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| − | <h1>Internal Tools</h1>
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| − | <h2>Number of mutations and mutated sequences</h2>
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| − | <p>Expected number of mutations in a single sequence:
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| − | $$p_{m} = \frac{N_{mutations}}{L_{Sequence}} = N_{generations} * r_{mutation} = t_{total} * \Phi * r_{mutation}$$
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| − | </p>
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| − | <p>The expected share of sequences that shows at least one mutation in \(L_{Sequence}\) bp is the probability that \(L_{sequence}\) basepairs stay unchanged when \(\frac{N_{mutations}}{L_{Sequence}}\) mutations are expected:
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| − | $$p_{M} = \frac{N_{mutated}}{N_{Sequences}} = 1 - p(N_{mutations}=0) = 1 - (1-p_{m})^{L_{Sequence}} $$
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| − | </p>
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| − | <p>With this equation we can also calculate the number of sequences \(N_{Sequences}\) that have to be sequenced in order to find a mutated one with a probability of \(p(N_{mutated} > 0)\).
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| − | $$ N_{Sequences} = \frac{p(N_{mutated} > 0)}{p_{M}} $$
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| − | </p>
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| − | <p>The probability to find at least one mutated sequence under the given conditions is
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| − | $$p(N_{mutated}>0) = 1 - (1-p_{M})^{N_{sequences}}$$
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| − | which gives
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| − | $$N_{Sequences} = \frac{ln(1-p(N_{mutated}>0))}{ln(1-p_{M})}$$
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| − | </p>
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| − | <p>Set \(\Phi\) to zero to use the number of generations for the calculation. If \(\Phi\) and the number of generations are given, \(\Phi\) is used.</p>
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| − | <p>Consider \(L_{Sequence}\) as the number of basepairs that is expected to be mutated. If half of the sequence you are interested in, is highly conserved choose a lower \(L_{Sequence}\).</p>
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| − |
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| − | </div>
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| − | <form action="" id="form1">
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| − | <section>
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| − | <h2>Get your mutations</h2>
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| − | <ul class="input-list style-1 clearfix">
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| − | <li>
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| − | <label>
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| − | Mutation rate \(r_{mutation} [bp/generation]\)
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="mr" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Flow troughLagoon \(\Phi_{lagoon} [Volumes/h]\)
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="phi" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Total time<br> in lagoon \(t_{total} [h]\)
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="tt" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Number<br> of generations \(N_{generations}\)
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ng" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Length of sequence that can mutate \(L_{Sequence} [bp]\)<br>
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ls" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Number of sequences that are sequenced \(N_{Sequences}\)<br>
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ns" value="0" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <label>
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| − | Probability to get at least one mutated result \(p(N_{mutated}>0) \)
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| − | <br>
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| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="pm" value="0.9" lang='en-150' step="any">
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| − | </label>
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| − | </li>
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| − | <li>
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| − | <div style="padding-top: 30px;">
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| − | <input type="button" value="Submit" id="input_form" onclick="return number_mutations();">
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| − | </div>
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| − | </li>
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| − | </ul>
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| − | </section>
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| − | </form>
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| − |
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| − | <br>
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| − | <p id="number_generations"></p>
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| − | <p>\(p_{m} =\) <span id="amount_mutations"></span> %(bp/bp).</p>
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| − | <p>\(N_{mutations} =\) <span id="number_mutations"></span> bp per sequence.</p>
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| − | <p>The share of sequences that shows at least one mutation in \(L_{Sequence}\) bp is \(p_{M}=\) <span id="amount_mutated"></span> % of sequences</p>
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| − | <p id="number_to_seq"></p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − |
| |
| − | <section id="footer-sec">
| |
| − | <div class="container">
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| − | <div class="row" style="padding-top: 30px;">
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| − | <div class="col-md-3">
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| − | <h4>ABOUT US </h4>
| |
| − | <p>"We are an extremely motivated team of young students competing in the worlds biggest synthetic biology competition"</p>
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| − |
| |
| − | </div>
| |
| − | <div class="col-md-3">
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| − | <h4> Useful <strong>Links</strong> </h4>
| |
| − |
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| − | <li>
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| − | <a href="#">
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| − | <i class="fa fa-angle-right">
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| − | </i>
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| − | Special pages
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| − | </a>
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| − | </li>
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| − | <li>
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| − | <a href="#">
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| − | <i class="fa fa-angle-right">
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| − | </i>
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| − | Main Page
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| − | </a>
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| − | </li>
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| − | </div>
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| − | <div class="col-md-3">
| |
| − | <h4> Follow us on </h4>
| |
| − | <a href="#" target="_blank" id="facebook"><i class="fa fa-facebook-square fa-3x"></i></a>
