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
We here present our poster, MASSIVELY-
PARALLEL COMPUTATIONAL STRATEGIES FOR ANALYSES OF MULTIELECTRODE
, 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
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-
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
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
(version 3.0.1 or greater). Please
see the detailed Version
for more information. To download the new release please go to the
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
) and writing (
) continuous data (e.g., LFP). Function
is now able to handle continuous data; see the new demo
Please see the detailed
for more information. To download the new release please go to the
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
. To download the new release please go to the
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
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
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.