[Comp-neuro] Article on data sharing/analysis of multielectrode array

I'd like to highlight the following article from our group that I hope
will be of use to the community. Code and data are available via the
project site: http://www.damtp.cam.ac.uk/user/sje30/waverepo

Best wishes, Stephen

----------------------------------------------------------------------
Eglen SJ, Weeks M, Jessop M, Simonotto J, Jackson T, Sernagor E (2014)

A data repository and analysis framework for spontaneous neural activity
recordings in developing retina. Gigascience 3:3.

Paper: http://dx.doi.org/10.1186/2047-217X-3-3


Background

During early development, neural circuits fire spontaneously, generating
activity episodes with complex spatiotemporal patterns. Recordings of
spontaneous activity have been made in many parts of the nervous system
over the last 25 years, reporting developmental changes in activity
patterns and the effects of various genetic perturbations.

Results

We present a curated repository of multielectrode array recordings of
spontaneous activity in developing mouse and ferret retina. The data
have been annotated with minimal metadata and converted into HDF5. This
paper describes the structure of the data, along with examples of
reproducible research using these data files. We also demonstrate how
these data can be analysed in the CARMEN workflow system. This article
is written as a literate programming document; all programs and data
described here are freely available.

Conclusions

1. We hope this repository will lead to novel analysis of spontaneous
activity recorded in different laboratories. 2. We encourage published
data to be added to the repository. 3. This repository serves as an
example of how multielectrode array recordings can be stored for
long-term reuse.

Keywords:

Retinal waves; Spontaneous activity; Electrophysiology; HDF5;
Multielectrode arrays
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[Comp-neuro] DENDRITES 2014, July 1-4, Crete: LAST CALL & LOWER REGISTRATION

Apologies for cross-posting!

Please distribute to interested parties.

many thanks!

Yiota Poirazi

-------------------------------------------------------

DENDRITES 2014

4^th NAMASEN Training Workshop

Heraklion, Crete, Greece. 

July 1-4, 2014

http://dendrites2014.gr/

info@dendrites2014.gr

 

* * * * * FINAL DEADLINE EXTENSION* * * * *

Abstract submission for poster and oral presentation has been extended to April 14th, 2014. This is the final submission date.

* * * * * REGISTRATION WAIVERS FOR STUDENTS/POSTDOCS* * * * *

Several registration waivers are still available!!
Waivers are provided by IBRO PERC funding for Symposia, Workshops & Meetings. Students and postdocs presenting an abstract are eligible. To request a waiver, please send an email to info@dendrites2014.org including information about your submitted abstract.

Travel funds might also become available and will be announced on the web site.

* * * * * LOWER REGISTRATION FEES if registering by April 30th, 2014* * * * *

We are happy to announce that, given the availability of new sponsorships, we can provide lower registration fees (-40 Euro) for attendants registering by April 30th, 2014. People who registered already will get reimbursed.

* * * * * EMBO KEYNOTE LECTURE* * * * *

We are happy to announce that Prof.  Tonegawa's lecture will be supported by EMBO, as the "EMBO Keynote Lecture". This award, given to EMBO members presenting in major international scientific meeting, highlights the international standing of DENDRITES 2014.

----------------------------------------

Dendrites 2014 aims to bring together scientists from around the world to present their research on dendrites, ranging from the molecular to the anatomical and biophysical levels.  The Workshop will take place in the beautiful island of Crete, just after the AREADNE meeting (areadne.org) which takes place in the nearby island of Santorini. Note that Santorini is just a 2 hour boat ride from Crete. One could combine two meetings in a single trip to Greece!

FORMAT AND SPEAKERS

The meeting consists of the Main Event (July 1-3) and the Soft Skills Day (July 4).  Invited speakers for the Main Event include: 

* Susumu Tonegawa (Nobel Laureate),  

* Angus Silver, 

* Tiago Branco, 

* Alcino J. Silva, 

* Michael Häusser, 

* Julietta U. Frey, 

* Stefan Remy, and

* Kristen Harris. 

 

For the Soft Skills Day, Kerri Smith, Nature podcast editor, is going to present on communication and dissemination of scientific results.  Alcino J. Silva (UCLA) will present his recent work on developing tools for integrating and planning research in Neuroscience. There will be a hands on session on tools used to model neural cells/networks and a talk about the advantages of publishing under the Creative Commons License.

