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<!DOCTYPE html>
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<title>DSGRN Documentation</title>
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<body class="article toc2 toc-right">
<div id="header">
<h1>DSGRN Documentation</h1>
<div class="details">
<span id="author" class="author">Shaun Harker</span><br>
<span id="email" class="email"><a href="mailto:[email protected]">[email protected]</a></span><br>
<span id="revnumber">version 1.0,</span>
<span id="revdate">2015-05-21</span>
</div>
<div id="toc" class="toc2">
<div id="toctitle">Table of Contents</div>
<ul class="sectlevel1">
<li><a href="#_purpose">Purpose</a></li>
<li><a href="#_installation">Installation</a></li>
<li><a href="#_dependencies">Dependencies</a></li>
<li><a href="#_about_the_installation">About the installation</a>
<ul class="sectlevel2">
<li><a href="#_mac_os_x">Mac OS X:</a></li>
<li><a href="#_linux">Linux:</a></li>
</ul>
</li>
<li><a href="#_network_components">Network Components</a>
<ul class="sectlevel2">
<li><a href="#_logics_and_partitions">Logics and Partitions</a></li>
<li><a href="#_description_files">Description Files</a></li>
</ul>
</li>
<li><a href="#_parameter_representation">Parameter Representation</a>
<ul class="sectlevel2">
<li><a href="#_binning_representation">Binning Representation</a></li>
<li><a href="#_hex_representation">Hex Representation</a></li>
<li><a href="#_comparison">Comparison</a></li>
<li><a href="#_conversion">Conversion</a></li>
</ul>
</li>
<li><a href="#_networks">Networks</a>
<ul class="sectlevel2">
<li><a href="#_network_spec_files">Network Spec Files</a></li>
<li><a href="#_network_builder">Network Builder</a></li>
</ul>
</li>
<li><a href="#_high_level_api">High-level API</a>
<ul class="sectlevel2">
<li><a href="#_dsgrn_tutorial">DSGRN Tutorial</a></li>
<li><a href="#_database_tutorial">Database Tutorial</a></li>
</ul>
</li>
<li><a href="#_low_level_api">Low-level API</a>
<ul class="sectlevel2">
<li><a href="#_network_interface">Network Interface</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="content">
<div class="sect1">
<h2 id="_purpose">Purpose</h2>
<div class="sectionbody">
<div class="paragraph">
<p>Here we document technical information regarding the <a href="https://github.com/shaunharker/DSGRN">DSGRN</a> (<em>Dynamic Signatures Generated by Regulatory Networks</em>) project.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_installation">Installation</h2>
<div class="sectionbody">
<div class="paragraph">
<p>The installation proceeds in two stages.
First, install the prerequisites.
Second, build and install the DSGRN software.</p>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_dependencies">Dependencies</h2>
<div class="sectionbody">
<div class="paragraph">
<p>The dependencies are:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>C++11 compiler</p>
</li>
<li>
<p>Boost 1.58</p>
</li>
<li>
<p>Open MPI</p>
</li>
<li>
<p><a href="https://github.com/shaunharker/cluster-delegator.git">cluster-delegator</a></p>
</li>
<li>
<p>sqlite3</p>
</li>
</ul>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_about_the_installation">About the installation</h2>
<div class="sectionbody">
<div class="paragraph">
<p>DSGRN is installed by invoking the <code>install.sh</code> script in the source root.
The location it installed is determined by the so-called installation prefix.
This can be specified as in the following example:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code>./install.sh --prefix=/opt/local</code></pre>
</div>
</div>
<div class="paragraph">
<p>If the installation prefix is not specified than a default value is used.
This value is <code>/usr/local</code>. If, however, you do not have write privileges to <code>/usr/local</code>,
then the installer will check to see if you have a directory named <code>~/.local</code>.
