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| − | <div class="t-container">
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| − | <div class="t-col t-col_12">
| |
| − | <div class="container-fluid" style="margin-top: 10px;" id="container1">
| |
| − | <h1>Internal Tools</h1>
| |
| − | <h2>Number of mutations and mutated sequences</h2>
| |
| − | <p>Expected number of mutations in a single sequence:
| |
| − | $$p_{m} = \frac{N_{mutations}}{L_{Sequence}} = N_{generations} \cdot r_{mutation} = t_{total} \cdot \Phi \cdot r_{mutation}$$
| |
| − | </p>
| |
| − | <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:
| |
| − | $$p_{M} = \frac{N_{mutated}}{N_{Sequences}} = 1 - p(N_{mutations}=0) = 1 - (1-p_{m})^{L_{Sequence}} $$
| |
| − | </p>
| |
| − | <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 \(p(N_{mutated} > 0)\).
| |
| − | $$ N_{Sequences} = \frac{p(N_{mutated} > 0)}{p_{M}} $$
| |
| − | </p>
| |
| − | <p>The probability to find at least one mutated sequence under the given conditions is
| |
| − | $$p(N_{mutated}>0) = 1 - (1-p_{M})^{N_{sequences}}$$
| |
| − | which gives
| |
| − | $$N_{Sequences} = \frac{ln(1-p(N_{mutated}>0))}{ln(1-p_{M})}$$
| |
| − | </p>
| |
| − | <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>
| |
| − | <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>
| |
| − |
| |
| − |
| |
| − | <form action="" id="form1">
| |
| − | <section>
| |
| − | <h2>Get your mutations</h2>
| |
| − | <ul class="input-list style-1 clearfix">
| |
| − | <li>
| |
| − | <label>
| |
| − | Mutation rate \(r_{mutation} \:[bp/generation]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="mr" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Flow troughLagoon \(\Phi_{lagoon} \: [Volumes/h]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="phi" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Total time<br> in lagoon \(t_{total} \: [h]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="tt" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Number<br> of generations \(N_{generations}\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ng" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Length of sequence that can mutate \(L_{Sequence} \: [bp]\)<br>
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ls" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Number of sequences that are sequenced \(N_{Sequences}\)<br>
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ns" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Probability to get at least one mutated result \(p(N_{mutated}>0) \)
| |
| − | <br>
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="pm" value="0.9" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <div style="padding-top: 30px;">
| |
| − | <input type="button" value="Submit" id="input_form" onclick="return number_mutations();">
| |
| − | </div>
| |
| − | </li>
| |
| − | </ul>
| |
| − | </section>
| |
| − | </form>
| |
| − | </div>
| |
| − | <div class="container-fluid" style="margin-top: 10px;" id="container2">
| |
| − | <p id="warnings_mutations"></p>
| |
| − | <br>
| |
| − | <p id="number_generations"></p>
| |
| − | <p>\(p_{m} =\) <span id="amount_mutations"></span> %(bp/bp).</p>
| |
| − | <p>\(N_{mutations} =\) <span id="number_mutations"></span> bp per sequence.</p>
| |
| − | <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>
| |
| − | <p id="probability_positive_sequencing"></p>
| |
| − | <p id="number_to_seq"></p>
| |
| − |
| |
| − |
| |
| − | <div class="container-fluid" style="margin-top: 10px;" id="container1">
| |
| − | <h2>Diff tool</h2>
| |
| − | <p>Marks differences in two strings, ignores newlines.
