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Software/Data Downloads

Active software projects

  • Online Spike sorting: Osort - a Matlab implementation of my online spike sorting/unsupervised clustering algorithm. Available together with example files, documentation and the original paper.

  • Closed-loop visual stimulus display: StimOmatic - Software package (Matlab/Python) for closed-loop control and visual stimulus display, conditional on phase and power of oscillations in the LFP measured in realtime.

  • Neuralynx file reader and writer (neurophysiology file formats) for matlab on unix / linux / Mac OS X. Project homepage.

  • Implementing DFAs with Winner-take all networks: Matlab/Java package for automatically converting arbitrary deterministic state automatons to winner-take-all networks. Accompanies our recently published paper. Includes a tutorial.

Data downloads

  • Example single-neuron recordings: Provided as part of Osort.
  • Single-neuron dataset during recognition memory: Scientific Data data descriptor and data release (Dryad) of over 1500 human single neurons during new/old recognition memory task.
  • NIH NDAR releases for our projects: Project 2449 and Project 2417
  • Eye tracking. Zenodo open archive of eye tracking data and model code for our binocular rivalry study Marx et al.

Inactive software projects

  • ABI: Adaptive Building Intelligence. An opensource java framework for online learning from sparse events. Its usefulness is demonstrated by applying it to an intelligent building (integration with LON). The original ABI can be found here. New versions, originally based on ABI, can be found here.
  • Java SCEP: A SCEP (Cisco Simple Certificate Enrollment Protocol) client, including proxy for PKCS#12 key requests so that browsers can use SCEP for key requests. A SCEP server can be found here. The JAVA SCEP client is available here.


    A completely retyped version in latex (courtesy of Akram S. Sadek, Caltech) of the classic Probabilistic logics and the synthesis of reliable organisms from unreliable components by J. von Neumann, originally published in C. E. Shannon and J. McCarthy (editors), Automata Studies, 1956. Also note the article "Parallel information and computation with restitution for noise-tolerant nanoscale logic networks" by Akram S Sadek et al 2004 Nanotechnology 15:192-210 for an application to new physical substractes of computation (link).

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