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

Research team from UNESP-Brazil reports its works on Genomics: from basic science to biotechnology

2016-06-22T10:37:42+01:00

Gui Valente joins us for a special journal club session.

This lecture is made possible through an international partnership between Prof. Fitt and Dr. Stotz (University of Hertfordshire) with Dr. Valente (São Paulo State University, UNESP-Brazil) with funding from the Santander Bank. The aim of this meeting it to report what Valente's team has been doing in science to establish future international cooperation between both universities as a result of Santander funding.

Dr. Valente leads the Systems Biology and Genomics Lab. at the São Paulo State University, Brazil (UNESP). Despite being a quite new group (2015), they have worked on several biological topics, including biofuel, health science, plant research and basic sciences (genome organization and evolution). They focus on using bioinformatics as an important "toolbox" for better understanding biological questions. This, the presentation will therefore introduce Valente's research group, showing projects they are working on right now. He will show results on ncRNAs, HIV+HCV/HBV evolution, B chromosome science, genomic entropies, enzyme discoveries in plants and S. cerevisiae ethanol tolerance.

Date: 24/06/2016
Time: 16:00
Location: LB252

UH Biocomputation Group - Bioinformatics

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

References/URLs

Research team from UNESP-Brazil reports its works on Genomics: from basic science to biotechnology