| |
| − | </p>
| |
| − |
| |
| − |
| |
| − | <form action="" id="form2">
| |
| − | <section>
| |
| − | <ul class="input-list style-1 clearfix">
| |
| − | <li>
| |
| − | <label>
| |
| − | String 1
| |
| − | <br>
| |
| − | <textarea id="str1" lang='en-150' rows=8 cols=50></textarea>
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | String 2
| |
| − | <br>
| |
| − | <textarea id="str2" lang='en-150' rows=8 cols=50></textarea>
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − |
| |
| − | <label for="case_sensitive">Case sensitive <input type="checkbox" Name="Case sensitive" id="case_sensitive" value="True" checked> </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <div style="padding-top: 30px;">
| |
| − | <input type="button" value="Submit" id="input_form2" onclick="return differences();">
| |
| − | </div>
| |
| − | </li>
| |
| − | </ul>
| |
| − | </section>
| |
| − | </form>
| |
| − | </div><p>Comparison:</p>
| |
| − | <div style="overflow-x:scroll !important; overflow-y:hidden !important; max-height: 100px !important; background-color: whitesmoke;">
| |
| − | <p id="outstr1" style="display:inline !important; overflow: hidden !important; white-space: nowrap !important; font-family: monospace !important;"></p>
| |
| − | <br>
| |
| − | <p id="outstr2" style="display:inline !important; overflow: hidden !important; white-space: nowrap !important; font-family: monospace !important;"></p>
| |
| − | </div>
| |
| − | <p id="diffinfo"></p>
| |
| − |
| |
| − |
| |
| − | <h2>Glucose Concentratoin</h2>
| |
| − | <p>
| |
| − | Calculate the ideal glucose concentration in the medium used for either a turbidostat or a single flask.
| |
| − | </p>
| |
| − | <p> The glucose concentration in the <b>turbidostat</b> \(c_{G_{T}}\) is increased with the incoming medium with a flow rate of \(\Phi\) and a glucose concentration of \(c_{G_{M}}\). It is decreased by with the medium that leaves the turbidostat with the same flow rate, but a glucose concentration of \(c_{G_{T}}\). Additionally E. coli take up glucose with a concentration of \(c_{E}\) and a rate of \(q\).
| |
| − | $$
| |
| − | \frac{\partial c_{G_{T}}(t)}{\partial t} = \Phi \cdot c_{G_{M}} - \Phi \cdot c_{G_{T}} - c_{E} \cdot q
| |
| − | $$
| |
| − | In the case of a turbidostat we can assume a dynamic equilibrium:
| |
| − | $$
| |
| − | \frac{\partial c_{G_{T}}(t)}{\partial t} = 0
| |
| − | $$
| |
| − | This results in
| |
| − | $$
| |
| − | c_{G_{T}} = c_{G_{M}} - \frac{c_{E. coli} \cdot q}{\Phi}
| |
| − | $$ $$
| |
| − | \Leftrightarrow c_{G_{M}} (c_{G_{T}}) = c_{G_{T}} + \frac{c_{E} \cdot q}{\Phi}
| |
| − | $$
| |
| − | </p>
| |
| − | <br>
| |
| − | <p>If the concentration of glucose in a <b>flask</b>, \(c_{G_{F}}\) needs to be determined, the functional dependencies are as follows.</p>
| |
| − | <p>
| |
| − | As there is no incoming medium, or medium that leaves the flask, the concentration of glucose is only changed by <i>E. coli</i> degrading it.
