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  Computational Neuroinformatics Tools for Analysis of Spike Train Data



November 21, 2011 News


The recent Society for Neuroscience meeting, this summer's CNS*2011, and our successful Stockholm GPU-parallel workshop have all confirmed both the increasing interest in GPU computing for neurophysiology and also the community consensus that careful program design is needed to achieve the close-to-two-order-of-magnitude speedup potential.

We here present our poster, MASSIVELY- PARALLEL COMPUTATIONAL STRATEGIES FOR ANALYSES OF MULTIELECTRODE RECORDINGS, shown and discussed at SfN 2011.

January 6, 2011 News


Further confirming the very high potential significance of GPU-parallel processing for spike train analysis and many other areas of neurophysiology and computational neuroscience, this summer's CNS*2011 Computational Neuroscience meeting will feature a Workshop we have organized, entitled: "Enabling Super-Computational Neuroscience: Low-Cost GPU-Parallel Analyses And Simulations."

With nine confirmed speakers so far, both multielectrode neurophysiologists and computational modelers, the workshop will review the demonstrated ability, and explore the enormous potential, of GPU-parallelization. There will be an emphasis on selecting appropriate algorithms, and necessary adaptations to the GPU architecture.

Open to the many CNS*2011 registrants, the workshop will also solicit additional short talks or poster presentations. In all cases, the emphases will be on identifying areas where GPUs can have the greatest impact on multielectrode neurophysiology and other areas of computational neuroscience, and on community-enabling open source software to most appropriately leverage GPU architecture and capabilities.

This is currently planned for all day on July 27th at the CNS*2011 meeting in Stockholm. Further details, including exact scheduling and venue (either the Karolinska or the KTH Royal institute of Technology), will be forthcoming both here at neuroanalysis.org and at www.cnsorg.org/2011/.

Dec 21, 2010 News


Toward the 2011 Biophysical Society Annual Meeting, we have posted our abstract for the poster that will present our initial estimates and projections (now in progress) of the greater-than-order-of- magnitude speedups for our in-development Neurophysiology Extended Analysis Tool NEAT. Our poster 510 will be displayed on Sunday, 6 March 2011 in the Neuronal Systems & Modeling session.

Also, we have posted the PowerPoint slides from the lab's presentation on the current status of neuroanalysis.org and STAToolkit and on initial plans for the GPU-parallel implementation, given in Nanosymposium 838 at the 2010 SfN Annual Meeting.

Sep 30, 2010 News


At the 2011 Biophysical Society Annual Meeting, we will offer our initial estimates and projections of the greater-than-order-of-magnitude speedups for our in-development Neurophysiology Extended Analysis Tool NEAT. Program information will be posted in early December along with the abstract, and a PDF of the presentation following the Baltimore meeting in early March, 2011.

Aug 17, 2010 News


For the growing number of investigators with cortical and other multielectrode recording systems, we are beginning development of new GPU-enabled analysis routines. These will include versions of popular STAToolkit analyses as well as others most needed by the community. The goal is to enable online real-time analyses that are now possible only offline, and to allow others that are not now performed because the computations on even multicore CPUs are too extended.

At the 2010 SfN Annual Meeting, we offer the latest neuroanalysis.org and STAToolkit related event: Neuroanalysis.org will be included in Wednesday (November 17) afternoon's Nanosymposium 838 in room 10, San Diego Convention Center. PowerPoint slides will be posted after the session.

Feb 12, 2010 News


We are proud to announce a new release of the STAToolkit, version 1.5! The STAToolkit now works with Octave (version 3.0.1 or greater). Please see the detailed Version History for more information. To download the new release please go to the Download page.

Jan 29, 2010 News


We are proud to announce a new release of the STAToolkit, version 1.4! This version augments the input data format and input data structures to allow for reading (staread) and writing (stawrite) continuous data (e.g., LFP). Function binless is now able to handle continuous data; see the new demo. Please see the detailed Version History for more information. To download the new release please go to the Download page.