 

CALL FOR ABSTRACTS

Submission of abstracts for poster and oral presentations are due by 14 April 2014. We welcome both experimental and theoretical contributions addressing novel findings related to dendrites. For details, please see http://dendrites2014.gr/call/. 

 

Electronic abstract submission is hosted on the Frontiers platform, where extended abstracts will be published as an online, open access special issue (in Frontiers in Cellular Neuroscience, Impact factor 4.5). One of the authors has to register for the main event as a presenting author. In case an abstract is not accepted for presentation, the registration fee will be refunded. 

 

FOR FURTHER INFORMATION

Please see the conference web site (http://dendrites2014.gr/), subscribe to our twitter (https://twitter.com/dendrites2014) or RSS feeds (http://dendrites2014.gr/rss_feed/news.xml), or send an email to info@dendrites2014.org.

--   Panayiota Poirazi, Ph.D.  Research Director  Institute of Molecular Biology and Biotechnology (IMBB)  Foundation of Research and Technology-Hellas (FORTH)  Vassilika Vouton, P.O.Box 1385  GR 711 10 Heraklion, Crete, GREECE    Tel: +30 2810 391139  Fax: +30 2810 391101  Εmail: poirazi@imbb.forth.gr  http://www.dendrites.gr

[Comp-neuro] models of structural plasticity

Dear colleagues,

 

We would like to draw your attention to a series of recent papers dedicated to models of structural plasticity. Developing as well as mature brains are much less hard-wired than traditionally thought. Formation of new connections and breaking of existing connections (structural plasticity) by dendritic spine and axonal bouton turnover, as well as re-routing of axonal branches, can cause a dramatic rewiring of brain connectivity, which so far has largely been disregarded in neuronal network models.

 

The following papers describe novel models of structural plasticity:

 

Homeostatic structural plasticity increases the efficiency of small-world networks

Markus Butz, Ines D. Steenbuck and Arjen van Ooyen

Front. Synaptic Neurosci., 01 April 2014. DOI: 10.3389/fnsyn.2014.00007

(Open access) http://journal.frontiersin.org/Journal/10.3389/fnsyn.2014.00007/abstract

 

A simple rule for dendritic spine and axonal bouton formation can account for cortical reorganization after focal retinal lesions

Markus Butz and Arjen van Ooyen

PloS Computational Biology, 10 October 2013. DOI: 10.1371/journal.pcbi.1003259

(Open access) http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003259

 

Further reading:

Van Ooyen, A. (2011). Using theoretical models to analyse neural development. Nature Reviews Neuroscience 12: 311-326.

Butz, M., Worgotter, F., and Van Ooyen, A. (2009). Activity-dependent structural plasticity. Brain Research Reviews 60: 287-305.

 

Kind regards,

Markus Butz

Arjen van Ooyen

[Comp-neuro] Bernstein Workshop "Characterizing Natural Scenes": Call for Abstracts/Contributed Talks

Bernstein workshop: Characterizing Natural Scenes: Retinal Coding and Statistical Theory

Call for Abstracts/Contributed Talks

You are invited to participate in the pre-conference Bernstein workshop "Characterizing Natural Scenes: Retinal Coding and Statistical Theory", taking place in in Göttingen, Germany, on September 2-3, 2014. Please find the preliminary schedule on workshop URL: https://sites.google.com/site/jiankliu/Meetings/2014bccn_workshop

The workshop chairs will select a couple of abstracts for short oral presentation at the workshop. All the abstracts will be presented as posters during the Bernstein conference on September 3-4. However, the workshop could hold a separate poster session based on the number and quality of abstracts that we receive.

To participate in the workshop please submit the abstract (the extended version is preferred) as a PDF attachment via email to Jian Liu (jian.liu@med.uni-goettingen.de) or Arno Onken (arno.onken@iit.it). The deadline for submission is August 1.

REGISTRATION:

Please refer to the Bernstein Conference 2014 for registration and venue information.

http://www.bernstein-conference.de/

WORKSHOP DESCRIPTION:

How does the retina process natural visual inputs? What role do the many types of retinal ganglion cells (RGCs) play in this? Experiments with specific artificial stimuli have suggested that individual types of RGCs may have specific functional roles in visual processing, yet it is not clear how these simplified functional investigations relate to the processing of natural images and movies. An important ingredient for future analysis will be a better understanding of the complex statistical properties of natural scenes, as revealed by theoreticians.