| |
| − | $$
| |
| − | \frac{\partial c_{G_{F}}(t)}{\partial t} = q \cdot c_{E}(t)
| |
| − | $$
| |
| − | Exponential growth of the <i>E. coli</i> is assumed, resulting in
| |
| − | $$c_{G_{F}}(t) = c_{G_{F}}(t_{0}) - q \cdot c_{E}(t) \cdot t
| |
| − | $$
| |
| − | $$
| |
| − | = c_{G_{F}}(t_{0}) -q \cdot \int_{t_{0}}^{t} c_{E}(t_{0}) \cdot exp\left(\frac{t}{t_{E}}\right) dt
| |
| − | $$
| |
| − | $$
| |
| − | = c_{G_{F}}(t_{0}) - q \cdot c_{E}(t_{0}) \cdot t_{E} \cdot \left(exp\left(\frac{t}{t_{E}}\right) - exp\left(\frac{t_{0}}{t_{E}}\right)\right)
| |
| − | $$
| |
| − | So the glucose starting concentration \(c_{G_{F}}(t_{0})\) needed to get a concentration of \(c_{G_{f}}(t)\) afer a duration of \(t\) is calculated by
| |
| − | $$
| |
| − | c_{G_{F}}(t_{0}) = c_{G_{F}}(t) + q \cdot c_{E}(t_{0}) \cdot t_{E} \cdot \left(exp\left(\frac{t}{t_{E}}\right) - exp\left(\frac{t_{0}}{t_{E}}\right)\right)
| |
| − | $$
| |
| − |
| |
| − | </p>
| |
| − | <br>
| |
| − | <p><b>Further calculations</b> for simplification of entering data:</p>
| |
| − | <p class="basictext">
| |
| − | $$
| |
| − | c_{E. coli_{DW}} = c_{E. coli_{OD600}} \cdot 0.36
| |
| − | $$
| |
| − | according to <i>Milo et al.</i><x-ref>Milo2009</x-ref>.
| |
| − | $$
| |
| − | q = 0.183 g_{Glucose} \: g_{DW}^{-1} \: h^{-1}
| |
| − | $$
| |
| − | according to <i>Neubauer et al.</i><x-ref>Neubauer2001</x-ref>.
| |
| − | </p>
| |
| − | <p>
| |
| − | Because turbidstats are operated at a constant cell density, the flow rate \(Phi\) can be calculated from the generation time \(t_{E}\).
| |
| − | $$
| |
| − | \Phi = \frac{ln(2)}{t_{E}}
| |
| − | $$
| |
| − | </p>
| |
| − | <p>If the <i>E. coli</i> titer in \(g_{DW}/l\) is zero, it is calculated from the OD, else the dryweight value is used. If the glucose concentration in \(mmol/l\) not zero, it is used for the calulation. If the generation time \(t_{E}\) is not zero, it is used to calculate the flow rate \(\Phi\). </p>
| |
| − |
| |
| − |
| |
| − | <form action="" id="form1">
| |
| − | <section>
| |
| − | <h2>Get the ideal concentration</h2>
| |
| − | <ul class="input-list style-1 clearfix">
| |
| − | <li>
| |
| − | <label>
| |
| − | Glucose concentration <br> \(c_{G_{T}} \: [g/l]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="cturbidostat" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Glucose concentration <br> \(c_{G_{T}} \: [mmol/l]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="cturbidostatmol" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Flow rate <br>\(\Phi \:[Volumes/h]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="fr" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Generation time <br>\(t_{E} \:[min]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="te" value="30" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | <i>E. coli</i> titer<br> \(c_{E. coli} \:[OD600]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ectiterod" value="0.8" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | <i>E. coli</i> titer<br> \(c_{E. coli} \:[g_{DW}/l]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ectiterdw" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Glucose degradation<br>\(q \: [g_{glucose} \: g_{DW}^{-1} h^{-1}]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="q" value="0.183" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | Time <br>\(t \: [min]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="gluc_time" value="90" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | <i>E. coli</i> start concentration<br>\(c_{E} \: [g/L]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ec0dw" value="0" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − | <li>
