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51  <title>piRNAi app</title>
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54
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56
57</head>
58<body>
59  <div class="container-fluid">
60    <style type="text/css">.js-irs-none .irs-single, .js-irs-none .irs-bar-edge, .js-irs-none .irs-bar {
61                          background: transparent;
62                          border-top-color: transparent;
63                          border-bottom-color: transparent;
64                          border-left-color: transparent;
65                          border-right-color: transparent}
66               .navbar-default .navbar-brand:hover {color: #ffffff;}
67               </style>
68    <style type="text/css">#AdvancedFragment {white-space: pre-wrap;}</style>
69    <style type="text/css">#SimpleFragment {white-space: pre-wrap;}</style>
70    <style type="text/css">#piBoxes .form-group {margin-bottom: 0px; margin-top: 0px;}</style>
71    <style type="text/css">
72                   table {
73  font-family: arial, sans-serif;
74  border-collapse: collapse;
75  width: 100%;
76}
77
78td, th {
79  border: 1px solid #dddddd;
80  text-align: left;
81  padding: 8px;
82}
83
84tr:nth-child(even) {
85  background-color: #dddddd;
86}
87                   </style>
88    <nav class="navbar navbar-default navbar-static-top" role="navigation">
89      <div class="container-fluid">
90        <div class="navbar-header">
91          <span class="navbar-brand">
92            <a id="link_to_tabpanel_title" href="#" class="action-button"><b>piRNAi</b></a>
93          </span>
94        </div>
95        <ul class="nav navbar-nav shiny-tab-input" id="panels" data-tabsetid="3152">
96          <li class="active">
97            <a href="#tab-3152-1" data-toggle="tab" data-value="Designer">Designer</a>
98          </li>
99          <li>
100            <a href="#tab-3152-2" data-toggle="tab" data-value="Downloads">Downloads</a>
101          </li>
102          <li>
103            <a href="#tab-3152-3" data-toggle="tab" data-value="About">About</a>
104          </li>
105        </ul>
106      </div>
107    </nav>
108    <div class="container-fluid">
109      <div class="tab-content" data-tabsetid="3152">
110        <div class="tab-pane active" data-value="Designer" id="tab-3152-1">
111          <div class="col-sm-8">
112            <h2>Design piRNAi fragments</h2>
113            <h4>Target <i>C. elegans</i> and <i>C. briggsae</i> genes</h4>
114            <div class="tabbable">
115              <ul class="nav nav-tabs" data-tabsetid="1370">
116                <li class="active">
117                  <a href="#tab-1370-1" data-toggle="tab" data-value="Simple">Simple</a>
118                </li>
119                <li>
120                  <a href="#tab-1370-2" data-toggle="tab" data-value="Advanced">Advanced</a>
121                </li>
122              </ul>
123              <div class="tab-content" data-tabsetid="1370">
124                <div class="tab-pane active" data-value="Simple" id="tab-1370-1">
125                  <br/>
126                  <div class="form-group shiny-input-container">
127                    <label class="control-label" for="geneinput">Target gene</label>
128                    <textarea id="geneinput" class="form-control" placeholder="WormbaseID, transcript or gene name" style="  resize: none;" rows="1"></textarea>
129                  </div>
130                  <button id="actiongenesearch" type="button" class="btn btn-default action-button">Search</button>
131                  <hr/>
132                  <div id="DesignControls" class="shiny-html-output"></div>
133                  <hr/>
134                  <pre id="ErrorMessage" class="shiny-text-output noplaceholder"></pre>
135                  <div id="SelPiTabSummary" class="shiny-html-output"></div>
136                  <div id="SelPiTab" class="shiny-html-output"></div>
137                  <pre id="SimpleFragment" class="shiny-text-output noplaceholder"></pre>
138                  <div id="RefMesSim" class="shiny-html-output"></div>
139                  <div id="downloadseq" class="shiny-html-output"></div>
140                </div>
141                <div class="tab-pane" data-value="Advanced" id="tab-1370-2">
142                  <h3>Select individual synthetic guide piRNAs</h3>
143                  <div class="row">
144                    <div id="clustercon" style="width: 100%;" class="form-group shiny-input-radiogroup shiny-input-container shiny-input-container-inline">
