From a115a83e6b4e89b1cb357a79fc8d65b7c55d2252 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Mon, 2 Jun 2025 17:44:39 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.md | 52 ++++++++++++++++++ index.html | 156 ----------------------------------------------------- 2 files changed, 52 insertions(+), 156 deletions(-) create mode 100644 README.md delete mode 100644 index.html diff --git a/README.md b/README.md new file mode 100644 index 0000000..4aa599a --- /dev/null +++ b/README.md @@ -0,0 +1,52 @@ +# Model Code: Ca²⁺ current vs. Ca²⁺ channel cooperativity + +[CalC Download](http://web.njit.edu/%7Ematveev/calc.html) | [CalC Manual](http://web.njit.edu/%7Ematveev/calc/manual.html) | [CalC Scripts](http://web.njit.edu/%7Ematveev/calc/scripts.html) | [CalC Publications](http://web.njit.edu/%7Ematveev/calc/calc_pub.html) | [Victor's Homepage](http://web.njit.edu/%7Ematveev/) + + +The scripts following below reproduce the simulation results presented in the manuscript: + +| | +|----------------------------------------------------------------------------------------------------------------------------------------| +| Victor V. Matveev, Richard Bertram and Arthur Sherman (2009) +**Ca²⁺ current vs. Ca²⁺ channel cooperativity of exocytosis** +*Journal of Neuroscience*, **29**(39): 12196-12209. +[Abstract](http://www.jneurosci.org/cgi/content/abstract/29/39/12196) [Full Text](http://www.jneurosci.org/cgi/content/full/29/39/12196) | + + +♦ [Fig1.par](http://web.njit.edu/%7Ematveev/Scripts/MvsN/Fig1.par) +This CalC script generates the first figure of the manuscript. It requires a single command-line parameter, the total buffer concentration (in μM) (e.g. run `calc Fig1.par 100`). The simulation produces an ASCII data file with five columns: +1. single-channel Ca²⁺ current (varied from 0.001 to 1 pA); +2. maximal release produced by a 1ms-long current pulse; +3. corresponding maximal [Ca²⁺] at release site, 30 nm from channel; +4. maximal volume-averaged [Ca²⁺]; +5. time to peak release after simulation start. + + +♦ [Fig1.m](http://web.njit.edu/%7Ematveev/Scripts/MvsN/Fig1.m) +A MATLAB m-file that generates Figure 1 using data produced by CalC script `Fig1.par` above. + + +♦ [Fig7_8.par](http://web.njit.edu/%7Ematveev/Scripts/MvsN/Fig7_8.par) +This CalC script generates data for Figures 7 and 8 of the manuscript. The simulation produces an ASCII data file used by MATLAB script `Fig7_8.m` below. + + +♦ [Fig7_8.m](http://web.njit.edu/%7Ematveev/Scripts/MvsN/Fig7_8.m) +A MATLAB m-file that generates Figures 7 and 8 using data produced by CalC script `Fig7_8.par` above. + + +♦ [process2D.m](http://web.njit.edu/%7Ematveev/Scripts/MvsN/process2D.m) +A simple MATLAB data parsing script required by MATLAB m-files `Fig1.m` and `Fig7_8.m`. + + +--- + +Supported in part by the **National Science Foundation** grant **DMS 0817703** to Victor Matveev + + +Victor Matveev +This server is running a [Redhat](http://www.redhat.com/) distribution of [Linux](http://www.linux.org/). +Last modified: January 8, 2010 + +--- + +2025-06-02: Converted README to Markdown. \ No newline at end of file diff --git a/index.html b/index.html deleted file mode 100644 index 43f161a..0000000 --- a/index.html +++ /dev/null @@ -1,156 +0,0 @@ - - - - - - - - - -Code for manuscript "Ca<sup>2+</sup> current vs. -Ca<sup>2+</sup> channel cooperativity of exocytosis" (2009) -Matveev Bertram Sherman - - - - - - - - - - - -
Model Code: Ca2+ current vs. Ca2+ channel cooperativity
CalC Download CalC Manual CalC Scripts CalC Publications Victor's Homepage

