Standards and Tools in Neuroscience: a report on the Open Source Brain Workshop 2019

2019-10-01T10:52:42+01:00

While scientific work and output was traditionally limited to relatively small expert communities, the landscape is rapidly changing. Modern Science is far too complex to be carried out in isolation, and the need to increase the uptake of scientific output in society now seems far more pressing. As a result, scientific communities are pushing to make Science more Open.

The Neuroscience research community has also made this commitment. The philosophy of Free/Open Science, however, must be backed by Free/Open standards and tools. The Open Source Brain project is one of many initiatives that focus on developing Free/Open tools and standards for Neuroscience. A recent publication summarises their work.

While initially targeting computational Neuroscience, following the renewal of their funding from the Wellcome Trust, the Open Source Brain project are expanding their deliverables to support experimental data as well. With this in mind, they organised a workshop in September to discuss two key themes:

Accessible sharing of cellular Neuroscience data: by supporting the Neurodata Without Borders (NWB) format.
Modelling the cortex across scales: by further expanding the NeuroML model description language.

Since I was fortunate enough to attend this workshop, in this talk, I will summarise the main points that were discussed here. Time permitting, I will hope to begin a discussion in our group on how we can ensure that we follow and contribute to these standards and tools to make our research work and its outputs "default to Free/Open".

I will conclude with a (another?) short marketing pitch for our NeuroFedora project which shares these goals.

References/URLs

Open Science: https://en.wikipedia.org/wiki/Open_science
Free/Open Source Software: https://www.fsf.org/blogs/community/user-liberation-watch-and-share-our-new-video/
Open letter committing to the use of Open Source for Neuroscience: http://opensourceforneuroscience.org/
Open Source Brain: http://www.opensourcebrain.org
Neurodata Without Borders (NWB): https://nwb.org
NeuroML: https://www.neuroml.org
NeuroFedora: https://neuro.fedoraproject.org

Date: 04/10/2019
Time: 16:00
Location: D449

NeuroFedora: a ready to use Free/Open source platform for neuroscientists

2018-12-04T13:39:23+00:00

In this seminar, I introduce the NeuroFedora initiative to the group. I explain our goals, our philosophy, our methods, our current state and, solicit feedback on our work.

The (current) goal of the NeuroFedora SIG is to provide a ready to use platform for neuroscientists. We aim to do this by making commonly used Neuroscience software easily installable on a Fedora Linux system.

Neuroscience is an extremely multidisciplinary field. It brings together mathematicians, chemists, biologists, physicists, psychologists, engineers (electrical and others), computer scientists, and more. A lot of software is used nowadays in Neuroscience for:

data collection, analysis, and sharing.
image processing (a lot of ML is used here, think Data Science).
simulation of brain networks (NEURON, Nest, Moose, PyNN, Brian).
dissemination of scientific results (peer reviewed and otherwise, think LaTeX).

Given that a large proportion of neuroscientists are not trained in computer science, a lot of resources are spent setting up systems, installing software (often building whole dependency chains from source). This can be especially hard for people not well-versed in software development and related fields.

So, at NeuroFedora, we aim to enable Neuroscience research by providing a ready to use Fedora based system for researchers to work with. NeuroFedora is Free software and is therefore free to all to use, modify, study, and share.

Date: 07/12/2018
Time: 16:00
Location: D120

UH Biocomputation Group - Community

Standards and Tools in Neuroscience: a report on the Open Source Brain Workshop 2019

References/URLs

NeuroFedora: a ready to use Free/Open source platform for neuroscientists