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  Welcome to the BrainML Data Server at Neurodatabase.org



This site hosts a public neurophysiology database. You may access the database, contribute to it, or learn more about it here.

Use the links at left to navigate. Click on the logo at top left or use the "back" button to return to this page.

Please see also the newest projects of the Laboratory of Neuroinformatics:
- our Spike Train Analysis Toolkit; and
- our very new plans to develop essential neurophysiology analyses for the enabling platform of GPU-parallel processor cards.




News

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 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 (on neuroanalysis.org) for more information. To download the new release please go to the Download page.

July 25, 2007

Updated list of submissions to indicate large datasets with long loading times. Users are also provided alternate links to avoid the large datasets and thus provide quicker browsing of metadata. Datasets are now viewed using the Lab of Neuroinformatics' Visual Oscilloscope Tool (a Java application) that provides more dynamic viewing options. Previously, datasets were viewed only through static images. Submissions now display 50 traces per view at a time. This is intended to reduce the loading time of the submission.


December 15, 2006

Open Source Version 1.0 released. You may now download the source code for the repository and web start applications at neurodatabase.org here. Robustness improvements and bug fixes.


May 31, 2006

Version 3.1 released. Archiving and upgrade capabilities added. Metadata display improvements. Plots now appear in popup window. Robustness improvements and bug fixes.


April 6, 2006

Version 3.0 released. Java Upload Tool added in updated form. Unique, human readable IDs used for all submissions. Visualization and CSV download capability added to server. Robustness improvements and bug fixes.


January 27, 2006

Version 2.1 (beta2) released. Bug fixes and aesthetic improvements.


November 11, 2005

The BrainML Data Server Version 2.0 (beta1) is now on line. This software replaces what was formerly known as the Common Data Model (CDM) Cortical Neurodatabase. It fully configured dynamically at runtime to serve data conforming to a selected data model at brainml.org.

Using this software, a custom neuroscience data repository may be created for any data model with no custom programming, by writing simple XML interface specification files. This software will be released open source once it reaches a mature state.




The BrainML project is funded by the Human Brain Project-Informatics initiative via MH/NS57153 from the NIMH and NINDS (with related and past additional funding from NSF, NINDS, and NIMH) and is directed by:

Daniel Gardner


Weill Medical College of Cornell University
dan@aplysia.med.cornell.edu

 




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Weill Medical College of Cornell University