The relationship between natural visual statistics and retinal coding provides a promising direction for improving our understanding of the visual system. But we still lack a systematic framework for understanding the underlying mechanisms of how relevant features of natural scenes are encoded by the retina.

In this workshop, we expect mutual benefits for both natural scene statistics and retinal coding. We will bring together experimentalists and theoreticians in order to highlight recent progress, encourage exchange of insights, and stimulate new ideas for future work with the following core questions:

1) How can we develop useful descriptions of the statistics of natural scenes that are relevant for retinal coding?

2) How can we characterize the functional roles of different RGC types in processing natural scenes?

3) Which coding strategies are present at the level of RGC populations?

4) How can we unify the acquired knowledge of natural scenes and neural data to develop better tools for analysis?

CONFIRMED SPEAKERS:

* Vijay Balasubramanian (University of Pennsylvania)

* Philipp Berens (BCCN, Tübingen)

* Thomas Euler (University of Tübingen)

* Felix Franke (ETH Zurich)

* Olivier Marre (Vision Institute, Paris)

* Aman Saleem (University College London)

* Maneesh Sahani (University College London)

* Rava A. da Silveira (ENS, Paris)

We are looking forward to seeing you in Göttingen.

Workshop organizers:

Jian Liu (University Medical Center Göttingen and BCCN Göttingen)

Arno Onken (Center for Neuroscience and Cognitive Systems, Istituto Italiano di Tecnologia Rovereto)

**************************************************************************
Jian K. Liu, Ph.D. Mathematics
Department of Ophthalmology
University Medical Center Goettingen
Waldweg 33, 37073 Goettingen
Phone: +49 (0)551 39-91248
Fax: +49 (0)551 39-13541
email: jian.liu@med.uni-goettingen.de
Webpage: https://sites.google.com/site/jiankliu
**************************************************************************

[Comp-neuro] Fully funded Postdoc position in Computational Neuroscience

Fully funded Postdoc position (Experienced Researcher) in Computational Neuroscience

 

New approaches for the analysis of neuronal spike trains (ER3)

 

within the Marie Curie Initial Training Network - 'Neural Engineering Transformative Technologies' (NETT) at the Institute of Complex Systems (ISC), CNR, Florence, Italy.

 

Gross Salary per annum:  64,701 € (Living Allowance) plus 9,290 - 13,272 € (Mobility Allowance) depending on circumstances

 

Required title:  PhD in Physics, Engineering, Applied Mathematics, or Computational Neuroscience

 

Applications:   Please first send an informal enquiry to Dr. Thomas Kreuz (thomas.kreuz@cnr.it) and/or Dr. Alessandro Torcini (alessandro.torcini@cnr.it). Once you are preselected (you will receive a reply within a few days), a full application has to be submitted according to the rules stated here [http://neuro.fi.isc.cnr.it/index.php?page=how-to-apply].

 

Closing date for the position:  May 15, 2014

 

 

Applications are invited for the above post to work with Dr. Thomas Kreuz [http://www.fi.isc.cnr.it/users/thomas.kreuz/] and Dr. Alessandro Torcini [http://www.fi.isc.cnr.it/users/alessandro.torcini/] in the Computational Neuroscience group [http://neuro.fi.isc.cnr.it/] at ISC, Florence. This world leading group combines theoretical investigations (e.g., on non-trivial collective phenomena in neuronal populations) with practical applications (such as spike train analysis). The group is one of the main participants in the Center for the Study of Complex Dynamics (CSDC) created with the purpose of coordinating interdisciplinary training and research activities. CSDC researchers include physicists, control engineers, mathematicians, biologists and psychologists.

 

This full-time post will begin on the 1^st of September 2014 (at the latest) and will be offered on a fixed-term contract for a period of 24 months. The fellowship will include a six-month stay (probably at the end) with NETT partner Prof. Bert Kappen [http://www.snn.ru.nl/~bertk/] at the Radboud University Nijmegen, Netherlands.

 

The Florence part of the project will mainly consist of two parts: Development of new approaches for (multivariate) data analysis and analysis of electrophysiological data (in particular neuronal spike trains). During the six-month stay in the Netherlands the project will investigate the applicability of methods derived from latent state models, sequential Monte Carlo sampling, and path integral control to analyze neural time-series data, such as spike trains.

 

The candidate should have a strong background in at least one of the following fields: computational neuroscience, data analysis, and nonlinear dynamics as well as solid experience in scientific programming (Matlab).