145                      <label class="control-label" for="clustercon">Select piRNA cluster
146                                                     [<a href="" onclick="$('#explain_cluster_adv').toggle(); return false;">info</a>]
147                                                     </label>
148                      <div class="shiny-options-group">
149                        <label class="radio-inline">
150                          <input type="radio" name="clustercon" value="1" checked="checked"/>
151                          <span>Standard piRNA transgene (Cluster<sub>E</sub>, six sg-piRNAs)</span>
152                        </label>
153                        <label class="radio-inline">
154                          <input type="radio" name="clustercon" value="2"/>
155                          <span>Cluster<sub>G</sub> (six sg-piRNAs)</span>
156                        </label>
157                        <label class="radio-inline">
158                          <input type="radio" name="clustercon" value="3"/>
159                          <span>Cluster<sub>O</sub> (seven sg-piRNAs)</span>
160                        </label>
161                        <label class="radio-inline">
162                          <input type="radio" name="clustercon" value="4"/>
163                          <span>Cluster<sub>F</sub> (eight sg-piRNAs)</span>
164                        </label>
165                      </div>
166                    </div>
167                    
168                     <p align="justify"><div class="explain" style="display: none" id="explain_cluster_adv">
169            We recommend using the standard piRNAi Cluster<sub>E</sub> (centered on the <i>21ur-1224</i> piRNA loci). <b>Note:</b> Cluster<sub>O</sub> and Cluster<sub>F</sub> were tested with six sg-piRNAs but can accomodate additional sg-piRNAs, which may improve silencing.
170                                     </div></p>
171                     
172                    <div data-display-if="input.clustercon==1" data-ns-prefix="">
173                      <div class="col-sm-4">
174                        <div id="piBoxes" class="my_class">
175                          <div class="form-group shiny-input-container">
176                            <label class="control-label" for="piRNAseq1_1"></label>
177                            <textarea id="piRNAseq1_1" class="form-control" placeholder="sg-piRNA 1" style="  resize: none;" rows="1" cols="21"></textarea>
178                          </div>
179                          <div class="form-group shiny-input-container">
180                            <label class="control-label" for="piRNAseq2_1"></label>
181                            <textarea id="piRNAseq2_1" class="form-control" placeholder="sg-piRNA 2" style="  resize: none;" rows="1" cols="21"></textarea>
182                          </div>
183                          <div class="form-group shiny-input-container">
184                            <label class="control-label" for="piRNAseq3_1"></label>
185                            <textarea id="piRNAseq3_1" class="form-control" placeholder="sg-piRNA 3" style="  resize: none;" rows="1" cols="21"></textarea>
186                          </div>
187                          <div class="form-group shiny-input-container">
188                            <label class="control-label" for="piRNAseq4_1"></label>
189                            <textarea id="piRNAseq4_1" class="form-control" placeholder="sg-piRNA 4" style="  resize: none;" rows="1" cols="21"></textarea>
190                          </div>
191                          <div class="form-group shiny-input-container">
192                            <label class="control-label" for="piRNAseq5_1"></label>
193                            <textarea id="piRNAseq5_1" class="form-control" placeholder="sg-piRNA 5" style="  resize: none;" rows="1" cols="21"></textarea>
194                          </div>
195                          <div class="form-group shiny-input-container">
196                            <label class="control-label" for="piRNAseq6_1"></label>
197                            <textarea id="piRNAseq6_1" class="form-control" placeholder="sg-piRNA 6" style="  resize: none;" rows="1" cols="21"></textarea>
198                          </div>
199                        </div>
200                        <br/>
201                      </div>
202                    </div>
203                    <div data-display-if="input.clustercon==2" data-ns-prefix="">
204                      <div class="col-sm-4">
205                        <div id="piBoxes" class="my_class">
