UH Biocomputation Group - Computational Frameworkshttp://biocomputation.herts.ac.uk/2019-10-01T10:52:42+01:00Standards and Tools in Neuroscience: a report on the Open Source Brain Workshop 20192019-10-01T10:52:42+01:002019-10-01T10:52:42+01:00Ankur Sinhatag:biocomputation.herts.ac.uk,2019-10-01:/2019/10/01/standards-and-tools-in-Neuroscience-a-report-on-the-open-source-brain-workshop-2019.html<p class="first last">Ankur Sinha's journal club session where he reports on the
information presented and discussions held at the <a class="reference external" href="http://www.opensourcebrain.org/docs/Help/Meetings#OSB_2019">Open Source Brain
Workshop</a> in September, 2019.</p>
<p>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 <a class="reference external" href="https://en.wikipedia.org/wiki/Open_science">Open</a>.</p>
<p>The Neuroscience research community has also made this commitment. The
philosophy of <a class="reference external" href="https://www.fsf.org/blogs/community/user-liberation-watch-and-share-our-new-video/">Free/Open</a>
Science, however, must be backed by <a class="reference external" href="http://opensourceforneuroscience.org/">Free/Open standards and tools</a>. The <a class="reference external" href="http://www.opensourcebrain.org/">Open Source Brain</a> project
is one of many initiatives that focus on developing Free/Open tools and
standards for Neuroscience. A recent <a class="reference external" href="https://www.cell.com/neuron/fulltext/S0896-6273(19)30444-1">publication</a> summarises
their work.</p>
<p>While initially targeting computational Neuroscience, following the renewal of
their funding from the Wellcome Trust, the <a class="reference external" href="http://www.opensourcebrain.org/">Open Source Brain</a> project are
expanding their deliverables to support experimental data as well.
With this in mind, they organised a <a class="reference external" href="https://www.fsf.org/blogs/community/user-liberation-watch-and-share-our-new-video/">workshop</a>
in September to discuss two key themes:</p>
<ul class="simple">
<li>Accessible sharing of cellular Neuroscience data: by supporting the
<a class="reference external" href="https://www.nwb.org/">Neurodata Without Borders (NWB)</a> format.</li>
<li>Modelling the cortex across scales: by further expanding the <a class="reference external" href="https://www.neuroml.org/">NeuroML</a> model description language.</li>
</ul>
<p>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".</p>
<p>I will conclude with a (another?) short marketing pitch for our <a class="reference external" href="https://neuro.fedoraproject.org">NeuroFedora</a> project which shares these goals.</p>
<div class="section" id="references-urls">
<h2>References/URLs</h2>
<ul class="simple">
<li>Open Science: <a class="reference external" href="https://en.wikipedia.org/wiki/Open_science">https://en.wikipedia.org/wiki/Open_science</a></li>
<li>Free/Open Source Software: <a class="reference external" href="https://www.fsf.org/blogs/community/user-liberation-watch-and-share-our-new-video/">https://www.fsf.org/blogs/community/user-liberation-watch-and-share-our-new-video/</a></li>
<li>Open letter committing to the use of Open Source for Neuroscience: <a class="reference external" href="http://opensourceforneuroscience.org/">http://opensourceforneuroscience.org/</a></li>
<li>Open Source Brain: <a class="reference external" href="http://www.opensourcebrain.org">http://www.opensourcebrain.org</a></li>
<li>Neurodata Without Borders (NWB): <a class="reference external" href="https://nwb.org">https://nwb.org</a></li>
<li>NeuroML: <a class="reference external" href="https://www.neuroml.org">https://www.neuroml.org</a></li>
<li>NeuroFedora: <a class="reference external" href="https://neuro.fedoraproject.org">https://neuro.fedoraproject.org</a></li>
</ul>
<div class="line-block">
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</div>
<p><strong>Date:</strong> 04/10/2019 <br />
<strong>Time:</strong> 16:00 <br />
<strong>Location</strong>: D449</p>
</div>
Open Position: PhD studentship in Biocomputation Research Group2018-05-31T12:43:55+01:002018-05-31T12:43:55+01:00Shabnam Kadirtag:biocomputation.herts.ac.uk,2018-05-31:/2018/05/31/open-position-phd-studentship-in-biocomputation-research-group.html<p class="first last">Applications are invited for a PhD studentship on Computational
frameworks for high-dimensional neural data with Dr. Shabnam Kadir in
the Biocomputation Research Group in the Centre for Computer Science