| |
| − | <label>
| |
| − | <i>E. coli</i> start concentration<br>\(c_{E} \: [OD600]\)
| |
| − | <input type="number" pattern="[0-9]+([,\.][0-9]+)?" id="ec0od" value="0.01" lang='en-150' step="any">
| |
| − | </label>
| |
| − | </li>
| |
| − |
| |
| − | <li>
| |
| − | <div style="padding-top: 30px;">
| |
| − | <input type="button" value="Calculate Continuous" id="input_form" onclick="return glucosecont();">
| |
| − | </div>
| |
| − | </li>
| |
| − | <li>
| |
| − | <div style="padding-top: 30px;">
| |
| − | <input type="button" value="Calculate Discontinuous" id="input_form" onclick="return glucosedis();">
| |
| − | </div>
| |
| − | </li>
| |
| − | <li>
| |
| − | <div style="padding-top: 30px;">
| |
| − | <input type="button" value="Calculate Discontinuous in new plot" id="input_form" onclick="return glucosedisnew();">
| |
| − | </div>
| |
| − | </li>
| |
| − | </ul>
| |
| − | </section>
| |
| − | </form>
| |
| − | <p id="glucoseout"></p>
| |
| − | <br>
| |
| − | <div style="overflow-x: auto !important;">
| |
| − | <div style="min-width: 700 !important;" id="glucoseplot">
| |
| − | </div>
| |
| − | </div>
| |
| − | <br>
| |
| − | <p class="basictext" id="references"></p>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − | </div>
| |
| − |
| |
| − | <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script>
| |
| − | <script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
| |
| − | <script src="https://cdnjs.cloudflare.com/ajax/libs/numjs/0.13.1/numjs.js"></script>
| |
| − | <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
| |
| − | <script src="http://evanplaice.github.io/jquery-csv/src/jquery.csv.min.js"></script>
| |
| − | <script src="https://2017.igem.org/common/MathJax-2.5-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
| |
| − |
| |
| − | <script>
| |
| − |
| |
| − | //example that contains everything needed
| |
| − | function dummy(){
| |
| − | //get the values
| |
| − | var mr = Number(document.getElementById('mr').value);
| |
| − |
| |
| − | //initialise variables
| |
| − | var a_mutations = 0;
| |
| − |
| |
| − | //calculate
| |
| − | if(phi==0){
| |
| − | a_mutations = ng * mr;
| |
| − | }
| |
| − |
| |
| − | //return the results
| |
| − | $("#amount_mutated").html((Math.round(100000 * a_mutated))/1000);
| |
| − | $("#number_generations").html(ng_out);
| |
| − |
| |
| − | //end the function
| |
| − | return false;
| |
| − | }
| |
| − |
| |
| − | function number_mutations(){
| |
| − |
| |
| − | //get the values
| |
| − | var mr = Number(document.getElementById('mr').value);
| |
| − | var phi = Number(document.getElementById('phi').value);
| |
| − | var ng = Number(document.getElementById('ng').value);
| |
| − | 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;
| |
| − | var probability_positive_sequencing = ''
| |
| − | var warnings = ""
| |
| − |
| |
| − | //Check, if given values make sense:
| |
| − |
| |
| − | if(mr>1){
| |
