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| − | {{Heidelberg/header}}
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| − | {{#tag:html|
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| − | <script>
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| − | {{Heidelberg/title|Safetynet}}
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| − | </script>
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| − | {{Heidelberg/navbar
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| − | {{Heidelberg/main|
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| − | Software|
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| − | SafetyNet|
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| − | https://static.igem.org/mediawiki/2017/1/1b/T--Heidelberg--2017_background_web.jpg|turk|
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| − | {{Heidelberg/abstract|
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| − | https://static.igem.org/mediawiki/2017/e/eb/T--Heidelberg--2017_SafetyNet_GA.jpg|
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| − | When performing large scale, automated directed evolution experiments a manual assertion of every sequence in the library is impossible. However profound background and quality checks on sequences are crucial in the automated context as the experimentator has no direct control of the processes. This especially holds true for <i>in silico</i> evolution, where the immediate effect of a mutation is not assessable.
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| − | In order to safeguard our <i>in vivo</i> and <i>in silico</i> directed evolution experiments we developed Safetynet.
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| − | Safetynet is a web available, neural network based sequence check. It does not only infer the function and species of origin, but does also assert the safety level assigned to the origin species and the potential harm of an input sequence. We applied SafetyNet throughout our directed evolution experiments to ensure safe and flawless sequence improvement all the while preventing the unintended emergence of harmful traits.
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| − | }}
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| − | {{Heidelberg/templateus/Contentsection|
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| − | {{#tag:html|
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| − | {{Heidelberg/formblank|{{#tag:html|
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| − | <a href="https://2017.igem.org/Team:Heidelberg/Model/Mutagenesis_Induction#glucose">
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| − | <img padding="50" height="30" src="https://static.igem.org/mediawiki/2017/thumb/2/2e/T--Heidelberg--Team_Heidelberg_2017_modeling-logo.png/320px-T--Heidelberg--Team_Heidelberg_2017_modeling-logo.png">
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| − | Theory behind this tool
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| − | </a>
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| − | }}|#005498|||}}
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| − | To save the user from having to convert values, some of the input is redudant. For the glucose concentration \(c_{G}\), <i>E. coli</i> concentration \(c_{E}\) and the <i>E. coli</i> capacity two unit are accepted. For the glucose concentration the value in mmol has the higher priority, for the <i>E. coli</i> values, the gram dryweight value has the higher priority.
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| − | <br>
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| − | The generation time \(t_{E}\) is redundant to the flow rate \(\Phi_{T}\) in the context of a turbidostat. Here, \(t_{E}\) is prioritised.
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| − | <br>
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| − | The different buttons trigger different calculations. The buttons first word specifies the glucose concentration of which vessel is calculated, the word in braces defines the vessel of which the glucose concentration is given in \(c_{G}\).
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| − | <br>
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| − | A new clean plot can be generated using the "New" option, that means all data plotted so far is lost.
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| − | <br>
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| − | The exponential mode of the model can be enabled witht he "Exponential" option. The default is logistic growth.
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| − | <br>
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| − | When a comma-separted file is uploaded via the "Choose File" button, data from the csv is plottet into the graph.
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| − | The csv must have the following format:<br>
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| − |
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| − | <code class="html">t; E. coli 1; Glucose 1</code><br>
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| − | <code class="html">0; 0.01; 1.0</code><br>
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| − | <code class="html">20; 0.02; 0.9</code><br>
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| − | <code class="html">40; 0.04; 0.8</code><br>
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| − | <code class="html">60; 0.08; 0.7</code><br>
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| − | <code class="html">80; 0.16; 0.6</code><br>
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| − | <code class="html">100; 0.32; 0.5</code><br>
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| − | The first row is the header providing names for all colums. The first row is interpreted as the time. All other rows are interpreted as datapoints for the point in time that is specified in the first column. The separator is <code class="html">';'</code>, the row separator is newline.
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| − | {{Heidelberg/boxopen|Parameter overview|
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| − | {{Heidelberg/templateus/Tablebox|
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| − | Table 1: Variables and Parameters used for the calculation of the glucose and <i>E. coli</i> concentrations |
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| − | {{#tag:html|
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| − | <table class="table table-bordered mdl-shadow--4dp" XSSCleaned="overflow-x: scroll !important">
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| − | <thead style="background-color: #005493 !important;">
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| − | <tr>
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| − | <th>Symbol</th>
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| − | <th>Value and Unit</th>
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| − | <th>Explanation</th>
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| − | </tr>
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| − | </thead>
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| − | <tbody>
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| − | <tr>
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| − | <td>\(c_{G_{T} }\)</td>
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| − | <td>[g/ml] or [mmol/ml]</td>
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| − | <td>Glucose concentration in Turbidostat</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(c_{G_{M} }\)</td>
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| − | <td>[g/ml] or [mmol/ml]</td>
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| − | <td>Glucose concentration in medium</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(c_{G_{L} }\)</td>
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| − | <td>[g/ml] or [mmol/ml]</td>
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| − | <td>Glucose concentration in lagoon</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(t\)</td>
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| − | <td>[min]</td>
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| − | <td>Time</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(\Phi_{T}\)</td>
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| − | <td>[ml/min]</td>
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| − | <td>Flow rate through Turbidostat</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(\Phi_{L}\)</td>
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| − | <td>[ml/min]</td>
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| − | <td>Flow rate through Lagoon</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(c_{E}\)</td>
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| − | <td>[cfu/ml] or OD600</td>
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| − | <td><i>E. coli</i> concentration</td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(q\)</td>
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| − | <td>\([g_{glucose} \: g_{DW}^{-1} h^{-1}]\)</td>
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| − | <td>Glucose consumption by <i>E. coli</i><x-ref>Neubauer2001</x-ref></td>
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| − | </tr>
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| − | <tr>
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| − | <td>\(t_{E}\)</td>
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| − | <td>[min]</td>
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| − | <td><i>E. coli</i> generation time</td>
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| − | </tr>
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| − | </tbody>
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| − | </table>
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| − | }}|
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| − | List of all paramters and variables used in the numeric solution of this model.