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- - - - - - - - - - - - - - - - - - - - - -
- - -The scripts following below reproduce the simulation results presented in the manuscript: -

-
-Victor V. Matveev, Richard Bertram and Arthur Sherman (2009)
-Ca2+ current vs. Ca2+ channel cooperativity of exocytosis
-Journal of Neuroscience, 29(39): 12196-12209. -[ Abstract ] -[ Full Text ] -
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-
-
-♦ Fig1.par - -This CalC script generates the first figure of the manuscript. It requires a single command-line parameters, the -total buffer concentration (in μM) (e.g. run calc Fig1.par 100). The simulation -produces an ASCII data file with five columns: -(1) single-channel Ca2+ current (varied from 0.001 to 1 pA); -(2) maximal release produced by a 1ms-long -current pulse; -(3) corresponding maximal [Ca2+] at release site, 30 nm from channel; -(4) maximal volume-averaged [Ca2+]; -(5) time to peak release after simulation start. - -

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-♦ Fig1.m - -A MATLAB m-file that generates Figure 1 using data produced by CalC script Fig1.par above. - -

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-♦ Fig7_8.par - -This CalC script generates data for Figures 7 and 8 of the manuscript. The simulation -produces an ASCII data file used by MATLAB script Fig7_8.m below. -

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-♦ Fig7_8.m - -A MATLAB m-file that generates Figures 7 and 8 using data produced by CalC script Fig7_8.par above. - -

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-♦ process2D.m - -A simple MATLAB data parsing script required by MATLAB m-files and Fig1.m and Fig7_8.m. - -

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-Supported in part by the National Science Foundation grant -DMS 0817703 to Victor Matveev -

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- -Victor Matveev - -
- -This server is running a -Redhat distribution of -Linux. -
- - -Last modified: January 8, 2010 - - - - \ No newline at end of file From be34d1bd39e7f2ad65e0054762eb66becb3d2cb1 Mon Sep 17 00:00:00 2001 From: rsakai Date: Tue, 3 Jun 2025 17:43:41 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 4aa599a..315bcc2 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,13 @@ The scripts following below reproduce the simulation results presented in the manuscript: -| | -|----------------------------------------------------------------------------------------------------------------------------------------| -| Victor V. Matveev, Richard Bertram and Arthur Sherman (2009) -**Ca²⁺ current vs. Ca²⁺ channel cooperativity of exocytosis** -*Journal of Neuroscience*, **29**(39): 12196-12209. -[Abstract](http://www.jneurosci.org/cgi/content/abstract/29/39/12196) [Full Text](http://www.jneurosci.org/cgi/content/full/29/39/12196) | +Victor V. Matveev, Richard Bertram and Arthur Sherman (2009) +**Ca²⁺ current vs. Ca²⁺ channel cooperativity of exocytosis** +*Journal of Neuroscience*, **29**(39): 12196-12209. +[Abstract](http://www.jneurosci.org/cgi/content/abstract/29/39/12196) | [Full Text](http://www.jneurosci.org/cgi/content/full/29/39/12196) +---- ♦ [Fig1.par](http://web.njit.edu/%7Ematveev/Scripts/MvsN/Fig1.par) This CalC script generates the first figure of the manuscript. It requires a single command-line parameter, the total buffer concentration (in μM) (e.g. run `calc Fig1.par 100`). The simulation produces an ASCII data file with five columns: 1. single-channel Ca²⁺ current (varied from 0.001 to 1 pA); @@ -45,8 +44,7 @@ Supported in part by the **National Science Foundation** grant **DMS 0817703** t Victor Matveev This server is running a [Redhat](http://www.redhat.com/) distribution of [Linux](http://www.linux.org/). -Last modified: January 8, 2010 --- - -2025-06-02: Converted README to Markdown. \ No newline at end of file +Last modified: January 8, 2010 +Converted README to Markdown: June 2, 2025