| − | warnings += "A mutation rate that is above one mutation per basepair, per generation does not make sense. 100 % should be enough, right? ";
| |
| − | mr = 1;
| |
| − | }
| |
| − |
| |
| − | if(pm>1){
| |
| − | warnings += "A probability of 100 % should be enough, right?. ";
| |
| − | pm = 1;
| |
| − | }
| |
| − |
| |
| − | //calculate
| |
| − | if(phi*tt==0){
| |
| − | a_mutations = 1 - Math.pow((1 - mr), ng);
| |
| − | ng_out = "";
| |
| − | }
| |
| − | else{
| |
| − | a_mutations = 1 - Math.pow((1 - mr), tt*phi);
| |
| − | ng = tt*phi;
| |
| − | ng_out = "The conditions result in " + ng + " generations.";
| |
| − | }
| |
| − |
| |
| − | n_mutations = ls * a_mutations;
| |
| − | a_mutated = 1 - Math.pow((1-a_mutations), ls);
| |
| − |
| |
| − | if(ns!=0){
| |
| − | probability_positive_sequencing = ns*a_mutated;
| |
| − | $("#probability_positive_sequencing").html("Sequencing " + ns + " sequences results in a " + ((Math.round(probability_positive_sequencing*100))/100) + "% probabiltiy of finding at least one mutated sequence.");
| |
| − | }
| |
| − | else{
| |
| − | $("#probability_positive_sequencing").html("");
| |
| − | }
| |
| − |
| |
| − | if(pm!=0){
| |
| − | number_to_seq = Math.max(1, Math.round((Math.log(1-pm))/(Math.log(1-a_mutated))));
| |
| − | if(isNaN(number_to_seq)){
| |
| − | if(pm==1){
| |
| − | number_to_seq_out = "To be 100 % sure, sequence infinitely many sequences.";
| |
| − | }
| |
| − | else{
| |
| − | number_to_seq_out = "Unluckily we were unable to calculate the number of sequences to sequence to have a " + (pm*100) + "% probability for a positive result.";
| |
| − | }
| |
| − | }
| |
| − | else{
| |
| − | 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);
| |
| − | $("#warnings_mutations").html(warnings);
| |
| − |
| |
| − |
| |
| − | //end the function
| |
| − | return false;
| |
| − | }
| |
| − |
| |
| − |
| |
| − |
| |
| − | function glucosecont(){
| |
| − | glucose('cont');
| |
| − | }
| |
| − |
| |
| − | function glucosedis(){
| |
| − | glucose('dis');
| |
| − | }
| |
| − | function glucosedisnew(){
| |
| − | glucose('disnew');
| |
| − | }
| |
| − |
| |
| − | function glucose(mode){
| |
| − |
| |
| − | //get the values
| |
| − | var cturbidostat = Number(document.getElementById('cturbidostat').value);
| |
| − | var cturbidostatmol = Number(document.getElementById('cturbidostatmol').value);
| |
| − | var fr = Number(document.getElementById('fr').value);
| |
| − | var ectiterod = Number(document.getElementById('ectiterod').value);
| |
| − | var ectiterdw = Number(document.getElementById('ectiterdw').value);
| |
| − | var q = Number(document.getElementById('q').value);
| |
| − | var te = Number(document.getElementById('te').value);
| |
| − | var gluc_time = Number(document.getElementById('gluc_time').value);
| |
| − | var ec0dw = Number(document.getElementById('ec0dw').value);
| |
| − | var ec0od = Number(document.getElementById('ec0od').value);
| |
| − |
| |
| − | //initialise variables
| |
| − | var glucoseout = "";
| |
| − | var glucosemedium = 0;
| |
| − | var gl_OD = 0.36;
| |
| − |
| |
| − | if(ectiterdw == 0){
| |
| − | ectiterdw = ectiterod * gl_OD;
| |
| − | }
| |
| − | else{
| |
| − | ectiterod = ectiterdw/gl_OD;
| |
| − | }
| |
| − |
| |
| − | if(cturbidostatmol != 0){
| |
| − | cturbidostat = cturbidostatmol * 180.1559/1000.0;
| |
| − | }
| |
| − | else{
| |
