Tools that contain the Simulator Tool Topic : Utility

(Performs operating system-level procedures such as searching for filenames in paths.)
1. Convert NEURON vectors to sine wave "wav" audio files At the suggestion of Ann Stuart and John Moore a matlab translation program was written which converts vectors written from NEURON to "wav" audio files.
2. Data thief-like python script that converts paper figures to NEURON vector dat files Retrieve (approximate) values from graphs! By first using inkscape (available for free from equivalent) to prepare a file created by clicking on traces on a graph, this python script,, will create vector dat files suitable for reading into NEURON. See readme.txt for detailed usage instructions.
3. Destexhe methods for creating movies from NEURON This tutorial explains a couple of ways to create an mpeg movie from NEURON. This file is available from Alain's web site:
4. emacs mode scripts for hoc and mod files These ".el" emacs mode files were supplied by Karoly Antal.
5. fftilt Low-pass filtering using NEURON's fft() routine
6. Find a file within the paths supplied by an environment variable. See the readme.txt below for a sample use and a listing of this function.
7. mknrndll shortcut for Windows v2.0 (Shailesh Appukuttan) This NEURON plug-in would provide a shortcut for compiling .mod files by adding ‘mknrndll’ as an option to mouse right-click context menu. It also avoids having to specify the compile directory by implicitly accepting the folder inside which you right-clicked as the location. See included 'ReadMe.pdf' file for screenshots and more details.
8. Modification of the built-in NetStim.mod of NEURON 6.1 (Johannes Luthman) Changes from NetStim: The output events can be set to follow gamma distributions of order 1-6, where 1 corresponds to the original Poisson process generated by NetStim.mod. The gamma process is generated in the same way as that given by timetable.c in GENESIS 2.3. A refractory period has been added. The output length is determined by duration in ms instead of number of events.
9. netconinc is a general summed synapse mechanism based on <br> <br> Lytton WW. Optimizing synaptic conductance calculation for network simulations <br> Neural Computation, 8:501--510, 1996. <br> <br> eg <br> COMMENT <br> USAGE: for most receptors <br> ***************************************************************************** <br> NEURON { <br> POINT_PROCESS NAME <br> } <br> <br> PARAMETER { <br> Cdur = 1.08 (ms) : transmitter duration (rising phase) <br> Alpha = 1 (/ms mM) : forward (binding) rate <br> Beta = 0.02 (/ms) : backward (unbinding) rate <br> Erev = -80 (mV) : reversal potential <br> } <br> <br> INCLUDE "" <br> ***************************************************************************** <br>
10. NeuGen NeuGen is a tool for the efficient generation and description of dendritic and axonal morphology of realistic neurons and neural networks in 3D. The 'in silico' neurons are based on cells of cortical columns in the neocortex. NeuGen can generate hoc files suitable for simulation with NEURON. The NeuGen development team includes Jens P. Eberhard, Alexander Wanner, Simone Eberhard, and Sergei Wolf. For documentation and download, see <a href=""></a>
11. NeuroidNet Simulator (Gunay and Maida 2003) extension of (Valiant 1994) Simulator used in Gunay C, Maida AS. "Temporal binding as an inducer for connectionist recruitment learning over delayed lines". Neural Netw. 2003 Jun-Jul;16(5-6):593-600. The Neuroidal framework was proposed by Valiant in "Circuits of the Mind," 1994. This version extends the neuroidal networks to use integrate-and-fire spiking neurons and analyze timing issues in networks with asymmetric topologies. The simulator is flexible such that other network topologies or computing units can easily be employed.
12. NQS NQS is a databasing program with a query command modeled loosely on the SQL select command. <p> Please see the manual NQS.pdf for details of use.<P> An NQS database must be populated with data to be used. You may wish to download (model fingerprint) which provides an example of NQS use. <p>
13. PANDORA Neural Analysis Toolbox <p>PANDORA is a Matlab Toolbox that makes database management accessible from your electrophysiology project. <p>PANDORA works by extracting user-defined characteristics from raw neural data (e.g., voltage traces) and creating numerical database tables from them. These tables can then be subjected to further analyses, such as invariant effects, statistical, correlation, and principal components. Publication-ready plots can be produced with an embedded plotting system. <p> PANDORA's features are: <ul> <li>Works offline within Matlab; <li>requires no external software; <li>is object oriented and allows easy extensions; <li>can easily tie with existing Matlab scripts; <li>can query a database as in SQL. </ul> <p>See <a href="">the PANDORA website</a> for finding documentation and the latest version of the toolbox.
14. Robust formant tracking (Mustafa and Bruce 2006) "Several algorithms have been developed for tracking formant frequency trajectories of speech signals, however most of these algorithms are either not robust in real-life noise environments or are not suitable for real-time implementation. The algorithm presented in this paper obtains formant frequency estimates from voiced segments of continuous speech by using a time-varying adaptive filterbank to track individual formant frequencies. The formant tracker incorporates an adaptive voicing detector and a gender detector for formant extraction from continuous speech, for both male and female speakers. ..."
15. Section Copy Tool (Shailesh Appukuttan) Copies biophysical data (Distributed Mechanisms & L, nseg, Ra) from a specified section to all sections contained in the given SectionList
16. ThetaStim mechanism for NEURON models A Theta Stimulation protocol is one where a smaller group of spikes say 4 at 50 Hz is repeated at a longer interval, for example every 100 ms. Run the demo to experiment with different settings.
17. timer return amount of processor time used by a hoc call<br> only tested under LINUX (other UNIX systems may require changing #include -- see 'man clock') <br> // time("job()") will return processor time required to run job<br> // if tmstr is set then time() will run job listed there (default "run()")<br> // prints out date before and after as well as processor time so can assess loading<br> // if CPU is unloaded real elapsed time should equal processor time<br>
18. union Union allows storage of a double, string or object <br/> It is useful as a localobj in an obfunc since it will permit returning anything <br/> It also makes it easy to pick up any kind of value out of a list, vector or array <br/> USAGE: XO=new Union(val) where val can be a number string or object <ul> <li> XO=new Union(list,index) will pick up a string or object from list <li> XO=new Union(vec,index) will pick up a number from vector <li> XO=new Union(&dbl,index) will pick up a number from double array </ul>