206                          <div class="form-group shiny-input-container">
207                            <label class="control-label" for="piRNAseq1_2"></label>
208                            <textarea id="piRNAseq1_2" class="form-control" placeholder="sg-piRNA 1" style="  resize: none;
208" rows="1" cols="21"></textarea>
209                          </div>
210                          <div class="form-group shiny-input-container">
211                            <label class="control-label" for="piRNAseq2_2"></label>
212                            <textarea id="piRNAseq2_2" class="form-control" placeholder="sg-piRNA 2" style="  resize: none;" rows="1" cols="21"></textarea>
213                          </div>
214                          <div class="form-group shiny-input-container">
215                            <label class="control-label" for="piRNAseq3_2"></label>
216                            <textarea id="piRNAseq3_2" class="form-control" placeholder="sg-piRNA 3" style="  resize: none;" rows="1" cols="21"></textarea>
217                          </div>
218                          <div class="form-group shiny-input-container">
219                            <label class="control-label" for="piRNAseq4_2"></label>
220                            <textarea id="piRNAseq4_2" class="form-control" placeholder="sg-piRNA 4" style="  resize: none;" rows="1" cols="21"></textarea>
221                          </div>
222                          <div class="form-group shiny-input-container">
223                            <label class="control-label" for="piRNAseq5_2"></label>
224                            <textarea id="piRNAseq5_2" class="form-control" placeholder="sg-piRNA 5" style="  resize: none;" rows="1" cols="21"></textarea>
225                          </div>
226                          <div class="form-group shiny-input-container">
227                            <label class="control-label" for="piRNAseq6_2"></label>
228                            <textarea id="piRNAseq6_2" class="form-control" placeholder="sg-piRNA 6" style="  resize: none;" rows="1" cols="21"></textarea>
229                          </div>
230                        </div>
231                        <br/>
232                      </div>
233                    </div>
234                    <div data-display-if="input.clustercon==3" data-ns-prefix="">
235                      <div class="col-sm-4">
236                        <div id="piBoxes" class="my_class">
237                          <div class="form-group shiny-input-container">
238                            <label class="control-label" for="piRNAseq1_3"></label>
239                            <textarea id="piRNAseq1_3" class="form-control" placeholder="sg-piRNA 1" style="  resize: none;" rows="1" cols="21"></textarea>
240                          </div>
241                          <div class="form-group shiny-input-container">
242                            <label class="control-label" for="piRNAseq2_3"></label>
243                            <textarea id="piRNAseq2_3" class="form-control" placeholder="sg-piRNA 2" style="  resize: none;" rows="1" cols="21"></textarea>
244                          </div>
245                          <div class="form-group shiny-input-container">
246                            <label class="control-label" for="piRNAseq3_3"></label>
247                            <textarea id="piRNAseq3_3" class="form-control" placeholder="sg-piRNA 3" style="  resize: none;" rows="1" cols="21"></textarea>
248                          </div>
249                          <div class="form-group shiny-input-container">
250                            <label class="control-label" for="piRNAseq4_3"></label>
251                            <textarea id="piRNAseq4_3" class="form-control" placeholder="sg-piRNA 4" style="  resize: none;" rows="1" cols="21"></textarea>
252                          </div>
253                          <div class="form-group shiny-input-container">
254                            <label class="control-label" for="piRNAseq5_3"></label>
255                            <textarea id="piRNAseq5_3" class="form-control" placeholder="sg-piRNA 5" style="  resize: none;" rows="1" cols="21"></textarea>
256                          </div>
257                          <div class="form-group shiny-input-container">
258                            <label class="control-label" for="piRNAseq6_3"></label>
259                            <textarea id="piRNAseq6_3" class="form-control" placeholder="sg-piRNA 6" style="  resize: none;
259" rows="1" cols="21"></textarea>