| − | cturbidostatmol = cturbidostat/(180.1559/1000.0);
| |
| − | }
| |
| − |
| |
| − | if(te != 0){
| |
| − | fr = Math.LN2/te;
| |
| − | }
| |
| − | else{
| |
| − | te = fr * Math.LN2;
| |
| − | }
| |
| − |
| |
| − | if(ec0dw == 0){
| |
| − | ec0dw = ec0od * gl_OD;
| |
| − | }
| |
| − | else{
| |
| − | ec0od = ec0dw/gl_OD;
| |
| − | }
| |
| − |
| |
| − | if(mode=='cont'){
| |
| − | //calculate
| |
| − | glucosemedium = cturbidostat + ((ectiterdw * q)/fr);
| |
| − |
| |
| − | var glucosemediummol = glucosemedium/(180.1559/1000.0);
| |
| − |
| |
| − | //return the results
| |
| − | glucoseout = "With a <b>glucose concentration of " + (0.01*Math.round(100*glucosemedium)) + " g/L, " +(0.01*Math.round(100*glucosemediummol)) + "mmol/l in the medium</b>, a flow rate of " + (0.01*Math.round(100*fr)) + " Volumes/h, or a generation time of " + Math.round(te) + " min, an <i>E. coli</i> titer of " + (0.01*Math.round(100*ectiterdw)) + " g/l, an OD600 of " + (0.01*Math.round(100*ectiterod)) + " and a degradation rate of " + (0.01*Math.round(100*q)) + " g l<sup>-1</sup>cfu<sup>-1</sup>h<sup>-1</sup> a concentration of " + (0.01*Math.round(100*cturbidostat)) + " g/L, " + (0.01*Math.round(100*cturbidostatmol)) + " mmol/l is maintained.";
| |
| − |
| |
| − | $("#glucoseplot").html('');
| |
| − |
| |
| − | }
| |
| − | else{
| |
| − | //calculate
| |
| − | glucosemedium = cturbidostat + q * ec0dw * te * (Math.exp(gluc_time/te) - 1);
| |
| − |
| |
| − | var glucosemediummol = glucosemedium/(180.1559/1000.0);
| |
| − |
| |
| − | //return the results
| |
| − | glucoseout = "With a <b>glucose concentration of " + (0.01*Math.round(100*Math.max(0,glucosemedium))) + " g/L, " +(0.01*Math.round(100*Math.max(0,glucosemediummol))) + "mmol/l in the medium</b>, a generation time of " + (0.01*Math.round(100*te)) + " min, an <i>E. coli</i> starting titer of " + (0.01*Math.round(100*ec0dw)) + " g/l, an OD600 of " + (0.01*Math.round(100*ec0od)) + " and a degradation rate of " + (0.01*Math.round(100*q)) + " g l<sup>-1</sup>cfu<sup>-1</sup>h<sup>-1</sup> a concentration of " + (0.01*Math.round(100*cturbidostat)) + " g/L, " + (0.01*Math.round(100* cturbidostatmol)) + " mmol/l is reached after " + gluc_time + " minutes.";
| |
| − | }
| |
| − |
| |
| − | $("#glucoseout").html(glucoseout);
| |
| − |
| |
| − | //plot glucose concentration and e. coli titer
| |
| − | if(mode!='cont'){
| |
| − | var glucoseplot = document.getElementById('glucoseplot');
| |
| − |
| |
| − | var gluc_time_exp = 1.2 * gluc_time;
| |
| − | var t = new Array(501);
| |
| − | var cecoli = new Array(501);
| |
| − | var cg = new Array(501);
| |
| − |
| |
| − | for(var it = 0; it <=500; it++){
| |
| − | t[it] = it*gluc_time_exp/500;
| |
| − |
| |
| − | cecoli[it] = Math.max(0, ec0od * Math.exp(t[it]/te));
| |
| − |
| |
| − | cg[it] = Math.max(0, glucosemedium - (q * ec0dw * te * (Math.exp((t[it]/te)) - 1.0)));
| |
| − | }
| |
| − |
| |
| − | var glucosedata = [{x: t,
| |
| − | y: cg,
| |
| − | name: 'Glucose [g/l]'},
| |
| − | {x: t,
| |
| − | y: cecoli,
| |
| − | name: 'E. coli [OD600]',
| |
| − | yaxis: 'y2'
| |
| − | }];
| |
| − |
| |
| − | var layout = {
| |
| − | title: 'Glucose concentration and phage titer in discontinuous culture',
| |
| − | showlegend: true,
| |
| − | width: glucoseplot.width,
| |
| − | legend: {
| |
| − | orientation: 'v',
