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Neuroscience Runs on GNU/Linux

Michael Hanke, Yaroslav O. Halchenko
2011 Frontiers in Neuroinformatics  
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.  ...  Windows-users themselves most often run a GNU/Linux OS inside a VM (Fig. 1A) .  ...  We believe that these results provide ample support for considering GNU/Linux as the current standard computing environment in neuroscience research.  ... 
doi:10.3389/fninf.2011.00008 pmid:21779243 pmcid:PMC3133852 fatcat:2g4oy4km4zctfosd4o3kvmw65a

Simulation platform: cloud-computing meets computational neuroscience

Tadashi Yamazaki, Hidetoshi Ikeno, Yoshihiro Okumura, Shunji Satoh, Yoshimi Kamiyama, Yutaka Hirata, Keiichiro Inagaki, Akito Ishihara, Takayuki Kannon, Shiro Usui
2011 BMC Neuroscience  
Computational models and theoretical tools are essential components in computational neuroscience.  ...  Simulation Platform is a cloud of virtual machines running GNU/Linux.  ...  BMC Neuroscience 2011 12(Suppl 1):P346.  ... 
doi:10.1186/1471-2202-12-s1-p346 pmcid:PMC3240463 fatcat:tglofr5pqnhyjpezmm3opk7jz4

A primer of visual stimulus presentation software

Rolf Kötter
2009 Frontiers in Neuroscience  
Acknowledgments This work was supported by the Initiative and Networking Fund of the Helmholtz Association within the Helmholtz Alliance on Systems Biology.  ...  Furthermore, the primary development platform of the Vision Egg is GNU/Linux, while it appears to be Windows for PsychoPy.  ...  Straw The visual system has been the most widely studied sensory system in neuroscience during the last decades.  ... 
doi:10.3389/neuro.01.021.2009 pmid:20228860 pmcid:PMC2751622 fatcat:otyc4fndgbdipk4c4ikd5hx7gu

Simulation Platform: A cloud-based online simulation environment

Tadashi Yamazaki, Hidetoshi Ikeno, Yoshihiro Okumura, Shunji Satoh, Yoshimi Kamiyama, Yutaka Hirata, Keiichiro Inagaki, Akito Ishihara, Takayuki Kannon, Shiro Usui
2011 Neural Networks  
Simulation Platform is a cloud of virtual machines running GNU/Linux.  ...  When a user posts a request, a virtual machine is assigned to the user, and the simulation starts on that machine.  ...  Acknowledgments We would like to thank Nilton Liuji Kamiji for valuable comments on the manuscript. We appreciate reviewers' proposals of new functionality in Simulation Platform.  ... 
doi:10.1016/j.neunet.2011.06.010 pmid:21741207 fatcat:uhy6oyc22fbafbx3en4sqcuwym

Open is Not Enough. Let's Take the Next Step: An Integrated, Community-Driven Computing Platform for Neuroscience

Yaroslav O. Halchenko, Michael Hanke
2012 Frontiers in Neuroinformatics  
We are indebted to our colleagues for their critical comments, and to Alex Waite for his work on improving the readability of this manuscript.  ...  The Debian OS has been ported to numerous hardware architectures and runs natively on any hardware relevant for neuroscience research.  ...  Over 50 packages have successfully migrated from NeuroDebian into Debian, which are now officially part of the Debian OS and its more than 100 10 derived GNU/Linux distributions, such as Ubuntu 11 (developed  ... 
doi:10.3389/fninf.2012.00022 pmid:23055966 pmcid:PMC3458431 fatcat:zxlo5qdytnbcffvwodshqzb7li

RPG: A low-cost, open-source, high-performance solution for displaying visual stimuli [article]

Vivian Imbriotis, Adam Ranson, William M Connelly
2020 bioRxiv   pre-print
The development of new high throughput approaches for neuroscience such as high-density silicon probes and 2-photon imaging have led to a renaissance in visual neuroscience.  ...  Specifically, the Raspberry Pi is a low-cost, credit card sized computer with general purpose input/output pins, allowing RPG to be triggered to deliver stimuli and to provide real-time feedback on stimulus  ...  Methods Raspberry Pi RPG has been developed and tested on the Model B Raspberry Pi 3, which are powered by a quad core Cortex A53 (1.2 GHz) with 1GB of RAM and running the default Raspbian GNU/Linux  ... 
doi:10.1101/2020.03.05.979724 fatcat:louq2oxqwbgjdco23nd3mydavm

Measuring Software Timing Errors in the Presentation of Visual Stimuli in Cognitive Neuroscience Experiments

Pablo Garaizar, Miguel A. Vadillo, Diego López-de-Ipiña, Helena Matute, Suliann Ben Hamed
2014 PLoS ONE  
However, external factors, often related to the technology used to display the visual information, can have a noticeable impact on the actual performance and may be easily overlooked by researchers.  ...  PsychoPy is a multiplatform software package that can run natively in Microsoft Windows, GNU/Linux and Apple Mac OS X.  ...  In addition, it runs under the most popular generalpurpose operating systems (i.e., Microsoft Windows, GNU/Linux and Mac OS X) and is even able to take advantage of the reliability provided by real-time  ... 
doi:10.1371/journal.pone.0085108 pmid:24409318 pmcid:PMC3883681 fatcat:sptuixlo7ffmnmlabxyfxejp2q

