hg.stevelosh.com > random.stevelosh.com

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        <title>Tornado Plot Demo</title>
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        <p>The graph is 100kb wide.  The histogram is frequency of reads.</p>

        <ul>
            <li><b>cells:</b> number of cells in the population.</li>
            <li><b>synthesis time:</b> simulated synthesis time (seconds).</li>
            <!-- <li><b>firing model:</b> whether to simulate exponential firing (uses firing half-life), or linear firing (uses firing probability).</li> -->
            <!-- <li><b>firing half-life:</b> the half-life of the origin with respect to firing (seconds), e.g. a value of 5 means that this origin will fire in half of the cells after 5 seconds. Only used when exponential firing is selected.</li> -->
            <li><b>firing probability:</b> the probability this origin will fire each second.
                <!-- Only used when linear firing is selected. -->
            </li>
            <li><b>ori:</b> position of the origin.</li>
            <li><b>left/right fork rates:</b> how fast each fork progresses (nt/second).</li>
            <li><b>rate noise:</b> how much noise to add to each fork's rate (per fork, proportion of total rate).</li>
            <li><b>undercut rate:</b> proportion of reads that get missed due to undercutting.</li>
            <li><b>overcut rate:</b> proportion of reads to cut apart after generation.</li>
            <li><b>overcut exponent:</b> kludge to change distribution of cut positions (1 to cut uniformly, higher to tend to cut closer to ends).</li>
            <li><b>block locations:</b> position of blocking elements (does nothing if block time is zero).</li>
            <li><b>block times:</b> how long to pause at a particular block (seconds).</li>
        </ul>
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author	Steve Losh <steve@stevelosh.com>
date	Sun, 05 Nov 2023 13:43:36 -0500
parents	26d94a234232
children	829a5fc659a5