260                          </div>
261                          <div class="form-group shiny-input-container">
262                            <label class="control-label" for="piRNAseq7_3"></label>
263                            <textarea id="piRNAseq7_3" class="form-control" placeholder="sg-piRNA 7" style="  resize: none;" rows="1" cols="21"></textarea>
264                          </div>
265                        </div>
266                        <br/>
267                      </div>
268                    </div>
269                    <div data-display-if="input.clustercon==4" data-ns-prefix="">
270                      <div class="col-sm-4">
271                        <div id="piBoxes" class="my_class">
272                          <div class="form-group shiny-input-container">
273                            <label class="control-label" for="piRNAseq1_4"></label>
274                            <textarea id="piRNAseq1_4" class="form-control" placeholder="sg-piRNA 1" style="  resize: none;" rows="1" cols="21"></textarea>
275                          </div>
276                          <div class="form-group shiny-input-container">
277                            <label class="control-label" for="piRNAseq2_4"></label>
278                            <textarea id="piRNAseq2_4" class="form-control" placeholder="sg-piRNA 2" style="  resize: none;" rows="1" cols="21"></textarea>
279                          </div>
280                          <div class="form-group shiny-input-container">
281                            <label class="control-label" for="piRNAseq3_4"></label>
282                            <textarea id="piRNAseq3_4" class="form-control" placeholder="sg-piRNA 3" style="  resize: none;" rows="1" cols="21"></textarea>
283                          </div>
284                          <div class="form-group shiny-input-container">
285                            <label class="control-label" for="piRNAseq4_4"></label>
286                            <textarea id="piRNAseq4_4" class="form-control" placeholder="sg-piRNA 4" style="  resize: none;" rows="1" cols="21"></textarea>
287                          </div>
288                          <div class="form-group shiny-input-container">
289                            <label class="control-label" for="piRNAseq5_4"></label>
290                            <textarea id="piRNAseq5_4" class="form-control" placeholder="sg-piRNA 5" style="  resize: none;" rows="1" cols="21"></textarea>
291                          </div>
292                          <div class="form-group shiny-input-container">
293                            <label class="control-label" for="piRNAseq6_4"></label>
294                            <textarea id="piRNAseq6_4" class="form-control" placeholder="sg-piRNA 6" style="  resize: none;" rows="1" cols="21"></textarea>
295                          </div>
296                          <div class="form-group shiny-input-container">
297                            <label class="control-label" for="piRNAseq7_4"></label>
298                            <textarea id="piRNAseq7_4" class="form-control" placeholder="sg-piRNA 7" style="  resize: none;" rows="1" cols="21"></textarea>
299                          </div>
300                          <div class="form-group shiny-input-container">
301                            <label class="control-label" for="piRNAseq8_4"></label>
302                            <textarea id="piRNAseq8_4" class="form-control" placeholder="sg-piRNA 8" style="  resize: none;" rows="1" cols="21"></textarea>
303                          </div>
304                        </div>
305                        <br/>
306                      </div>
307                    </div>
308                    <div data-display-if="input.clustercon==5" data-ns-prefix="">
309                      <div class="col-sm-4">
310                        <div id="piBoxes" class="my_class">
311                          <div class="form-group shiny-input-container">
312                            <label class="control-label" for="piRNAseq1_5"></label>
313                            <textarea id="piRNAseq1_5" class="form-control" placeholder="sg-piRNA 1" style="  resize: none;" rows="1" cols="21"></textarea>
314                          </div>
315                          <div class="form-group shiny-input-container">
316                            <label class="control-label" for="piRNAseq2_5"></label>
317                            <textarea id="piRNAseq2_5" class="form-control" placeholder="sg-piRNA 2" style="  resize: none;
317" rows="1" cols="21"></textarea>
318                          </div>