| |
| − | x: 1.15,
| |
| − | xanchor: 'left',
| |
| − | y: 1
| |
| − | },
| |
| − | xaxis: {
| |
| − | title: 'Duration [min]',
| |
| − | titlefont: {
| |
| − | family: 'Courier New, monospace',
| |
| − | size: 18,
| |
| − | color: '#7f7f7f'
| |
| − | },
| |
| − | showgrid: false
| |
| − | },
| |
| − | yaxis: {
| |
| − | title: 'Glucose concentration [g/l]',
| |
| − | titlefont: {
| |
| − | family: 'Courier New, monospace',
| |
| − | size: 18,
| |
| − | color: '#7f7f7f'
| |
| − | },
| |
| − | showgrid: false
| |
| − | },
| |
| − | yaxis2: {
| |
| − | title: 'E. coli titer [OD600]',
| |
| − | side: 'right',
| |
| − | overlaying: 'y',
| |
| − | titlefont: {
| |
| − | family: 'Courier New, monospace',
| |
| − | size: 18,
| |
| − | color: '#7f7f7f'
| |
| − | },
| |
| − | showgrid: false
| |
| − | },
| |
| − | shapes: [{
| |
| − | type: 'line',
| |
| − | x0: gluc_time,
| |
| − | x1: gluc_time,
| |
| − | y0: 0,
| |
| − | y1: cg[0],
| |
| − | line:{
| |
| − | width: 1,
| |
| − | color: '#7f7f7f'
| |
| − | }
| |
| − | }]
| |
| − | };
| |
| − | if(mode=='disnew'){
| |
| − | Plotly.newPlot(glucoseplot, glucosedata, layout);
| |
| − | }
| |
| − | else{
| |
| − | Plotly.plot(glucoseplot, glucosedata, layout);
| |
| − | }
| |
| − | }
| |
| − | }
| |
| − |
| |
| − |
| |
| − | function differences(){
| |
| − | //get the values
| |
| − | var str1 = document.getElementById('str1').value;
| |
| − | var str2 = document.getElementById('str2').value;
| |
| − | str1 = str1.replace(/(\r\n|\n|\r)/gm,"");
| |
| − | str2 = str2.replace(/(\r\n|\n|\r)/gm,"");
| |
| − |
| |
| − | //initialise variables
| |
| − | var diff = [];
| |
| − | var outstr1 = "";
| |
| − | var outstr2 = "";
| |
| − | var diffs = 0;
| |
| − | var lendiffs = 0;
| |
| − | var sharedlen = 0;
| |
| − | var diffinfo = "";
| |
| − | var str1_comp = str1;
| |
| − | var str2_comp = str2;
| |
| − |
| |
| − | //calculate
| |
| − |
| |
| − | if(document.getElementById("case_sensitive").checked == false){
| |
| − | str1_comp = str1.toLowerCase();
| |
| − | str2_comp = str2.toLowerCase();
| |
| − | }
| |
| − |
| |
| − | var i = 0;
| |
| − | while(i < str1.length){
| |
| − | if(i==str2.length){
| |
| − | break;
| |
| − | }
| |
| − | if(str1_comp[i]==str2_comp[i]){
| |
| − | outstr1 += str1[i];
| |
| − | outstr2 += str2[i];
| |
| − | }
| |
| − | else{
| |
| − | diffs += 1;
| |
| − | outstr1 += '<span style="color: red">' + str1[i] + '</span>';
| |
| − | outstr2 += '<span style="color: red">' + str2[i] + '</span>';
| |
| − | }
| |
| − | i++;
| |
| − | }
| |
| − | sharedlen = i;
| |
| − | while(i < str1.length){
| |
| − | outstr1 = outstr1 + '<span style="color: blue">' + str1[i] + '</span>';
| |
| − | i++;
| |
| − | lendiffs++;
| |
| − | }
| |
| − | while(i < str2.length){
| |
| − | outstr2 = outstr2 + '<span style="color: blue">' + str2[i] + '</span>';
| |
| − | i++;
| |
| − | lendiffs++;
| |
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| |
| − | diffinfo = "The strings are different for " + diffs + " from " + sharedlen + " positions (" + (0.01*Math.round(10000*(diffs/sharedlen))) + "%)and their length differs by " + lendiffs + " positions.";
| |
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| − | title="Permanent link to this revision of the page">Permanent link</a>
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