Tools that contain the Simulator Tool Topic : File manipulation

(These utilities process files.)
No.ToolDescription
1. 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!
2. 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.
3. 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
4. emacs mode scripts for hoc and mod files These ".el" emacs mode files were supplied by Karoly Antal.
5. 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
6. 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="http://software.incf.org/software/pandora">the PANDORA website</a> for finding documentation and the latest version of the toolbox.
7. SimTracker - Parallel NEURON network model simulation management & analysis The SimTracker tool streamlines the entire modeling process, from code writing/versioning and simulation design to execution of simulations on a variety of machines (local, remote supercomputer, NSG) to organization and analysis of simulation results. It also provides tools to: - characterize model components (cells, synapses, ion channels) in experimentalist-friendly ways - read in experimental data and fit model components using that data (in conjunction with NEURON's Multiple Run Fitter) - Explore the parameter space of the model - Share model specifications and results online in an interactive manner, as an alternative to placing all the figures/tables into a supplemental PDF for a publication, although LaTeX code for a PDF can also be generated.