Tools that contain the Modeling Application : NEURON (Home Page)

(NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons. It is particularly well-suited to problems where cable properties of cells play an important role, possibly including extracellular potential close to the membrane), and where cell membrane properties are complex, involving many ion-specific channels, ion accumulation, and second messengers. It evolved from a long collaboration between Michael Hines and John W. Moore at the Department of Neurobiology, Duke University. Their express goal was to create a tool designed specifically for solving the equations that describe nerve cells.)
No.ToolDescription
1. AP halfwidth measurement for NEURON This simple example shows how to measure half width of Action Potentials (in milliseconds).
2. Average a data file to make a smaller data file This utility will read the file specified in the hoc program and write the file specified in the hoc program with blocks of the input file averaged into a single time point. (See top of hoc file for settings) This is a very simple program!
3. Cross Correlation Tool This GUI tool wraps the Vector.correl function http://www.neuron.yale.edu/neuron/docs/help/neuron/general/classes/vector/vect2.html#$Since Vector.correl is implemented using the fast fourier transform this tool interpolates the vectors in the domain tbegin to tend onto a grid with number of points equal to a power of 2. To do this an "actual dt" is selected which is near the "nominal dt" grid spacing and satisfies (tend-tbegin)/"actual dt" = 2^n where n is an integer.
4. Data thief-like python script that converts figures to NEURON vector dat files By first preparing a polyline(s) file written by idraw, this python script, traces2vecs.py, will create vector dat files suitable for reading into NEURON. See readme.txt for usage instructions. An idraw that imports tif files can be installed on ubuntu with sudo apt-get install ivtools-bin
5. Demonstration of order of execution of blocks in NEURON mod files Demonstration of order of execution of blocks in NEURON mod files.
6. 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: http://cns.iaf.cnrs-gif.fr/alain_demos.html
7. emacs mode scripts for hoc and mod files These ".el" emacs mode files were supplied by Karoly Antal.
8. fftilt Low-pass filtering using NEURON's fft() routine
9. 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.
10. loadfiles perl script reads load_file() statements in a hoc file to create a single hoc output file with loaded hoc code inserted in place of the load_file statements uses HOC_LIBRARY_PATH to locate files several options available -- call without args for help limitations: 1. does not read xopen() commands 2. does not process 2 arg load_file() command 3. cannot handle a load_file() embedded in an if {} or other other control structure (this requires logical parsing of the whole file as can only be done by hoc parser) -- will generate an error
11. MFP For use with the NQS tool available in SimToolDB<p> Organizes conductance and tree information from ModelDB models into a relational database for data-mining.<p>
12. 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.
13. 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.
14. netconinc netcon.inc 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 "netsyn.inc" <br> ***************************************************************************** <br>
15. NEURON interface to GAUL (Neymotin and Lytton) This interface allows the use of genetic algorithms for optimization and search in high-dimensional spaces from within the NEURON environment. It includes converted .c,.h files from GAUL wrapped in proper MOD file syntax as well as MOD code interfacing to the library. It also comes with hoc utilitiy functions to make it easier to use the GA.
16. 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 MFP.zip (model fingerprint) which provides an example of NQS use. <p>
17. Sample Entropy (SampEn) method (Neymotin et al. 2010) "... To determine the complexity of the EEG time series, we calculated the sample entropy (SampEn) .... SampEn is the negative natural logarithm of an estimate of the conditional probability that subseries (epochs) of length m-1 that match pointwise within a tolerance r also match at the mth point. ..."
18. 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
19. Stretch reflex and gamma loop This network model by Sergiu Abramovici examines the stretch reflex and gamma loop.
20. 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.
21. 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>
22. Tutorial: Partially Demyelinated Axon In this study, the goal was to observe the action potential propagation of a partially demyelinated axon. The simulation was derived from Moore JW, Joyner RW, Brill MH, Waxman SD, Najar-Joa M (1978) Simulations of conduction in uniform myelinated fibers. Relative sensitivity to changes in nodal and internodal parameters. Biophys J 21:147-60
23. 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>