If you do, then that will be the installation prefix. Otherwise the installer fails.</p>
</div>
<div class="paragraph">
<p>Assuming an installation prefix of <code>/usr/local</code> the files installed are as follows:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code> /usr/local/bin (dsgrn)
/usr/local/lib (libdsgrn.a, libdsgrn.so, libdsgrn.dylib)
/usr/local/share (DSGRN/logic/*.dat)</code></pre>
</div>
</div>
<div class="sect2">
<h3 id="_mac_os_x">Mac OS X:</h3>
<div class="paragraph">
<p>On Mac OS X, C++11 and sqlite3 come along with the standard command line tools. For Boost and OpenMPI I recommend using the "homebrew" installer. Cluster-delegator can be retrieved from the git repository.</p>
</div>
<div class="paragraph">
<p>Example installation using homebrew:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code>brew install boost
brew install openmpi
git clone https://github.com/shaunharker/cluster-delegator.git
./cluster-delegator/install.sh
git clone https://github.com/shaunharker/DSGRN.git
./DSGRN/install.sh</code></pre>
</div>
</div>
</div>
<div class="sect2">
<h3 id="_linux">Linux:</h3>
<div class="paragraph">
<p>Logs of successful Linux installations are available from Travis CI:</p>
</div>
<div class="paragraph">
<p><a href="https://travis-ci.org/shaunharker/DSGRN" class="bare">https://travis-ci.org/shaunharker/DSGRN</a></p>
</div>
<div class="paragraph">
<p>You may find the included scripts</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code> ./.travis.yml
./.install/boost.sh
./.install/openmpi.sh
./.install/sqlite3.sh</code></pre>
</div>
</div>
<div class="paragraph">
<p>useful.</p>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_network_components">Network Components</h2>
<div class="sectionbody">
<div class="paragraph">
<p>A network component is a building block of a network. It consists of a node, the number of input edges, the number of output edges, and a <em>logic</em>, which is an algebraic combination of variables associated with the input edges. In particular, we assume this algebraic combination is a product of sums, each input variable occurs precisely once, and all coefficients are unity.</p>
</div>
<div class="sect2">
<h3 id="_logics_and_partitions">Logics and Partitions</h3>
<div class="paragraph">
<p>The logic \(L\), as a product of sums, can be associated with a partitioning of the inputs into \(k\) groups of sizes \(p_1, p_2, p_3, \cdots, p_k\), where \(p_1 + p_2 + p_3 + ... + p_k = n\) and without loss \(p_1 \leq p_2 \leq p_3 \leq \cdots \leq p_k\). We call \((p_1, p_2, \cdots, p_k)\) the <em>partition associated with the logic</em>.</p>
</div>
</div>
<div class="sect2">
<h3 id="_description_files">Description Files</h3>
<div class="paragraph">
<p>Given a network node, its <em>description triple</em> is the tuple \((n,m,(p_1, p_2, \cdots, p_k))\) where \(n\) is the number of inputs, \(m\) is the number of outputs, and \((p_1, p_2, \cdots, p_k)\) is the partition associated with the logic.</p>
</div>
<div class="paragraph">
<p>We maintain a repository of files which contain information about various network components. They are named in accordance to their description triple, using underscores as separators:</p>
</div>
<div class="paragraph">
<p><code>n_m_p1_p2_p3_..._pk</code></p>
</div>
<div class="paragraph">
<p>To clarify we give an example. Consider a network node named X1 with 3 inputs (X0, X3, and X4) and 2 outputs (X2 and X5), with a logic of \((\mathrm{X3}+\mathrm{X0})\mathrm{X4}\). See the following figure:</p>
</div>
<div id="NetworkComponentExample" class="imageblock">
<div class="content">
<img src="doc/images/network_component.png" alt="Network Component Example">
</div>
<div class="title">Figure 1. Network Component Example</div>
</div>
<div class="paragraph">
<p>Then we have \(n = 3\), \(m = 2\), and the logic \(L\) is associated with a partition of \(n\) into \(k=2\) groups of sizes \(p_1 = 1\) and \(p_2 = 2\). This results in the following name:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">3_2_1_2.txt</code></pre>
</div>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_parameter_representation">Parameter Representation</h2>
<div class="sectionbody">
<div class="paragraph">
<p>A parameter can be understood as a set of inequalities between various input combinations and output thresholds for a network node. We give two conventions for representing parameters. The first is the <em>binning representation</em> and the second is the <em>hex representation</em>. The binning representation is more succinct, but we will prefer the hex representation because it lends itself to a more convenient comparison of parameters.</p>
</div>
<div class="sect2">
<h3 id="_binning_representation">Binning Representation</h3>
<div class="paragraph">
<p>The <em>binning representation</em> of a parameter arises by giving the <em>bin</em> for each of the \(2^n\) input combinations. A bin is a number in \(\{0,1,\cdots,m\}\) which determines the comparison between the input combination and the output edge. In particular a bin number of \(k\) indicates that the input combination activates edges \(j\) for \(j < k\). More precisely, a <em>binning representation</em> of parameter is the function</p>
</div>
<div class="paragraph">
<p>\(p: \{0,1\}^n \rightarrow \{0,1,\cdots,m\},\)</p>
</div>
<div class="paragraph">
<p>where \(p(i) > j\) iff the input combination \(i\) activates edge \(j\).</p>
</div>
<div class="paragraph">
<p>Programmatically, \(p\) may be encoded as an array of \(2^n\) binning values. For example in our C++ implementation we store the binning representation as</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-cpp" data-lang="cpp">std::vector<int64_t> bin_;</code></pre>
</div>
</div>
<div class="admonitionblock note">
<table>
<tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">
This is not as space efficient as possible. A more careful implementation would only require \(2^n \lceil \log_2 m \rceil\) bits rather than \(64 \cdot 2^n\).