| |
| − | <span style="color: grey">&</span>
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| − | <a href="#" target="_blank" id="twitter"><i class="fa fa-twitter-square fa-3x"></i></a>
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| − | </div>
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| − | <div class="col-md-3">
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| − | <h4> Contact us </h4>
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| − | <li>
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| − | <i class="fa fa-map-marker fa-lg">
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| − | </i>
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| − | Im Neuenheimer Feld 267
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| − | <br>
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| − | 69120 Heidelberg
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| − | </li>
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| − | <li>
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| − | <i class="fa fa-phone">
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| − | Tel: XXXXXX
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| − | </li>
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| − | <a href="mailto:info@yourdomain.com">
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| − | bioquant@uni-heidelberg.de
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| − | </a>
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| − | </li>
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| − | </div>
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| − | </div>
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| − | </div>
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| − | </section>
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| − | <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
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| − | <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
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| − | <script src="https://cdnjs.cloudflare.com/ajax/libs/numjs/0.13.1/numjs.js"></script>
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| − | <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
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| − | <script src="http://evanplaice.github.io/jquery-csv/src/jquery.csv.min.js"></script>
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| − | <script src="https://2017.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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| − | <script>
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| − | //example that contains everything needed
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| − | function dummy(){
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| − | //get the values
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| − | var mr = Number(document.getElementById('mr').value);
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| − |
| |
| − | //initialise variables
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| − | var a_mutations = 0;
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| − |
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| − | //calculate
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| − | if(phi==0){
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| − | a_mutations = ng * mr;
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| − | }
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| − |
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| − | //return the results
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| − | $("#amount_mutated").html((Math.round(100000 * a_mutated))/1000);
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| − | $("#number_generations").html(ng_out);
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| − |
| |
| − | //end the function
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| − | return false;
| |
| − | }
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| − |
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| − | function number_mutations(){
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| − |
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| − | //get the values
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| − | var mr = Number(document.getElementById('mr').value);
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| − | var phi = Number(document.getElementById('phi').value);
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| − | var ng = Number(document.getElementById('ng').value);
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| − | var tt = Number(document.getElementById('tt').value);
| |
| − | var ls = Number(document.getElementById('ls').value);
| |
| − | var ns = Number(document.getElementById('ns').value);
| |
| − | var pm = Number(document.getElementById('pm').value);
| |
| − |
| |
| − | //initialise variables
| |
| − | var a_mutations = 0;
| |
| − | var n_mutations = '?';
| |
| − | var a_mutated = '?';
| |
| − | var ng_out = "";
| |
| − | var number_to_seq_out = "";
| |
| − | var number_to_seq = 0;
| |
| − |
| |
| − | //calculate
| |
| − | if(phi==0){
| |
| − | a_mutations = ng * mr;
| |
| − | }
| |
| − | else{
| |
| − | a_mutations = mr * tt/phi;
| |
| − | ng = tt*phi;
| |
| − | ng_out = "The conditions result in " + ng + " generations."
| |
| − | }
| |
| − |
| |
| − | n_mutations = ls * a_mutations;
| |
| − | if(ns!=0){
| |
| − | a_mutated = 1 - Math.pow((1-a_mutations), ls);
| |
| − | }
| |
| − | if(pm!=0){
| |
| − | //TODO: fix this calculation
| |
| − | number_to_seq = Math.max(1, Math.round((Math.log(1-pm))/(Math.log(1-a_mutated))));
| |
| − | number_to_seq_out = "Sequence " + number_to_seq + " clones to have a " + (pm*100) + " % probability to have at least one mutated under the results.";
| |
| − | }
| |
| − |
| |
| − | //return the results
| |
| − | $("#amount_mutations").html((Math.round(1000000 * a_mutations))/10000);
| |
| − | $("#number_mutations").html((Math.round(n_mutations*100))/100);
| |
| − | $("#amount_mutated").html((Math.round(100000 * a_mutated))/1000);
| |
| − | $("#number_generations").html(ng_out);
| |
| − | $("#number_to_seq").html(number_to_seq_out);
| |
| − |
| |
| − | //end the function
| |
| − | return false;
| |
| − | }
| |
| − |
| |
| − | function glucose(){
| |
| − | //get the values
| |
| − | var initial_concentration = Number(document.getElementById('initial_concentration').value);
| |
| − | var minimal_concentration = Number(document.getElementById('minimal_concentration').value);
| |
| − | var final_ecoli_concentration = Number(document.getElementById('final_ecoli_concentration').value);
| |
| − | var beginning_ecoli_concentration = Number(document.getElementById('beginning_ecoli_concentration').value);
| |
| − | var pace = Boolean(document.getElementById('pace').value);
| |
| − | var doubling_time = Number(document.getElementById('doubling_time').value);
| |
| − | var time_induction = Number(document.getElementById('time_induction').value);
| |
| − | var flow_lagoon = Number(document.getElementById('flow_lagoon').value);
| |
| − |
| |
| − | //initialise variables
| |
| − | var time_turbidostat = 0;
| |
| − | var time_lagoon = 0;
| |
| − |
| |
| − | //calculate
| |
| − | if(pace){
| |
| − | phi = Math.LN2/doubling_time; //vol/h, not L/h!
| |
| − | time_turbidostat = 1/phi; // as in the esvelt supplementaries?
| |
| − | time_lagoon = 1/flow_lagoon;
| |
| − | }
| |
| − |
| |
| − | //return the results
| |
| − | $("#amount_mutated").html((Math.round(100000 * a_mutated))/1000);
| |
| − | $("#number_generations").html(ng_out);
| |
| − |
| |
| − | //end the function
| |
| − | return false;
| |
| − | }
| |
| − |
| |
| − |
| |
| − |
| |
| − |
| |
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