For more news and information see our blog. Older news items are available on identi.ca. Follow us on identi.ca (preferred) or twitter to subscribe to the NeuroDebian news.
How to use this repository¶
To enable the NeuroDebian repository on your system, select your Debian or Ubuntu release and a repository mirror from the lists below. Upon selection a short command snippet will be displayed that can be copied and pasted into a terminal session. These commands will configure the system package manager with the NeuroDebian repository key and package source information.
After selecting a release the setup code will be shown here.
Once this is done, you have to update the package index and you are ready to install packages. Use your favorite package manager, e.g. synaptic, adept. In the terminal you can use apt-get:
sudo apt-get update
sudo apt-get install mricron
Note
Not every package is available for all distributions/releases. For information about which package version is available for which release and architecture, please have a look at the corresponding package pages.
Popularity Contest¶
We would strongly encourage you to participate in the popularity contest (popcon), which anonymously collects the list of packages you installed/use on your system. Collecting such statistics is of particular importance for research software projects as a prove of an existing user-base. If upon installation of the system you rejected the invitation to participate you can always change your decision by running:
sudo dpkg-reconfigure popularity-contest
Note
If you are deploying multiple systems through cloning, to not have all systems considered as one, it would be necessary to re-generate the random MY_HOSTID. Following commands ran as root should do it (as root) without any interactive dialog:
sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
In addition to popcon pages for your “core” distribution (e.g. Debian or Ubuntu) you can see/get statistics for submissions to NeuroDebian and know that you are already contributing back to the community.
Ways to use NeuroDebian¶
Virtual machine¶
If you are not running Debian on a particular machine a NeuroDebian Virtual Machine is provided as a convenient testing and evaluation environment. After a few simple steps to setup the virtual machine, you will be able to use NeuroDebian as an integral part of your existing working environment without any sacrifice. The virtual machine is also a suitable environment to temporarily deploy neuroscience software on machines running other operating systems, e.g. for the purpose of teaching a neuroimaging data analysis course in a multipurpose computer lab.
Debian installation¶
Having been exposed to the wonders of NeuroDebian you are no longer satisfied with your previous choice of operating system? We would recommend installing Debian to replace or complement (dual-boot) your existing OS. Please visit “Getting Debian” to obtain the images for your hardware architecture and then simply add NeuroDebian repositories.
The team¶
Our main goal is to provide neuroscience FOSS for Debian. Thus the whole project would not be possible without the work of over 3,000 Debian developers and contributors who are as enthusiastically pursuing a similar goal. To add our share – Debian packages of FOSS for neuroscience research – the Experimental Psychology Debian packaging project was created to formally join the forces of
A number of packages that are now available from the NeuroDebian repository were not packaged by our team, but similar Debian teams. Therefore we want to express particular gratitude to the Debian Med and Debian Science teams for all their work.
Contacts¶
Email us directly with any “private” communication. Otherwise please use our public mailing lists, which exist not only to provide user-support but also to establish communication channels within the NeuroDebian community
- neurodebian-users: Discussions and support of NeuroDebian users
- neurodebian-upstream: General discussions and knowledge sharing among developers of the neuroscience software. We will also use it to update you with summaries of recent relevant developments in Debian project
- neurodebian-devel: Technical mailing list for discussions on NeuroDebian development
You are welcome also to join #neurodebian IRC room on OFTC network if you have quick questions or want to join a live discussion.
Acknowledgements¶
We are grateful to Jim Haxby for his continued support and endless supply of Italian espresso.
Thanks to the following institutions and individuals for hosting a mirror:
- Department of Psychological and Brain Sciences at Dartmouth College [us-nh] (primary mirror)
- Department of Experimental Psychology at the University of Magdeburg [de]
- Neurobot at Aristotle University of Thessaloniki, Greece [gr]
- Paul Ivanov [us-ca]
- Medical-image Analysis and Statistical Interpretation lab at Vanderbilt [us-tn]
- Australia’s research and education network (AARNET) [au]
If your are interested in mirroring the repository, please see the Frequently Asked Questions.
Publications¶
Hanke, M. (2011). More than batteries included: NeuroDebian. Talk given at the Python in Neuroscience satellite of EuroScipy 2011, Paris, France.
Halchenko, Y. O. (2011). π’s in Debian or Scientific Debian: NumPy, SciPy and beyond. Talk given at EuroScipy 2011, Paris, France.
Hanke, M. & Halchenko, Y. O. (2011). Neuroscience runs on GNU/Linux. Frontiers in Neuroinformatics, 5:8.
Hanke, M., Halchenko, Y. O. & Haxby, J. V. (2011). NeuroDebian – versatile platform for brain-imaging research Poster presented at the annual meeting of the Organisation for Human Brain Mapping, Quebec City, Canada.
Hanke, M. (2011). Integrating Condor into the Debian operating system. Talk given at CondorWeek 2011, Madison, Wisconsin, USA.
Hanke, M. & Halchenko, Y. O. (2010). Report from the Debian booth at SfN2010. Annual meeting of the Society for Neuroscience, San Diego, USA.
Halchenko, Y. O., Hanke, M., Haxby, J. V., Pollmann, S. & Raizada, R. D. (2010). Having trouble getting your Nature paper? Maybe you are not using the right tools? Poster presented at the annual meeting of the Society for Neuroscience, San Diego, USA.
Hanke, M., Halchenko, Y. O. (2010). Debian: The ultimate platform for neuroimaging research. Talk given at DebConf10, New York City, USA. [video: low resolution, high resolution]
Hanke, M., Halchenko, Y. O., Haxby, J. V. & Pollmann, S. (2010). Improving efficiency in cognitive neuroscience research with NeuroDebian. Poster presented at the annual meeting of the Cognitive Neuroscience Society, Montréal, Canada.
Halchenko, Y. O., Hanke, M. (2009). An ecosystem of neuroimaging, statistical learning, and open-source software to make research more efficient, more open, and more fun. Talk given at Dartmouth College, New Hampshire, USA.