</td>
</tr>
</table>
</div>
</div>
<div class="sect2">
<h3 id="_hex_representation">Hex Representation</h3>
<div class="paragraph">
<p>In the <em>hex representation</em>, we explicitly record the status of each of the comparisons between the \(2^n\) input combinations and the \(m\) output thresholds. Generically, comparisons are either \(<\) or \(>,\) which we may represent respectively as the binary bits \(0\) or \(1\). Accordingly, a <em>hex representation</em> encodes a \(2^n m\) length sequence of bits as a hexadecimal code. The hex codes strings are presented in big-endian fashion, meaning that reading from left to right the most significant nybbles (4-bit characters) come first.</p>
</div>
<div class="paragraph">
<p>We choose the following convention for the ordering of the bits. For \(0 \leq i < 2^n\) and \(0 \leq j < m\), let \(b_{ij} = 1\) if input i activates output j and let \(b_{ij} = 0\) otherwise. We order the bits \(b_{ij}\) so that the \((mi + j)\)th binary digit (where the 0th digit is the least significant) is \(b_{ij}\).</p>
</div>
<div class="paragraph">
<p>To continue the above example (<a href="#NetworkComponentExample">Network Component Example</a>), we list the contents of the network component description file for the \((3,2,(1,2))\) component:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> cat 3_2_1_2.txt | tr '\n' ' '
0000 4000 4040 4400 4440 4444 5000 5040 5050 5400 5440 5444 5450 5454 5500 5540 5544 5550 5554 5555 C000 C040 C0C0 C400 C440 C444 C4C0 C4C4 CC00 CC40 CC44 CCC0 CCC4 CCCC D000 D040 D050 D0C0 D0D0 D400 D440 D444 D450 D454 D4C0 D4C4 D4D0 D4D4 D500 D540 D544 D550 D554 D555 D5D0 D5D4 D5D5 DC00 DC40 DC44 DCC0 DCC4 DCCC DCD0 DCD4 DCDC DD00 DD40 DD44 DD50 DD54 DD55 DDC0 DDC4 DDCC DDD0 DDD4 DDD5 DDDC DDDD F000 F040 F050 F0C0 F0D0 F0F0 F400 F440 F450 F4C0 F4D0 F4D4 F4F0 F4F4 F500 F540 F550 F554 F555 F5D0 F5D4 F5D5 F5F0 F5F4 F5F5 FC00 FC40 FCC0 FCC4 FCCC FCD0 FCD4 FCDC FCF0 FCF4 FCFC FD00 FD40 FD44 FD50 FD54 FD55 FDC0 FDC4 FDCC FDD0 FDD4 FDD5 FDDC FDDD FDF0 FDF4 FDF5 FDFC FDFD FF00 FF40 FF44 FF50 FF54 FF55 FFC0 FFC4 FFCC FFD0 FFD4 FFD5 FFDC FFDD FFF0 FFF4 FFF5 FFFC FFFD FFFF</code></pre>
</div>
</div>
<div class="admonitionblock note">
<table>
<tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">
The <code>cat</code> command reads the file and writes it to standard output, which is piped <code>|</code> to the <code>tr '\n' ' '</code> command, which replaces newlines with spaces. In the file itself the hex codes are separated by newlines.