and Informatics Research, University of Hertfordshire, U.K. The
short-listing process will begin on 25th June 2018. Details within.</p>
<p>Applications are invited for a PhD studentship on Computational frameworks for
high-dimensional neural data with Dr. Shabnam Kadir in the Biocomputation
Research Group in the Centre for Computer Science and Informatics Research,
University of Hertfordshire, U.K.</p>
<hr class="docutils" />
<p>New developments in experimental technology have led to petabytes of raw data
being produced by experimental neuroscientists, which are increasingly publicly
available, e.g. Allen Institute data (<a class="reference external" href="http://www.brain-map.org/">http://www.brain-map.org/</a>). In particular,
we are in the realm where population recordings of tens of thousands of neurons
are feasible thanks to, e.g. a new generation of large dense probes for
electrophysiological recordings, imaging using 2-photon microscopy coupled with
calcium fluorescent sensors. Large scale neuronal recordings require novel
approaches for both processing and quantitative analysis.</p>
<p>As well as using techniques from high-dimensional statistics, machine learning,
information theory, we aim to explore new approaches from mathematical fields
outside statistics, such as algebraic topology. The study of networks is a
particularly important topic in neuroscience: neurons communicate with each
other electrically via synapses, forming intricate networks. These networks can
be studied using techniques from computational topology (e.g. persistent
homology, clique topology). These could be used to extract information about
subnetworks and assemblies, both from large scale recordings, and via
connectomics derived from simulations (Blue Brain Project).</p>
<p>We aim in this project to go beyond spike sorting and develop new tools and
computational frameworks which would help interpret high dimensional data and
interrogate how information is being processed by the brain, e.g. How are
sensory stimuli (location in environment, visual and auditory stimuli) encoded?
How can we characterise the neural activity associated with memory, attention,
decision making and motor control?</p>
<p>We shall be collaborating with labs at Imperial, Pennsylvania State University
and UCL.</p>
<p>More information can be found here:
<a class="reference external" href="http://www.herts.ac.uk/__data/assets/pdf_file/0003/187455/Dec2017-computational-frameworks-for-high-dimensional-neural-data.pdf">http://www.herts.ac.uk/__data/assets/pdf_file/0003/187455/Dec2017-computational-frameworks-for-high-dimensional-neural-data.pdf</a></p>
<p>We are looking for candidates with the following profile:</p>
<ul class="simple">
<li>Strong first degree in a quantitative field such as mathematics, physics,
computer science, engineering, computational neuroscience.</li>
<li>Strong programming skills (e.g. Python, MATLAB, C++).</li>
<li>Interest in neuroscience and biology would be helpful.</li>
</ul>
<p>A studentship from the PhD Programme in Computer Science provides approximately
£14,750 per annum bursary plus the payment of student fees. Applicants from
outside the UK or EU are eligible.</p>
<p>Research in Computer Science at the University of Hertfordshire has been
recognised as excellent in the latest Research Excellence Framework Assessment
(2014), with 50% of the research submitted rated as internationally excellent
or world-leading. The Centre for Computer Science and Informatics Research
provides a very stimulating environment, offering a large number of specialised
and interdisciplinary seminars as well as general training and researcher
development opportunities. The University is situated in Hatfield, in the green
belt just north of London.</p>
<hr class="docutils" />
<p>Please contact Dr Shabnam Kadir (<code>s.kadir2 AT herts DOT ac DOT uk</code>) for informal enquiries.
Application forms are available under
<a class="reference external" href="http://www.herts.ac.uk/apply/schools-of-study/computer-science/our-research/the-phd-programme-in-computer-science">http://www.herts.ac.uk/apply/schools-of-study/computer-science/our-research/the-phd-programme-in-computer-science</a>
and should be returned to:</p>
<p>Ms Emma Thorogood, <br />
Research Student Administrator, <br />
University of Hertfordshire, College Lane, <br />
Hatfield, Herts, AL10 9AB, <br />
Tel: 01707 286083 <br />
E-mail: <code>doctoralcollegeadmissions AT herts DOT ac DOT uk</code>.</p>
<p>The short-listing process will begin on 25th June 2018.</p>