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Alan Garny agarny

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@agarny
agarny / runpath2rpath.c
Last active June 19, 2023 12:19
A simple program for converting a RUNPATH value to a RPATH value (for 64-bit libraries).
/*******************************************************************************
Copyright The University of Auckland
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
@agarny
agarny / pandit_hinch_niederer.cellml
Created October 22, 2015 15:31
CellML file for https://github.com/opencor/opencor/issues/581
<?xml version="1.0" encoding="UTF-8"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:semsim="http://www.bhi.washington.edu/SemSim#" xmlns:dcterms="http://purl.org/dc/terms/" name="niederer_replace_units">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<section id="sec_status">
<title>Model Status</title>
<para>This model is known to run in OpenCell and COR to reproduce the output shown in the publication. The units have been checked and they are consistent.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
@agarny
agarny / src_plugins_simulation_SingleCellView_src_singlecellviewwidget_cpp.html
Created July 10, 2014 16:47
Code used in https://github.com/opencor/opencor/issues/377
This file has been truncated, but you can view the full file.
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title>ExamDiff Pro Diff Report</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
<style type="text/css">
body {font-family: Lucida Console; font-size:13px; font-style: normal; font-weight:400; background-color:#C0C0C0;}
table {background-color:#FFFFFF;}
div {font-family: Lucida Console; font-size:13px; font-style: normal; font-weight:400; background-color:#FFFFFF;}
@agarny
agarny / gist:b051897560031a2591a2
Created July 10, 2014 16:03
parabola_as_dae_model.cellml
<?xml version="1.0" encoding="iso-8859-1"?>
<model
name="parabola_as_dae_model"
cmeta:id="parabola_as_dae_model"
xmlns="http://www.cellml.org/cellml/1.1#"
xmlns:cellml="http://www.cellml.org/cellml/1.1#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<component name="main" cmeta:id="main">
<variable name="time" units="dimensionless"/>
@agarny
agarny / LEMS_NML2_Ex9_FN.cellml
Created April 24, 2014 14:36
<?xml version='1.0' encoding='UTF-8'?>
<model name="net1" xmlns="http://www.cellml.org/cellml/1.1#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.cellml.org/cellml/1.1# http://www.cellml.org/cellml/cellml_1_1.xsd">
<!--
<documentation>
<p xmlns="http://www.w3.org/1999/xhtml">
This CellML file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.3.0
org.neuroml.model v1.3.0
jLEMS v0.9.5.2
@agarny
agarny / bondarenko_szigeti_bett_kim_rasmusson_2004_apical.cellml
Created March 24, 2014 04:19
<?xml version='1.0' encoding='utf-8'?>
<!--
This CellML file was generated on 04/12/2007 at 15:20:38 using:
COR (0.9.31.821)
Copyright 2002-2007 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk
CellML 1.0 was used to generate this cellular model
http://www.CellML.org/
@agarny
agarny / gist:5574882
Last active December 17, 2015 07:39
Ohara_Rudy_2011.cellml
<?xml version="1.0" encoding="utf-8"?>
<model name="MyModel1" cmeta:id="MyModel1" xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<units name="millisecond">
<unit units="second" prefix="milli"/>
</units>
<units name="per_millisecond">
<unit units="millisecond" exponent="-1"/>
</units>
<units name="millivolt">
<unit units="volt" prefix="milli"/>
@agarny
agarny / gist:5560821
Last active December 17, 2015 05:49
fink_slepchenko_moraru_watras_schaff_loew_2000v2.cellml
<?xml version='1.0' encoding='utf-8'?>
<model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="fink_slepchenko_moraru_watras_schaff_loew_2000_version01" cmeta:id="fink_slepchenko_moraru_watras_schaff_loew_2000_version01">
<units name="micromolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="micrometre">
<unit units="metre" prefix="micro"/>
</units>
@agarny
agarny / github-import-issues
Last active June 7, 2023 22:44
Import GitHub issues from one repository to another (incl. milestones, labels and comments).
#!/usr/bin/python
# -*- coding: utf-8 -*-
# This script came about after I removed several big files from a GitHub
# repository (see https://gist.github.com/agarny/5541082) and force pushed
# everything back to GitHub. However, cloning the 'new' GitHub repository still
# results in those big files being present in the git history. This is, among
# other things, due to some pull requests I have in that repository and which
# reference those big files. I contacted GitHub about this, but there seems to
# be nothing that they can do about it. So, I was left with no other choice but
@agarny
agarny / git-big-files
Created May 8, 2013 15:30
Retrieve and return the n largest files in a git repository
#!/bin/sh
# Retrieve and return the n largest files in a git repository
# Note: adapted from http://stubbisms.wordpress.com/2009/07/10/git-script-to-show-largest-pack-objects-and-trim-your-waist-line/
# Usage
function usage()
{
echo "Usage: `basename $0` [-n count]"