Michael eHanke

Yaroslav O Halchenko

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Michael Hanke

Yaroslav O. Halchenko

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Frontiers in Neuroinformatics

Neuroscience Runs on GNU/Linux

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Neuroscience runs on GNU/Linux

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NEUROINFORMATICS
Neuroscience runs on GNU/Linux
Michael Hanke1,2,3† and Yaroslav O. Halchenko1,2*†
1 Center for Cognitive Neuroscience, Dartmouth College, Hanover, NH, USA
2 Department of Psychological and Brain Sciences, Dartmouth College, Hanover, NH, USA
3 Department of Experimental Psychology, University of Magdeburg, Magdeburg, Germany
*Correspondence: michael.hanke@gmail.com; yaroslav.o.halchenko@onerussian.com
†Michael Hanke and Yaroslav O. Halchenko have contributed equally to this article.
In response to a recent grant application for 
a software development project, we received 
some reviewer comments that questioned 
the prevalence of GNU/Linux systems as 
a computing platform in neuroscience. 
Moreover, a concern was raised that virtu-
alization1 is not a feasible solution to over-
come limitations of any particular platform 
or to provide a convenient multi-platform 
working environment. We were surprised 
by these comments, because they are in 
contrast to what we experience daily while 
working with software developers world-
wide to integrate neuroscience software 
into the NeuroDebian2 project.
In an attempt to replace subjective 
experience with facts, in May 2011, we 
conducted an online survey3 in which we 
asked  neuroscientists to share some details 
about their computing environments. We 
tried to avoid a selection bias among par-
ticipants by using an uninformative short-
URL in the request for participation, and 
posted it to numerous neuroscience-related 
mailing lists, including thematic lists (e.g., 
comp-neuro4, connectionist5), as well as 
project-specific mailing lists for popular, 
cross-platform tools in various subfields of 
neuroscience. Within 12 days, a total of 583 
participants from 44 countries responded to 
the survey (three empty submissions were 
removed and 14 additional submissions 
were exclude after being identified as iden-
tical duplicates, sent from the same machine 
in short succession).
In the survey we asked participants to 
describe three computing environments 
they might be using: personal – a system 
with an operating system of their own 
choice, where they have permission to install 
arbitrary research software; managed – an 
environment that is provided and main-
tained by someone else (e.g., dedicated IT 
staff), without general permission to install 
arbitrary software; virtual – an environment 
that runs in a virtual machine (VM), pos-
sibly with multiple instances of operating 
systems running simultaneously on the 
same hardware.
The most striking result was that GNU/
Linux-based operating systems are the most 
commonly reported computing platform in 
our sample of neuroscience researchers. A 
total of 68% (95%-CI [64, 72]) of all par-
ticipants reported to be using such an OS 
in at least one of the described computing 
environments. For comparison, this statis-
tic yields 52% for Windows (CI [48, 56]) 
and 26% for Mac OS X(CI [23, 30]). This 
figure was even higher for participants that 
described themselves as “developing software 
to be used by other researchers” (n = 237; 75% 
Linux users, CI [69, 80]), than other non-
developer participants (n = 346; 64% Linux 
users, CI [58, 68]). Moreover, the prevalence 
of GNU/Linux was evident across research-
ers working with any of the nine different 
data modalities that were assessed by the 
survey (magnetic resonance imaging, CI 
[70, 79]; magneto/electro-encephalography, 
CI [61, 73]; electrophysiology, CI [55, 71]; 
behavioral data, CI [59, 70], simulations, CI 
[65, 78]; remaining modalities: CI [68, 84]).
Taking a closer look at the three types 
of computing environments, the survey 
revealed that in both, personal (n = 566) 
and managed (n = 371) computing envi-
ronments the largest fraction of participants 
use a GNU/Linux OS. In the managed envi-
ronment it is a majority of 61% (CI [56, 65]; 
Figure 1A). The data showed an expected 
difference between personal and managed 
computing environments: while 92% of all 
participants reported to use laptops, com-
modity desktops, or workstations for their 
personal environment, 68% indicated to 
be using high-end workstations, compute 
clusters, or grid/cloud computing infra-
structure in managed environments. Of all 
participants that reported to be using both 
personal and managed computing environ-
ments, the majority is using a GNU/Linux 
OS in both environments, followed by 
researchers that exclusively use Windows 
(Figure 1B top panel).
We also asked participants to rate 
their individual computing environments 
regarding various aspects by indicating how 
much they agree to a particular statement 
(four-level answer: definitely agree/mostly 
agree/disagree, encoded as evenly spaced 
numerical values within [−1, 1]; disagree-
ment being negative). We analyzed the data 
with respect to differences between users of 
individual operating systems – grouped into 
the major families: GNU/Linux, Windows6 
and Mac OS X7. All statistical analyses were 
implemented as ANOVA contrasts, and 
every test report includes the 95% confi-
dence intervals of parameter estimates for 
each OS group. First and foremost, we found 
that preference of GNU/Linux, Mac OS X, 
or Windows was not differentially moti-
vated by adequacy of hardware support, 
and availability of free support via web-
forums and similar channels. Interestingly, 
we observe that, in comparison to Mac 
OS X and Windows, GNU/Linux users 
are more likely to prefer this OS, because 
they see themselves as “having the necessary 
technical skills to maintain this environment 
themselves” (t = 2.796, df = 553, p < 0.01, 
CI
L
 [0.41, 0.54], CI
M
 [0.24, 0.42], CI
W
 [0.27, 
0.44]). Moreover, we found that they also, 
more than Mac- or Windows-users, see 
the “variety of available research software” 
as a reason for their platform preference 
(t = 4.456, df = 552, p < 0.001, CI
L
 [0.44, 
0.57], CI
M
 [0.24, 0.41], CI
W
 [0.20, 0.36]). 
1http://en.wikipedia.org/wiki/Hardware_ virtualization
2http://neuro.debian.net
3http://neuro.debian.net/survey/2011
4http://www.neuroinf.org/mailman/listinfo/comp-
neuro
5https://mailman.srv.cs.cmu.edu/mailman/listinfo/
connectionists
6http://www.windows.com
7http://www.apple.com/macosx
Frontiers in Neuroinformatics www.frontiersin.org July 2011 | Volume 5 | Article 8 | 1
OpiniOn Article
published: 07 July 2011
doi: 10.3389/fninf.2011.00008
Linux was only feasible with a good local 
system administrator, today the situation 
has changed and Windows or Mac OS X 
users are more likely to report “many of 
my colleagues use something similar” as a 
motivation for their platform choice than 
GNU/Linux users. (t = 3.779, df = 552, 
p < 0.001, CI
L
 [−0.05, 0.08], CI
M
 [0.14, 
0.30], CI
W
 [0.06, 0.22]). Moreover, exclud-
ing all reports from dedicate IT staff, GNU/
Linux users report the lowest average time 
they need to invest in maintenance of their 
personal computing environment (5.77 h/
month). This is not significantly differ-
ent from the average investment of a user 
of Apple’s Mac OS X (6.44 h/month) – a 
system that is widely known for its ease of 
maintenance. In contrast, Windows-users 
spend on average 13.97 h/month on sys-
tem maintenance, significantly more than 
GNU/Linux or Mac OS X users (t = 3.356, 
df = 497, p < 0.001, CI
L
 [1.92, 8.02], CI
M
 
