<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv=Content-Type content="text/html; charset=windows-1255"> <meta name=ProgId content=Word.Document> <meta name=Generator content="Microsoft Word 9"> <meta name=Originator content="Microsoft Word 9"> <link rel=File-List href="./ReadMe_files/filelist.xml"> <title>ReadMe</title> <!--[if gte mso 9]><xml> <o:DocumentProperties> <o:Author>Alon Korngreen</o:Author> <o:LastAuthor>Alon Korngreen</o:LastAuthor> <o:Revision>2</o:Revision> <o:TotalTime>20</o:TotalTime> <o:Created>2002-01-20T14:32:00Z</o:Created> <o:LastSaved>2002-01-20T14:32:00Z</o:LastSaved> <o:Pages>3</o:Pages> <o:Words>911</o:Words> <o:Characters>5196</o:Characters> <o:Company>utbi</o:Company> <o:Lines>43</o:Lines> <o:Paragraphs>10</o:Paragraphs> <o:CharactersWithSpaces>6381</o:CharactersWithSpaces> <o:Version>9.3821</o:Version> </o:DocumentProperties> </xml><![endif]--><!--[if gte mso 9]><xml> <w:WordDocument> <w:DrawingGridHorizontalSpacing>3 pt</w:DrawingGridHorizontalSpacing> <w:DrawingGridVerticalSpacing>8.15 pt</w:DrawingGridVerticalSpacing> <w:DisplayHorizontalDrawingGridEvery>0</w:DisplayHorizontalDrawingGridEvery> </w:WordDocument> </xml><![endif]--> <style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; text-align:right; mso-pagination:widow-orphan; direction:rtl; unicode-bidi:embed; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:21.0cm 842.0pt; margin:36.0pt 36.0pt 34.0pt 36.0pt; mso-header-margin:36.85pt; mso-footer-margin:36.85pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style> </head> <body lang=EN-US style='tab-interval:36.0pt'> <div class=Section1> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><b><span style='font-family:Arial;mso-fareast-language:EN-US'>Instructions for the demo version<o:p></o:p></span></b></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>The directory tree contains the code we developed for correcting space-clamp distortions of voltage-clamp recordings. The code is distributed in several sub directories. The example given here is a voltage clamp experiment of a 2 mm cable with an ideal two electrode voltage clamp inserted in the middle of the cable. In the simulated experiment (sub directory <b>Experimen</b>t) a homogeneous density of the kfast potassium channel (Korngreen and Sakmann 2000) is inserted into the cable and a series of steps from —80 to +70 mV is given. Then the active conductance is removed and the voltage clamp protocol is repeated to calculate the passive response of the cable. This passive response is subtracted from the first set of currents thus performing the process of leak subtraction. The leak-subtracted currents are then copied to the directory where they will be corrected for space-clamp (the <b>Fit </b>directory). In addition to this, the simulation is also run in a one-compartment model to obtain the correct kinetics of the current (directory <b>Kinetic</b>s).<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>The demo version will run only on computers with NEURON 5.0.0 or later.<span style="mso-spacerun: yes"> </span>There are two batch files provided that facilitates the process of model compilation and execution.<span style="mso-spacerun: yes"> </span>One is for Uinx and the other for Windows (in a DOS consol).<span style="mso-spacerun: yes"> </span>Due to the limitation of the Microsoft operating system you have to compile manually the nrnmech.dll in the following directories before running the batch file.<span style="mso-spacerun: yes"> </span>This is not necessary under Unix.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><b><span style='font-family:Arial;mso-fareast-language:EN-US'>Correction.Demo\Kinetics\mod<o:p></o:p></span></b></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><b><span style='font-family:Arial;mso-fareast-language:EN-US'>Correction.Demo\Experiment\mod<o:p></o:p></span></b></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><b><span style='font-family:Arial;mso-fareast-language:EN-US'>Correction.Demo\Fit\mod<o:p></o:p></span></b></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>NOTE: During the execution of the PC.bat batch file you will have to intervene and after each step close NEURON. Unlike in Unix, NEURON stays on after it finished. This stops the execution of the batch file. The execution will resume only after you close NEURON. Generally, the Unix version is more stable.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Regardless of the batch file you select, after some messages and calculations you will get a panel with the following options:<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>1. Load the leak-subtracted currents recorded from the cylinder and display them.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>2. Load the conductance density of the currents recorded from a spherical cell.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>3. Run the correction algorithm. This might take a while. On the Silicon Graphics<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Unix Origin 2000 this took 20 minutes, sun Sparc10 2.5 hours, 400 MHz Celeron<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>PC with windows 98 2 hours.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>4. This will plot the results of the correction.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>In addition to the panel you will see a graph that displays the true kinetics. The values of the time, voltage and the conductance will be updated for every step in the calculation. The value of the conductance will also be displayed on-line on top of the true conductance in a graph that should be opened automatically. For display purposes the conductance shown is the conductance after correction for the initial guess for the activation time constants. If you will press the Verbose button you will also get a text output to the consol.<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><b><span style='font-family:Arial;mso-fareast-language:EN-US'>Description of files:<o:p></o:p></span></b></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><u><span style='font-family:Arial;mso-fareast-language:EN-US'>Directory <b>Kinetic</b>s:<o:p></o:p></span></u></p> <table border=1 cellspacing=0 cellpadding=0 style='border-collapse:collapse; border:none;mso-border-alt:solid windowtext .5pt;mso-padding-alt:0cm 5.4pt 0cm 5.4pt'> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>cylinder.kin.par <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border:solid windowtext .5pt; border-left:none;mso-border-left-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>This HOC file parameters that control the simulation. Edit this file to change the kinetics in a spherical morphology. They are later used for display purposes<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Kinetics<span style="mso-spacerun: yes"> </span><o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>This file actually simulates the conductances.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>InOut.kin <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Input output routines.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Routines.kin <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>General routines used for generation of the conductances.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Cells <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>This folder contains only a one compartment model of a cell.