Jan 20, 2010 News


We are proud to announce a new release of the STAToolkit, version 1.3! This version includes a new information method, the context-tree weighting Markov chain Monte Carlo algorithm (CTWMCMC). For more information, please see the Introduction page, and the detailed Version History. To download the new release please go to the Download page.

Dec 29, 2009 News


To better guide users of STAToolkit and neuroanalysis.org, we have we have added new tutorial and informative material, including:
  • a new Primer: What will the Spike Train Analysis Toolkit tell me about my data?,
  • a new fast-track Getting Started section to the Introduction that concisely summarize how a neurophysiologist user can use the kind and amount of data recorded by his or her protocols to select appropriate STAToolkit methods, and
  • a newly-expanded Spike Train Analysis Toolkit Demonstrations page that now includes a tutorial on using our demo scripts to evaluate which methods best suit each user's data.
At the 2010 Biophysical Society Annual Meeting, our poster entitled Neuroanalysis.org: Information- Theoretic and Extended Analyses of Neural Coding, by Michael A. Repucci, David H. Goldberg, Eliza Chan, Ajit Jagdale, Jonathan D. Victor, Daniel Gardner, will be presented on board B609 in the Neuronal Systems & Modeling session on Sunday, 21 February 2010.

Nov 3, 2009 News


We have added two buttons to this site's homepage to encourage feedback from our users. The first links to a questionnaire intended for STAToolkit users to learn how they have used the toolkit. The second button links to a questionnaire soliciting ideas from current and future users about what direction better helps their research efforts.

Oct 7, 2009 News


At the SfN Annual Meeting, we offer two neuroanalysis.org and STAToolkit related events:
  • The STAToolkit will be one of Neuroinformatics' Greatest Hits presented at this year's Neuroinformatics Special Interest Social on Sunday, Oct 18, from 6:45 PM - 8:45 PM in McCormick Center Room N140.
  • Our poster detailing new and planned capabilities for neuroanalysis.org: Expansion and integration of neurodatabase.org and neuroanalysis.org toward enhanced data discovery and analysis by D. Gardner, E. Chan, D. H. Goldberg, A. Jagdale, M. A. Repucci, and J. D. Victor will be presented in the Methods for Extracellular Spike Train Analysis session Wednesday morning, Oct 21, as poster 789.10 on board HH2.
This project complements our development at neurodatabase.org of searchable neurophysiology databases containing spike train and other microelectrode data and allied descriptive metadata including recording site, technique, and stimulus. To aid data sharing and interoperability among neurodatabases, we have also created BrainML, an XML-based multilevel data description suite for neuroscience.


Our work in computational neuroinformatics is a component of the Human Brain Project, supported by the NIH and NSF via NIMH. To advance our understanding of neural coding, we have developed the STAToolkit, a suite of information-theoretic algorithms as a public resource for Open Source download. We are extending the capabilities of the STAToolkit with additional information-theoretic tools, as well as additional measures for synchrony, variability, and dimensional reduction to aid tractability of multineuron analyses.

To assist neurophysiologists in applying STAToolkit algorithms for computationally-intensive explorations of databased spike trains, we also offer the AnalysisServer, an open-access dedicated large-scale computational array. To schedule an analysis job for processing, please use the links above or to the left, or contact us at neurodatabase (AT) med.cornell.edu.

User feedback is essential to enhance the power and ease of use of our resources. Should you wish to be added to our growing user list for the STAT Toolkit, please email us at neurodatabase (AT) med.cornell.edu. We are also creating a wiki and additional tutorials for the downloadable STAToolkit and the AnalysisServer.


Funded by Human Brain Project/Neuroinformatics via MH68012 from NIMH, NINDS, NIA, NIBIB and NSF.

More information on this project can be found at the Spike Train Analysis Toolkit home page.




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