This is the readme for the NQS method presented in the paper: Lytton WW (2006) Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics 4:163-76 The following sequence will populate the NQS database with information from one of the models in ModelDB. In the following I downloaded model 44050 from ModelDB http://senselab.med.yale.edu/senselab/ModelDB/ShowModel.asp?model=44050 'CA1 pyramidal neuron: dendritic spike initiation, Gasparini et al 2004' This gave me a zip file named modeldb.zip which is included for convenience in this NQS archive. unzip NQS_with_MFP_and_model.zip // includes MFP and modeldb.zip (model accession number 44050, 2007-09-26) cp NQS/vecst.mod modeldb cd modeldb nrnivmodl setenv HOC_LIBRARY_PATH ../NQS:../MFP // run special; close native graphics nrngui forfig5A.hoc load_file("setup.hoc") load_file("mechs.hoc") trunc(nq,nq2) // create the shape databases // At this point you may wish to explore the databases by looking at various NQS commands; eg nq.gets() // show the headers nq.pr(10) // show the first 10 entries nq2.gets() // show the headers nq2.pr(10) // show the first 10 entries mechnqs(nq2) // add in the conductance densities // Now the conductances have been added to nq2; look again nq2.gets() // show the headers nq2.pr(10) // show the first 10 entries nrfp() // will graph out the conductance densities; graph may need // to be translated and resized Then hopefully you will see a result similar to fig 1 from the paper but for the Gaspirini et al. model: Note that some models may be far more complicated to load, having several different subdirectories with mod files, hoc files and templates. In such cases, it is necessary to find your way around these directories before using shape.hoc. In general, it will be necessary to recompile the model with vecst.mod included by moving vecst.mod to the directory with other mod files and then reexecuting 'nrnivmodl.' The resulting 'special' can then be run as before with nrngui and shape.hoc can be loaded with a load_file() command. Some models may cause failures when loading shape.hoc. This will occur when the underlying model to be tested defines something as an object reference or as a number that is then used differently in shape.hoc. For example, shape.hoc defines a procedure p_p(). If an underlying model executed eg 'objref p_p' or 'p_p=7.2' then an error will occur when loading shape.hoc (This problem occurs because I have not encapsulated shape.hoc in a template so as to protect its variables.) Changelog --------- 2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.