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>mod <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>A directory containing the MOD files of the additional mechanisms that were tested.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Output <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>The output is written to this folder<o:p></o:p></span></p> </td> </tr> </table> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><u><span style='font-family:Arial;mso-fareast-language:EN-US'>Directory <b>Experiment<o:p></o:p></b></span></u></p> <table border=1 cellspacing=0 cellpadding=0 style='border-collapse:collapse; border:none;mso-border-alt:solid windowtext .5pt;mso-padding-alt:0cm 5.4pt 0cm 5.4pt'> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>cylinder.exp.par <o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border:solid windowtext .5pt; border-left:none;mso-border-left-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>This HOC file contains the parameters that control the simulation. Edit this file to change the simulation.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Experiment<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>This file actually does the simulation<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>InOut.exp<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Input output routines for the simulated experiment<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Routines.exp<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>General routines for the simulated experiment.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>ReduceModel.cell<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Used to automatically reduce the number of compartments in a fully reconstructed neuron.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Cells<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>This folder contains the files defining the morphology. It now contains only the cylinder morphology.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>ClampCurrents<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>The results of the simulation are written to this folder. The *.iCl files are the input to the fitting algorithm. To apply the correction algorithm to data from an actual experiment you will need to generate a file in the format of the *.iCl files.<o:p></o:p></span></p> </td> </tr> <tr> <td width=189 valign=top style='width:4.0cm;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>mod<o:p></o:p></span></p> </td> <td width=670 valign=top style='width:402.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>A directory containing the MOD files of the additional mechanisms that were tested.<o:p></o:p></span></p> </td> </tr> </table> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><u><span style='font-family:Arial;mso-fareast-language:EN-US'>Directory <b>Fit.<o:p></o:p></b></span></u></p> <table border=1 cellspacing=0 cellpadding=0 style='border-collapse:collapse; border:none;mso-border-alt:solid windowtext .5pt;mso-padding-alt:0cm 5.4pt 0cm 5.4pt'> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>cylinder.fit.par<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border:solid windowtext .5pt; border-left:none;mso-border-left-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>This HOC file contains the parameters that control the fit. Edit this file to change the simulation.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Fit<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Main body of the fitting algorithm<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Leak<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Calculates the leak at all voltages and writes it to file<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Display<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Contains the graphic display functions used to show the results of the fit.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Algorithm.fit<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Several routines that are called during the minimization stages.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Minimize.Algorithm.fit<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Golden bisection routines from Numerical Recipes<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>InOut.fit<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Input output routines for the fit<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>InOut.leak<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Input output routines for leak calculation<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Routines.fit<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>General routines for the fitting algorithm.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;direction:ltr; unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Routines.leak<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;direction:ltr; unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>General routines used for leak generation.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>ReduceModel.cell<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>Used to automatically reduce the number of compartments in a fully reconstructed neuron.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Cells<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>This folder contains the files defining the morphology. It now contains only the cylinder morphology.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>ClampCurrents<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>The results of the simulation are written to this folder. The *.iCl files are the input to the fitting algorithm. To apply the correction algorithm to data from an actual experiment you will need to generate a file in the format of the *.iCl files.<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Mod<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>A directory containing the MOD file of the dummy conductance<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>Output<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>The results of the calculation are written to this folder<o:p></o:p></span></p> </td> </tr> <tr> <td width=209 valign=top style='width:125.4pt;border:solid windowtext .5pt; border-top:none;mso-border-top-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>SimLeak<o:p></o:p></span></p> </td> <td width=645 valign=top style='width:387.0pt;border-top:none;border-left: none;border-bottom:solid windowtext .5pt;border-right:solid windowtext .5pt; mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt; padding:0cm 5.4pt 0cm 5.4pt'> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><span style="mso-spacerun: yes"> </span>The simulated leak is written to this folder<o:p></o:p></span></p> </td> </tr> </table> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>NOTE: We separated the code into several files to help with debugging and make the<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>code more modular. However, this is still one program. If you change the code in one<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;mso-layout-grid-align: none;text-autospace:none;direction:ltr;unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>file you may have to do this also in one or two other files. SO, be careful when you<o:p></o:p></span></p> <p class=MsoNormal style='text-align:justify;line-height:150%;direction:ltr; unicode-bidi:embed'><span style='font-family:Arial;mso-fareast-language:EN-US'>modify the code in one of these files.<o:p></o:p></span></p> </div> </body> </html>