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| − | }}
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| − | |tab1|#005493}}
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| − | }}
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| − | }}
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| − | {{Heidelberg/templateus/Contentsection|
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| − | {{#tag:html|
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| − | {{Heidelberg/formblank|Get the ideal concentration|#005493|
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/forminput|Glucose concentration \(c_{G} \: [g/l]\)|number|cturbidostat|1}}
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| − | {{Heidelberg/forminput|Glucose concentration \(c_{G} \: [mmol/l]\)|number|cturbidostatmol|0}}
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| − | {{Heidelberg/forminput|Flow rate \(\Phi_{T} \:[Volumes/h]\)|number|fr|0}}
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| − | {{Heidelberg/forminput|Generation time \(t_{E} \:[min]\)|number|te|40}}
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| − | }}
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/forminput|<i>E. coli</i> titer \(c_{E} \:[OD600]\)|number|ectiterod|0.05}}
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| − | {{Heidelberg/forminput|<i>E. coli</i> titer \(c_{E} \:[g_{DW}/l]\)|number|ectiterdw|0}}
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| − | {{Heidelberg/forminput|Lagoon volume \(V_{L} \:[ml]\)|number|vl|0}}
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| − | {{Heidelberg/forminput|Lagoon flow rate \(\Phi_{L} \:[ml/min]\)|number|phil|0}}
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| − | }}
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/forminput|Glucose degradation \(q \: [g_{glucose} \: g_{DW}^{-1} h^{-1}]\)|number|q|0.183}}
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| − | {{Heidelberg/forminput|Time \(t \: [min]\)|number|gluc_time|120}}
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| − | {{Heidelberg/forminput|<i>E. coli</i> capacity \(c_{c} \: [g/L]\)|number|cmaxdw|0}}
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| − | {{Heidelberg/forminput|<i>E. coli</i> capacity \(c_{c} \: [OD600]\)|number|cmaxod|4.0}}
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| − | }}
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/formcheckbox|New|new}}
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| − | {{Heidelberg/formcheckbox|Exponential|exponential}}
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| − | }}
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/formbutton|Medium (Turbidostat)|glucosecont();}}
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| − | {{Heidelberg/formbutton|Medium (Lagoon)|glucosecont_lagoon();}}
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| − | {{Heidelberg/formbutton|Lagoon (Medium)|glucosecont_forward();}}
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| − | }}
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| − | {{Heidelberg/formrow|
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| − | {{Heidelberg/formbutton|Medium (Flask)|glucosedis();}}
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| − | {{Heidelberg/formbutton|Flask (Medium)|glucosedis_forward();}}
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| − | {{Heidelberg/formfilefix}}
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| − | }}|
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| − | }}
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| − | <div class="col-lg-12 col-md-12 col-xs-12", style="padding-left:0px;padding-right:0px">
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| − | <div class="mdl-shadow--4dp" style="padding:20px; float:left}">
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| − | <div style="width: 100% !important; overflow-x: auto !important;">
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| − | <div style="width: 100% !important; min-width: 700 !important;" id="glucoseplot"></div>
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| − | </div>
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| − | {{Heidelberg/formblank| |#005493| |{{#tag:html|
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| − |
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| − | <div class="img-caption title" style="text-align: justify !important;"> <strong><b>Changes in <i>E. coli</i> and glucose concentration over time</b></strong>
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| − | </div>
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| − | <div class="img-caption subtitle" style="text-align: justify !important;">
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| − | <div class=content id="glucoseout"></div>
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| − | </div>
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| − | }}}}
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| − | </div>
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| − | </div>
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| − | }}
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| − | }}
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| − | {{Heidelberg/formblank|{{#tag:html|
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| − | <a href="https://2017.igem.org/Team:Heidelberg/Model/Mutagenesis_Induction#glucose">
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| − | <img padding="50" height="30" src="https://static.igem.org/mediawiki/2017/thumb/2/2e/T--Heidelberg--Team_Heidelberg_2017_modeling-logo.png/320px-T--Heidelberg--Team_Heidelberg_2017_modeling-logo.png">
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| − | Theory behind this tool
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| − | </a>
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| − | }}|#005498|||}}
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| − | }}
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| − | {{Heidelberg/references2
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| − | }}
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| − | {{Heidelberg/footer
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| − | }}
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| − | {{Heidelberg/tools_induction}}
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| − | {{Heidelberg/formcode|ecgluc|userdata}}
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