-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathindex.html
138 lines (124 loc) · 9.24 KB
/
index.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>Welcome to DCProgs’s documentation! — DCProgs 0.9 documentation</title>
<link rel="stylesheet" href="_static/haiku.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '0.9',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="top" title="DCProgs 0.9 documentation" href="#" />
<link rel="next" title="User Guide" href="manual.html" />
</head>
<body role="document">
<div class="header" role="banner"><h1 class="heading"><a href="#">
<span>DCProgs 0.9 documentation</span></a></h1>
<h2 class="heading"><span>Welcome to DCProgs’s documentation!</span></h2>
</div>
<div class="topnav" role="navigation" aria-label="top navigation">
<p>
<a class="uplink" href="#">Contents</a>
  ::  
<a href="manual.html">User Guide</a>  »
</p>
</div>
<div class="content">
<div class="section" id="welcome-to-dcprogs-s-documentation">
<h1>Welcome to DCProgs’s documentation!<a class="headerlink" href="#welcome-to-dcprogs-s-documentation" title="Permalink to this headline">¶</a></h1>
<p>The goal of DCProgs is to provide a collection of tools for scientific research on ion channels. The
package is derived from the <a class="reference external" href="http://www.ucl.ac.uk/Pharmacology/dcpr95.html">DCPROGS</a> suite and will consist of a Python port and wrap of Fortran
code with ~30 years usage at University College London. The rationale is to preserve and cultivate
these tools for future research applications.</p>
<p>For a description of the methods involved, see <a class="reference internal" href="#colquhoun-1982" id="id1">[CH82]</a>, <a class="reference internal" href="#hawkes-1992" id="id2">[HJC92]</a>,
<a class="reference internal" href="#colquhoun-1995a" id="id3">[CH95b]</a>, <a class="reference internal" href="#colquhoun-1995b" id="id4">[CH95a]</a>, <a class="reference internal" href="#colquhoun-1996" id="id5">[CHS96]</a>.</p>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="manual.html">User Guide</a><ul>
<li class="toctree-l2"><a class="reference internal" href="manual/qmatrix.html">The <span class="math">\(Q\)</span>-matrix</a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/likelihood_of_Q.html">Likelihood <span class="math">\(L(Q)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/missedeventsG.html">Missed-Events Likelihood <span class="math">\({}^eG(t)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/idealG.html">Ideal Likelihood <span class="math">\(\mathcal{G}(t)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/occupancies.html">Occupancies</a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/exact_survivor.html">Exact Survivor Function <span class="math">\(R_A(t)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/approx_survivor.html">Approximate Survivor Function <span class="math">\(R_A(t)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/determinant_equation.html">Determinant Equation <span class="math">\(W(s) = sI - H(s)\)</span></a></li>
<li class="toctree-l2"><a class="reference internal" href="manual/roots.html">Searching for Roots</a></li>
<li class="toctree-l2"><a class="reference internal" href="manual.html#how-to-read-this-manual">How to read this manual</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="api.html">Application Programming Interface:</a><ul>
<li class="toctree-l2"><a class="reference internal" href="api/cpp.html">C++ API Reference</a></li>
<li class="toctree-l2"><a class="reference internal" href="api/python.html">Python API Reference</a></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="indices-and-tables">
<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
</ul>
<p id="bibtex-bibliography-index-0"><table class="docutils citation" frame="void" id="colquhoun-1982" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id1">[CH82]</a></td><td>D. Colquhoun and A. G. Hawkes. On the stochastic properties of bursts of single ion channel openings and of clusters of bursts. <em>Philosophical Transactions of the Royal Society of London. B, Biological Sciences</em>, 300(1098):1–59, December 1982. URL: <a class="reference external" href="http://rstb.royalsocietypublishing.org/content/300/1098/1">http://rstb.royalsocietypublishing.org/content/300/1098/1</a>, <a class="reference external" href="http://dx.doi.org/10.1098/rstb.1982.0156">doi:10.1098/rstb.1982.0156</a>.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="colquhoun-1995b" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id4">[CH95a]</a></td><td>D. Colquhoun and A. G. Hawkes. A q-matrix cookbook. In B Sakmann and E Neher, editors, <em>Single-channel recording</em>, pages 589–633. Plenum Press, New York, 2nd edition, 1995.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="colquhoun-1995a" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id3">[CH95b]</a></td><td>D. Colquhoun and A. G. Hawkes. The principles of the stochastic interpretation of ion channel mechanisms. In B Sakmann and E Neher, editors, <em>Single-channel recording</em>, pages 397–482. Plenum Press, New York, 2nd edition, 1995.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="colquhoun-1996" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id5">[CHS96]</a></td><td>D. Colquhoun, A. G. Hawkes, and K. Srodzinski. Joint distributions of apparent open and shut times of single-ion channels and maximum likelihood fitting of mechanisms. <em>Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences</em>, 354(1718):2555–2590, November 1996. URL: <a class="reference external" href="http://rsta.royalsocietypublishing.org/content/354/1718/2555">http://rsta.royalsocietypublishing.org/content/354/1718/2555</a>, <a class="reference external" href="http://dx.doi.org/10.1098/rsta.1996.0115">doi:10.1098/rsta.1996.0115</a>.</td></tr>
</tbody>
</table>
<table class="docutils citation" frame="void" id="hawkes-1992" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label"><a class="fn-backref" href="#id2">[HJC92]</a></td><td>A. G. Hawkes, A. Jalali, and D. Colquhoun. Asymptotic distributions of apparent open times and shut times in a single channel record allowing for the omission of brief events. <em>Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences</em>, 337(1282):383–404, September 1992. URL: <a class="reference external" href="http://rstb.royalsocietypublishing.org/content/337/1282/383">http://rstb.royalsocietypublishing.org/content/337/1282/383</a>, <a class="reference external" href="http://dx.doi.org/10.1098/rstb.1992.0116">doi:10.1098/rstb.1992.0116</a>.</td></tr>
</tbody>
</table>
</p>
</div>
</div>
</div>
<div class="bottomnav" role="navigation" aria-label="bottom navigation">
<p>
<a class="uplink" href="#">Contents</a>
  ::  
<a href="manual.html">User Guide</a>  »
</p>
</div>
<div class="footer" role="contentinfo">
© Copyright 2013-2016, University College London.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
</div>
</body>
</html>