 

Candidates must be in the first 5 years of their research careers and already be in possession of a doctoral degree in physics, engineering, applied mathematics, or computational neuroscience. Preference will be given to a candidate with experience in (non-linear) data analysis. As part of our commitment to promoting diversity we encourage applications from women. To comply with the Marie Curie Actions rule for mobility applicants must not have resided, worked or studied in Italy for more than 12 months in the 3 years prior to May 2014.

 

Thomas Kreuz
Institute for complex systems, CNR
Via Madonna del Piano 10
50119 Sesto Fiorentino (Italy)
Tel: +39-349-0748506
Email: thomas.kreuz@cnr.it
Webpage: http://www.fi.isc.cnr.it/users/thomas.kreuz/

[Comp-neuro] Postdoctoral Positions in Human Intracranial Physiology at the National Institutes of Health

Two full-time post-doctoral position focused on understanding the neural correlates of cognitive function and on the physiology of seizure onset and propagation are available in the Surgical Neurology Branch of the National Institute of Neurological Disorders and Stroke at the NIH. The first position involves studies focused on designing and investigating behavioral tasks related to memory encoding, decision making, and attention, and on analyzing and manipulating human intracranial signals, including single-unit activity, local field potentials, and electro corticography (ECoG), captured from patients with medically refractory epilepsy and from patients receiving deep brain stimulation surgery. The goal of this project is to investigate the neural mechanisms that underlie cognitive behavior. The second position involves studies focused on analyzing ictal and inter-ictal activity across multiple modalities from patients with medically refractory epilepsy, including ECoG r
ecordings and single-unit activity captured through implanted microwires. The goal of this project is to link these data with data captured using MEG, high-density scalp EEG, and functional MRI in order to gain insight into the seizure localization, onset, and spread. Post-doctoral fellows will join a laboratory aimed at understanding the neural mechanisms that underlie human cognitive function and abnormal seizure physiology and at developing novel and innovative techniques to decode and directly communicate with those circuits through electrical stimulation.

We are seeking candidates that are highly creative, motivated, and independent with a Ph.D. in neuroscience, psychology, biomedical engineering, or a related field. Candidates must have a strong research background, with a record of relevant publications. Candidates will be encouraged and expected to participate in independent laboratory research, and will be expected to write scholarly manuscripts. Candidates must be able to lead and work well in a team. Candidates should have strong computational, quantitative, and/or engineering skills, with proficiency in developing custom code for data analysis preferred. Past medical research is not required, but candidates must be willing to perform experiments in a clinical setting. Candidates will interact with clinical staff, graduate students, research fellows, and must have excellent spoken and written English skills.

Applicants should submit a brief statement of research activities and interests, a current CV, and names and contact information of at least three references. Salary will be commensurate with experience and accomplishments. To arrange a meeting with the PI and to send materials required for consideration for this appointment please contact Dr. Zaghloul at zaghloulka@mail.nih.gov.
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[Comp-neuro] 1 PhD +1 Postdoctoral position in Computational Neuroscience at CRM / IDIBAPS (Barcelona).

Dear Colleagues,


We are looking for one PhD student and one Postdoctoral fellow to work in a joint project between the labs of Alex Roxin (Centre de Reserca Matemàtica, CRM) and the lab of Jaime de la Rocha (IDIBAPS). The projects require the development of network models to investigate spontaneous activity in cortical circuits and the relation between neuronal and behavioral variability. The funding comes from an agreement between La Caixa and the Catalan Government to sponsor a training programme on Collaborative Mathematics presented by the CRM. Several positions are available within the training program which offers other projects. Candidates would be chosen on based on academic merit. Funding for the PhD position lasts 39 months and for the postdoctoral position lasts 3 years. Start dates from Fall to Winter 2014-2015 are preferred. The deadline to apply is April 16, 2014.

Information about how to apply and a description of the projects can be found here:

http://www.crm.cat/SiteAssets/Lists/Crides/EditForm/Calls_Collaborative%20Mathematical%20Research.pdf

If you have any questions please contact Alex Roxin (aroxin@crm.cat<mailto:aroxin@crm.cat>) or Jaime de la Rocha (jrochav@clinic.ub.es<mailto:jrochav@clinic.ub.es>).


Best

Jaime



Jaime de la Rocha
Ramón y Cajal researcher at IDIABPS
c. Roselló 149-153
Barcelona, 08036 Spain
Tel. +34 932275400 (4307)
http://neuro.fcrb.es/delaRochaLab





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