</td>
</tr>
</table>
</div>
<div class="paragraph">
<p>We see that the network component description file contains the 155 hex codes which represent the network node parameters.</p>
</div>
</div>
<div class="sect2">
<h3 id="_comparison">Comparison</h3>
<div class="paragraph">
<p>As mentioned, the binning representation (if implemented carefully) has a space advantage over the hex representation. The hex representation has its own advantages:</p>
</div>
<div class="ulist">
<ul>
<li>
<p>They can be encoded as a simple string</p>
</li>
<li>
<p>Adjacent parameters differ by one bit in this representation</p>
</li>
<li>
<p>They have meaning independent of the threshold ordering</p>
</li>
</ul>
</div>
</div>
<div class="sect2">
<h3 id="_conversion">Conversion</h3>
<div class="paragraph">
<p>The following C++ code converts between the binning representation and the hex representation:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-cpp" data-lang="cpp"> /// hex
/// Return a hex code X which represents the parameter. The
/// hex code represents a binary string in big-endian fashion.
/// For 0 <= i < 2^n and 0 <= j < m, let b_{ij} be the
/// the (i*m + j)th binary digit of X (where the 0th digit is
/// the least significant).
/// Then b_{ij} = 1 if input i activates output j
/// b_{ij} = 0 otherwise
std::string hex ( void ) const {
std::string X;
int64_t N = ( 1 << n );
char nybble = 0, mask = 1;
auto flush_nybble = [&] () {
// Hex digits 0-9
if ( nybble < 10 ) X.push_back((char)(nybble + '0'));
// Hex digits A-F
else X.push_back((char)(nybble - 10 + 'A'));
nybble = 0; mask = 1;
};
for ( int64_t i = 0; i < N; ++ i ) {
for ( int64_t j = 0; j < m; ++ j ) {
if ( bin_[i] > j ) nybble |= mask;
mask <<= 1; if ( mask == 16 ) flush_nybble();
}
}
if ( mask != 1 ) flush_nybble ();
// Put into big-endian form.
std::reverse( X . begin(), X . end () );
return result;
}</code></pre>
</div>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_networks">Networks</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_network_spec_files">Network Spec Files</h3>
<table class="tableblock frame-all grid-all spread">
<colgroup>
<col style="width: 33.3333%;">
<col style="width: 66.6667%;">
</colgroup>
<tbody>
<tr>
<td class="tableblock halign-center valign-top"><div><div id="NetworkSpecFile" class="imageblock">
<div class="content">
<img src="doc/images/network_graphviz.png" alt="Network Specification File Example" width="200" height="400">
</div>
<div class="title">Figure 2. Network Specification Example</div>
</div></div></td>
<td class="tableblock halign-left valign-top" rowspan="2"><div><div class="paragraph">
<p>A <em>network specification file</em> is a text file which describes the interactions in a gene regulatory network. The specification file contains newline separated lines which describe each network node and the structure of its inputs. Each line is of the form <code>X : L</code>, where <code>X</code> is the name of the network node (which we will call the <em>target of the line</em>, and <code>L</code> is an expression corresponding to the logic. Network node names may be any sequence of alphanumeric characters. In particular, spaces are not allowed. Logic expressions are sequences of node names joined together with whitespace, parentheses, <code>+</code> signs, and <code>~</code> signs. The whitespace and parentheses are optional and ignored except as separators. Nodes appearing in a logic are called <em>source nodes of the line</em> and indicate a repressing edge when prefixed by <code>~</code> and an activating edge otherwise. Source nodes are partitioned into <em>factors</em>: Consecutively appearing source nodes in a logic expression belong to the same factor provided there is an intervening <code>+</code> symbol, and we extend this to non-consecutive source nodes via transitive closure. The partitioning of source nodes into factors corresponds to the partition associated with the logic of the target node.</p>
</div>
<div class="paragraph">
<p>To the left we show a graphviz-rendering of a network specification file, where the activating edges are represented by normal arrowheads, the repressing edges are represented by blunt arrowheads, and the partitioning of input edges is represented by color coding.</p>
</div></div></td>
</tr>
<tr>
<td class="tableblock halign-left valign-top"><div><div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-xml" data-lang="xml">X : (X + Y3) ~Z ~W1
Y1 : X
Y2 : (Y1 + W1)
Y3 : Y2(~W1)
Z : X(~W2)
W1 : Y2(~W2)
W2 : W1</code></pre>
</div>
</div>
<div class="paragraph">
<p>Network Specification File</p>
</div></div></td>
</tr>
</tbody>
</table>
<div class="admonitionblock note">
<table>
<tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">
The syntax for network specification files will be extended to accommodate imposition of constraints on parameters such as threshold ordering and activation ordering. These extensions will be done in a backward-compatible way.