[1.70, 9.54], CI
W
 [9.49, 16.97]; again exclud-
ing all system administrators).
It is our impression that despite a clear 
user preference, commercial software and 
hardware vendors often do not provide 
adequate support for the GNU/Linux 
platform. GNU/Linux is often perceived 
as a huge heterogeneous family of distri-
butions that is impossible to support as a 
whole. However, our data show that the 
vast majority of all GNU/Linux-based 
neuroscientists use only two flavors of this 
different OS types for host and guest OS 
(i.e., Windows on a Mac). However, about 
21% of all participants report to be using 
the same OS family inside and outside a 
VM (Figure 1B bottom panel). The latter 
group of researchers is more likely to state 
that a VM provides them with the ability 
to “to easily create a snapshot of a whole 
analysis environment” (t = 3.678, df = 259, 
p < 0.001, CI
same
 [−0.05, 0.27], CI
diff
 [−0.30, 
−0.14]) and that they “can take a complete 
analysis environment with them and run it 
on different machines” (t = 3.073, df = 261, 
p < 0.01, CI
same
 [0.08, 0.43], CI
diff
 [−0.14, 
0.04]). On the other hand, researchers 
using different OS inside and outside 
the VM are more likely to state that a 
VM allows them to “run software that is 
otherwise incompatible with their system” 
(t = 5.047, df = 262, p < 0.001, CI
same
 [0.03, 
0.34], CI
diff
 [0.56, 0.72]). Windows is the 
most frequently used operating system 
inside a VM. Windows-users themselves 
most often run a GNU/Linux OS inside a 
VM (Figure 1A).
We believe that these results provide 
ample support for considering GNU/
Linux as the current standard computing 
environment in neuroscience research. 
Apparently, this platform has come a long 
way from being a playground for techni-
cally skilled “geeks,” to a robust and reliable 
environment for day to day research activi-
ties. While it used to be that using GNU/
There is evidence that Windows-users tend 
to be more exposed to vendor lock-in situ-
ations. They, more than users of any other 
major operating system, indicate that they 
“rely on a particular application that runs in 
this environment only” (t = 3.245, df = 553, 
p < 0.001, CI
L
 [−0.18, −0.03], CI
M
 [−0.17, 
0.03], CI
W
 [0.01, 0.20]). At the same time, 
researchers using Windows in managed 
environments are less likely to agree that 
it “provides them with the best available 
tools for their research,” in comparison to 
GNU/Linux and Mac OS X (t = 3.802, 
df = 361, p < 0.001, CI
L
 [0.22, 0.36], CI
M
 