PyMVPA: a unifying approach to the analysis of neuroscientific data

Michael Hanke
2009 Frontiers in Neuroinformatics  
Neuroscientists often focus on only one or a smaller subset of these neural modalities partly due to the kinds of questions investigated and partly due to the cost of learning to analyze data from these  ...  The recent rise of reciprocal interest between the machine learning (ML) and neuroscience communities is an example of the desire for an inter-disciplinary transfer of computational methods that can benefi  ...  number of RPM-based GNU/Linux distributions, such as OpenSUSE, RedHat, CentOS, Mandriva, and Fedora.  ... 
doi:10.3389/neuro.11.003.2009 pmid:19212459 pmcid:PMC2638552 fatcat:6dfxvlmjsbgcfflpmul5puuqce

Stimfit: quantifying electrophysiological data with Python

Segundo J. Guzman, Alois Schlögl, Christoph Schmidt-Hieber
2014 Frontiers in Neuroinformatics  
VALIDATION OF MEASUREMENT AND FITTING ALGORITHMS All validations were executed on a PC with a 2.5 GHz Intel Core i5 CPU running on GNU/Linux.  ...  Plotting times were measured for a 800 × 600 pixels window running on OS X.  ... 
doi:10.3389/fninf.2014.00016 pmid:24600389 pmcid:PMC3931263 fatcat:23usewsdardxtlo5lko3xeqwqi

Neural Responses to Naturalistic Clips of Behaving Animals in Two Different Task Contexts

Samuel A. Nastase, Yaroslav O. Halchenko, Andrew C. Connolly, M. Ida Gobbini, James V. Haxby
2018 Frontiers in Neuroscience  
All multivariate analyses were performed using PyMVPA (v2.6.3.dev1; http://www.pymvpa.org; Hanke et al., 2009; RRID:SCR_006099) in the NeuroDebian computational environment (Debian "jessie" 8.5 GNU/Linux  ...  Frontiers in Neuroscience | www.frontiersin.org May 2018 | Volume 12 | Article 316  ... 
doi:10.3389/fnins.2018.00316 pmid:29867327 pmcid:PMC5962655 fatcat:psviodchhbc63ki3dieufzhfz4

Developing a new experimental system for an undergraduate laboratory exercise to teach theories of visuomotor learning

Shoko Kasuga, Junichi Ushiba
2014 Journal of Undergraduate Neuroscience Education  
It can be downloaded for free, working on GNU/Linux, Mac OS X, and Windows. Processing has interactive programs with 2D, 3D graphics, or PDF output and OpenGL integration for accelerated 3D graphics.  ...  To uncover potential mechanisms, approaches based on computational neuroscience have been developed.  ... 
pmid:25565915 pmcid:PMC4281044 fatcat:xmiebpe7gfdblju6vlsd24ue4a

Gesture Language Translator Using Raspberry Pi

Supriya Pawar, Apoorva Bamgude, Sayali Kamthe, Arundhati Patil, Prof. Rajesh Barapte
2022 International Journal for Research in Applied Science and Engineering Technology  
/Linux distributions that can be run on the Raspberry Pi.  ...  features a 1.4 GHz quad-core ARMv8 64bit processor and a powerful VideoCore IV GPU. 4) Snappy Ubuntu Core, Raspbian, Fedora, and Arch Linux, as well as Microsoft Windows 10 IoT Core, are among the ARM GNU  ... 
doi:10.22214/ijraset.2022.42242 fatcat:irsyivzv2nckhbfpnlj27sjj2i

Neural ensemble communities: open-source approaches to hardware for large-scale electrophysiology

Joshua H Siegle, Gregory J Hale, Jonathan P Newman, Jakob Voigts
2015 Current Opinion in Neurobiology  
One often-overlooked factor when selecting a platform for largescale electrophysiology is whether or not a particular data acquisition system is 'open' or 'closed': that is, whether or not the system's  ...  The increasing difficulty of obtaining replacement parts motivated a total rewrite of the underlying code for National Instruments hardware and GNU/Linux.  ...  The requirement to run alongside a very different system forced ArtE to be modular, with data moving between independent processes running on different machines over the network, in the spirit of MEABench  ... 
doi:10.1016/j.conb.2014.11.004 pmid:25528614 pmcid:PMC4447530 fatcat:v4zhm2vozfh7xbtbtlfj3fy2du

Reproducibility of neuroimaging analyses across operating systems

Tristan Glatard, Lindsay B. Lewis, Rafael Ferreira da Silva, Reza Adalat, Natacha Beck, Claude Lepage, Pierre Rioux, Marc-Etienne Rousseau, Tarek Sherif, Ewa Deelman, Najmeh Khalili-Mahani, Alan C. Evans
2015 Frontiers in Neuroinformatics  
/Linux.  ...  differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU  ...  ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: Alzheimers Association;  ... 
doi:10.3389/fninf.2015.00012 pmid:25964757 pmcid:PMC4408913 fatcat:msaymuffgvgkpatyrf73sgqr3u

The Use of programming languages and computer software in psychological science

Nelson Torro-Alves, Bernardino Fernández-Calvo, José Antonio Aznar-Casanova, Armindo de Arruda Campos Neto, Natanael Antonio Santos
2014 Temas em Psicologia  
In addition, there are numerous functions for handling, import and export data, being multiplatform, with versions for Windows, MacOS, GNU/Linux and Unix.  ...  Given its characteristics, C is considered a general-purpose language that can run on any microprocessor that has its own C compiler.  ... 
doi:10.9788/tp2014.3-06 fatcat:6u6njpk4lbgmxlzvgk7bx4lea4
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