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Sunday, July 19 • 7:00pm - 8:00pm
P80: Comp-NeuroFedora, a Free/Open Source operating system for computational neuroscience: download, install, research

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Ankur Sinha, Aniket Pradhan, Qianqian Fang, Danny Lee, Danishka Navin, Alberto Rodriguez Sanchez, Luis Bazan, Luis M. Segundo, Alessio Ciregia, Zbigniew J˛edrzejewski-Szmek, Sergio Pascual, Antonio Trande, Victor Manuel Tejada Yau, Morgan Hough

Google Meet link: https://meet.google.com/rkx-siwq-dww


The promotion and establishment of Open Neuroscience[9] is heavily dependent on the availability of Free/Open Source Software (FOSS) tools that support the modern scientific process. While more and more tools are now being developed using FOSS driven methods to ensure free (as in freedom, and thus also free of cost) access to all, the complexity of these domain specific tools tends to hamper their uptake by the target audience---scientists hailing from multiple, sometimes non-computing, disciplines. The NeuroFedora initiative aims to shrink the chasm between the development of neuroscience tools and their usage[10].
Using the resources of the FOSS Fedora community[4] to implement current best practices in software development, NeuroFedora volunteers identify, package, test, document, and disseminate neuroscience software for easy usage on the general purpose Fedora Linux Operating System (OS). The result is the reduction of the installation/deployment process for this software to a simple two step process: install any flavour of the Fedora OS; install the required tools using the in-built package manager.

To make common computational neuroscience tools even more accessible, NeuroFedora now provides an OS image that is ready to download and use. In addition to a plethora of computational neuroscience software-Auryn[7], NEST[1], Brian[6], NEURON[2], GENESIS[3], Moose[5], Neurord[8], and others--- the image also includes various utilities that are commonly used along with modelling tools, such as the complete Python science stack. Further, since this image is derived from the popular Fedora Workstation OS, it includes the modern GNOME integrated application suite and retains access to thousands of scientific, development, utility, and other daily use tools from the Fedora repositories.

A complete list of available software can be found at the NeuroFedora documentation at neuro.fedoraproject.org. We invite students, trainees, teachers, researchers, and hobbyists to use Comp-NeuroFedora in their work and provide feedback. As a purely volunteer driven initiative, in the spirit of the Open Science and FOSS, we welcome everyone to participate, engage, learn, and contribute in whatever capacity they wish.

References

1. Linssen, C., Lepperød, M. E., Mitchell, J., Pronold, J., Eppler, J. M., et al. NEST 2.16.0 Aug. 2018-08.
2. Hines, M. L. & Carnevale, N. T. The NEURON simulation environment. Neural Computation 9, 1179–1209 (1997).
3. Bower, J. M., Beeman, D. & Hucka, M. The GENESIS simulation system (2003).
4. RedHat. Fedora Project 2008.
5. Dudani, N., Ray, S., George, S. & Bhalla, U. S. Multiscale modeling and interoperability in MOOSE. BMC Neuroscience 10, P54 (2009).
6. Goodman, D. F. M. & Brette, R. The brian simulator. Frontiers in neuroscience 3, 192 (2009).
7. Zenke, F. & Gerstner, W. Limits to high-speed simulations of spiking neural networks using general-purpose computers. Frontiers in neuroinformatics 8 (2014).
8. J˛edrzejewski-Szmek, Z. & Blackwell, K. T. Asynchronous τ-leaping. Journal of Chemical Physics 144, 125104 (2016).
9. Gleeson, P., Davison, A. P., Silver, R. A. & Ascoli, G. A. A Commitment to Open Source in Neuroscience. Neuron 96, 964–965 (2017).
10. Sinha, A., Bazan, L., Segundo, L. M., J˛edrzejewski-Szmek, Z., Kellner, C. J., et al. NeuroFedora: a ready to use Free/Open Source platform for Neuroscientists. English. BMC Neuroscience 20. ISSN : 1471-2202. https://neuro.fedoraproject.org (2019).

Speakers
avatar for Ankur Sinha

Ankur Sinha

Research Fellow, University College London, UK



Sunday July 19, 2020 7:00pm - 8:00pm CEST
Slot 10