</td>
</tr>
</table>
</div>
</div>
<div class="sect2">
<h3 id="_network_builder">Network Builder</h3>
<div class="paragraph">
<p>We provide a tool, <a href="https://shaunharker.github.io/DSGRN/software/NetworkBuilder/index.html">Network Builder</a>, for graphically constructing networks and outputting network specification files. This tool also determines the number of parameters associated with a given network. The tool is browser based — so in fact we can embed it in the documentation! Here it is:</p>
</div>
<iframe
id="frame"
src="https://shaunharker.github.io/DSGRN/software/NetworkBuilder/index.html"
width="100%"
height="700"
scrolling="no">
</iframe>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_high_level_api">High-level API</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_dsgrn_tutorial">DSGRN Tutorial</h3>
<div class="paragraph">
<p>To begin with, we tell DSGRN what network we are interested in. Let’s study the network <code>2D_Example_C.txt</code>:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">X : (X)(~Y)
Y : (~X)(Y)</code></pre>
</div>
</div>
<div class="paragraph">
<p>To do this we type:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn network ./networks/2D_Example_C.txt</code></pre>
</div>
</div>
<div class="paragraph">
<p>This produces a file called <code>dsgrn.session</code> in the current working directory. You can delete it when you are done. It just remembers which network we want to study. If you change directories and call <code>dsgrn</code> again, it won’t find the session file and will have forgotten about the network.</p>
</div>
<div class="paragraph">
<p>Anyhow, we can visualize the network using DSGRN by asking it for a graphviz representation of the network. To do this, we type:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn network draw > network.gv</code></pre>
</div>
</div>
<div class="paragraph">
<p>Here we used the shell redirection operator <code>></code> to pipe the output to the file <code>network.gv</code>. We can open this up with Graphviz and we get the following image:</p>
</div>
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
"http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!-- Generated by graphviz version 2.36.0 (20140111.2315)
-->
<!-- Title: %3 Pages: 1 -->
<svg width="80pt" height="116pt"
viewBox="0.00 0.00 80.00 116.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
<g id="graph0" class="graph" transform="scale(1 1) rotate(0) translate(4 112)">
<title>%3</title>
<polygon fill="aliceblue" stroke="none" points="-4,4 -4,-112 76,-112 76,4 -4,4"/>
<!-- X -->
<g id="node1" class="node"><title>X</title>
<ellipse fill="beige" stroke="black" cx="27" cy="-90" rx="27" ry="18"/>
<text text-anchor="middle" x="27" y="-86.3" font-family="Times,serif" font-size="14.00">X</text>
</g>
<!-- X->X -->
<g id="edge2" class="edge"><title>X->X</title>
<path fill="none" stroke="darkgoldenrod" d="M46.895,-102.432C59.688,-105.675 72,-101.531 72,-90 72,-81.6218 65.5006,-77.1433 57.0395,-76.5644"/>
<polygon fill="darkgoldenrod" stroke="darkgoldenrod" points="56.5019,-73.1004 46.895,-77.5679 57.191,-80.0665 56.5019,-73.1004"/>
</g>
<!-- Y -->
<g id="node2" class="node"><title>Y</title>
<ellipse fill="beige" stroke="black" cx="27" cy="-18" rx="27" ry="18"/>
<text text-anchor="middle" x="27" y="-14.3" font-family="Times,serif" font-size="14.00">Y</text>
</g>
<!-- X->Y -->
<g id="edge4" class="edge"><title>X->Y</title>
<path fill="none" stroke="darkgoldenrod" d="M21.1601,-72.411C20.1381,-63.0465 19.9768,-51.2238 20.6763,-41.0836"/>
<polygon fill="darkgoldenrod" stroke="darkgoldenrod" points="16.0529,-36.5208 26.0156,-37.3842 25.8429,-39.3767 15.8802,-38.5133 16.0529,-36.5208"/>
<polyline fill="none" stroke="darkgoldenrod" points="21.1206,-35.9562 20.6889,-40.9375 "/>
</g>
<!-- Y->X -->
<g id="edge1" class="edge"><title>Y->X</title>
<path fill="none" stroke="black" d="M32.8794,-35.9562C33.879,-45.3841 34.0178,-57.2161 33.2959,-67.3118"/>