[0.12, 0.50], CI
W
 [−0.10, 0.12]). Moreover, 
these researchers are also less likely to agree 
that “the support staff solves all their techni-
cal problems and addresses their demands 
in a timely fashion” (t = 2.248, df = 360, 
p < 0.05, CI
L
 [0.09, 0.24], CI
M
 [−0.01, 0.41], 
CI
W
 [−0.12, 0.12]) and that “there are always 
enough licenses for essential commercial soft-
ware tools” (t = 1.700, df = 354, p < 0.05, CI
L
 
[0.03, 0.17], CI
M
 [−0.09, 0.29], CI
W
 [−0.14, 
0.08]).
Even though we expected hardware 
virtualization to be a common tool on 
computing platforms in neuroscience, we 
were still surprised by the survey results. 
A total of 44% (CI [40, 48]) of all par-
ticipants reported to be using VMs as part 
of their research activities. Among these 
participants, we could identify two distinct 
usage patterns. The majority (79%) uses 
Figure 1 | (A) Distribution of operating systems (OS) by computing 
environment type. Each horizontal bar indicates the proportion of survey 
participants that reported to be using the respective operating system. The 
lower half of each bar displays the distribution of participants’ responses to the 
question “What fraction of your research activity time do you spend in this 
software environment as opposed to any other environment that you might have 
access to? ” (four-level answer). (B) Total number of reported combinations of 
operating systems in personal and managed environments (top), as well as host 
and guest operating systems of a virtual environment (bottom). Only those OS 
combinations were considered in this figure that were reported to be actually 
used, and not those that were merely indicated to be available to a particular 
researchers.
Hanke and Halchenko GNU/Linux prevalence in neuroscience computing
Frontiers in Neuroinformatics www.frontiersin.org July 2011 | Volume 5 | Article 8 | 2
Acknowledgements
We are grateful to Andrew Connolly, 
Swaroop Guntupalli, Rajeev Raizada, and 
Jim Haxby for their support and feedback 
on the survey and this manuscript.
Received: 2 6 May 2011; accepted: 27 June 2011; published 
online: 07 July 2011.
Citation: Hanke M and Halchenko YO (2011) Neuroscience 
runs on GNU/Linux. Front. Neuroinform. 5:8. doi: 10.3389/
fninf.2011.00008
Copyright © 2011 Hanke and Halchenko. This is an open-
access article subject to a non-exclusive license between the 
authors and Frontiers Media SA, which permits use, dis-
tribution and reproduction in other forums, provided the 
original authors and source are credited and other Frontiers 
conditions are complied with.
different native package format). We think 
that it is both feasible and in the interest of 
vendors to make themselves familiar with 
the GNU/Linux platform and support it for 
their products.
All survey data, as well as results of sup-
plementary analyses are publicly available 
on the survey website12. We plan to run 
a future version of this survey in spring 
of 2012 to track changes in this field and 
further investigate the details of the wide-
spread use of virtualization in neuroscience 
research.
 platform: Red Hat8-based, and Debian9-
based GNU/Linux distributions, with a 
preference for Debian-based systems in 
the personal environment (Figure 1A). Both 
flavors are known to offer a stable platform 
with predictable release cycles. Moreover, 
they follow common standards (e.g., Linux 
Standard Base10, Freedesktop11) that make 
them very similar to each other (despite a 
8http://www.redhat.com
9http://www.debian.org
10http://www.linuxfoundation.org/collaborate/
workgroups/lsb
11http://www.freedesktop.org 12http://neuro.debian.net/survey/2011
Hanke and Halchenko GNU/Linux prevalence in neuroscience computing
Frontiers in Neuroinformatics www.frontiersin.org July 2011 | Volume 5 | Article 8 | 3


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