<polygon fill="black" stroke="black" points="37.9091,-71.8604 27.9489,-70.9695 28.127,-68.9775 38.0873,-69.8683 37.9091,-71.8604"/>
<polyline fill="none" stroke="black" points="32.8399,-72.411 33.2853,-67.4308 "/>
</g>
<!-- Y->Y -->
<g id="edge3" class="edge"><title>Y->Y</title>
<path fill="none" stroke="black" d="M46.895,-30.4321C59.688,-33.6753 72,-29.5312 72,-18 72,-9.62183 65.5006,-5.14331 57.0395,-4.56444"/>
<polygon fill="black" stroke="black" points="56.5019,-1.10045 46.895,-5.56787 57.191,-8.06645 56.5019,-1.10045"/>
</g>
</g>
</svg>
<div class="paragraph">
<p>Next, we ask about parameters. Let’s find out how many parameters there are.</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn parameter</code></pre>
</div>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">There are 1600 parameters.</code></pre>
</div>
</div>
<div class="paragraph">
<p>Looks good. Later we should add a feature that tells us how many there are for each cohort of output orderings. In this case it happens to be 4 cohorts of 400, since there are 2 output orders for both \(X\) and \(Y\).</p>
</div>
<div class="paragraph">
<p>Let’s pick a parameter out of a hat: 126. Let’s ask DSGRN about parameter 126. First, we will ask it to give us a JSON-string representing the parameter:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn parameter json 126</code></pre>
</div>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">[["X",[2,2,"C0"],[0,1]],["Y",[2,2,"C0"],[0,1]]]</code></pre>
</div>
</div>
<div class="paragraph">
<p>This is telling us that for this parameter, node \(X\) has the logic <code>[2,2,"C0"]</code> associated with it (2 inputs, 2 outputs, and hex code <code>C0</code>) and the output ordering <code>[0,1]</code>. The outputs have a natural ordering inherited from the sequence in which they appear in the network file; the <code>[0,1]</code> indicates an identity permutation of this natural ordering. Thus the outputs are ordered <code>X</code> then <code>Y</code>. Had it been <code>[1,0]</code> this would mean the other way around! In general, the \(k\)th out-ordered edge is the <code>p[k]</code> th node, where <code>p</code> is the permutation array.</p>
</div>
<div class="paragraph">
<p>We can ask about which parameter inequalities this logic/order corresponds to:</p>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn parameter inequalities 126</code></pre>
</div>
</div>
<div class="listingblock">
<div class="content">
<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">["{
L(X,X) L(Y,X) < THETA(X,X),
U(X,X) L(Y,X) < THETA(X,X),
L(X,X) U(Y,X) < THETA(X,X),
THETA(X,Y) < U(X,X) U(Y,X)
},{
THETA(X,X) < THETA(X,Y)
}",
"{
L(X,Y) L(Y,Y) < THETA(Y,X),
U(X,Y) L(Y,Y) < THETA(Y,X),
L(X,Y) U(Y,Y) < THETA(Y,X),
THETA(Y,Y) < U(X,Y) U(Y,Y)
},{
THETA(Y,X) < THETA(Y,Y)
}"]</code></pre>
</div>
</div>
<div class="paragraph">
<p>Neat. Let’s try to turn around and find out the index (i.e. 126) from the JSON-string it hands us:</p>
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<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">> dsgrn parameter index '[["X",[2,2,"C0"],[0,1]],["Y",[2,2,"C0"],[0,1]]]'</code></pre>
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<pre class="highlightjs highlight"><code class="language-bash" data-lang="bash">libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: Feature not implemented</code></pre>
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<p><em>Oh no!</em> The function to make indices out of the internal representation of parameters hasn’t been written yet. Don’t worry, this will be implemented soon. (Maybe it already has been and I haven’t gotten around to updating this doc yet!) In the meantime, how do we know the internal representation is correct? Well, we can print out the parameter inequalities:</p>
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