319                          <div class="form-group shiny-input-container">
320                            <label class="control-label" for="piRNAseq3_5"></label>
321                            <textarea id="piRNAseq3_5" class="form-control" placeholder="sg-piRNA 3" style="  resize: none;" rows="1" cols="21"></textarea>
322                          </div>
323                          <div class="form-group shiny-input-container">
324                            <label class="control-label" for="piRNAseq4_5"></label>
325                            <textarea id="piRNAseq4_5" class="form-control" placeholder="sg-piRNA 4" style="  resize: none;" rows="1" cols="21"></textarea>
326                          </div>
327                          <div class="form-group shiny-input-container">
328                            <label class="control-label" for="piRNAseq5_5"></label>
329                            <textarea id="piRNAseq5_5" class="form-control" placeholder="sg-piRNA 5" style="  resize: none;" rows="1" cols="21"></textarea>
330                          </div>
331                          <div class="form-group shiny-input-container">
332                            <label class="control-label" for="piRNAseq6_5"></label>
333                            <textarea id="piRNAseq6_5" class="form-control" placeholder="sg-piRNA 6" style="  resize: none;" rows="1" cols="21"></textarea>
334                          </div>
335                          <div class="form-group shiny-input-container">
336                            <label class="control-label" for="piRNAseq7_5"></label>
337                            <textarea id="piRNAseq7_5" class="form-control" placeholder="sg-piRNA 7" style="  resize: none;" rows="1" cols="21"></textarea>
338                          </div>
339                          <div class="form-group shiny-input-container">
340                            <label class="control-label" for="piRNAseq8_5"></label>
341                            <textarea id="piRNAseq8_5" class="form-control" placeholder="sg-piRNA 8" style="  resize: none;" rows="1" cols="21"></textarea>
342                          </div>
343                        </div>
344                        <br/>
345                      </div>
346                    </div>
347                    <div class="col-sm-8">
348                      <pre id="AdvancedFragment" class="shiny-text-output noplaceholder"></pre>
349                      <div id="RefMesAdv" class="shiny-html-output"></div>
350                      <div id="downloadconstruct" class="shiny-html-output"></div>
351                    </div>
352                  </div>
353                  <div class="row">
354                    <div class="col-sm-2">
355                      <button id="actionclean" type="button" class="btn btn-default action-button">Reset</button>
356                    </div>
357                    <div class="col-sm-2">
358                      <button id="actionconstruct" type="button" class="btn btn-default action-button">Generate piRNAi cluster</button>
359                    </div>
360                  </div>
361                  <pre id="AdvancedErrorMessage" class="shiny-text-output noplaceholder"></pre>
362                  <hr/>
363                  <div class="form-group shiny-input-container">
364                    <label class="control-label" for="Advancedgeneinput">Gene target</label>
365                    <textarea id="Advancedgeneinput" class="form-control" placeholder="WormbaseID, transcript or gene name" style="  resize: none;" rows="1"></textarea>
366                  </div>
367                  <button id="actionAdvsearch" type="button" class="btn btn-default action-button">Search piRNAs</button>
368                  <br/>
369                  <br/>
370                  <div class="form-group shiny-input-container">
371                    <label class="control-label" for="FluoInput"><b>Common fluorophore
372                    [<a href="" onclick="$('#explain_n_fluo').toggle(); return false;">info</a>]</b></label>
373                    <div>
374                      <select id="FluoInput"><option value="ce-GFP (Froekjaer-Jensen lab)">ce-GFP (Froekjaer-Jensen lab)</option>
375<option value="ce-tagRFP (Froekjaer-Jensen lab)">ce-tagRFP (Froekjaer-Jensen lab)</option>
376<option value="GFP (Fire lab)">GFP (Fire lab)</option>
377<option value="mCherry (Oegema lab)">mCherry (Oegema lab)</option>
378<option value="mCherry (Seydoux lab)">mCherry (Seydoux lab)</option>
379<option value="mKate2 (Dickinson lab)">mKate2 (Dickinson lab)</option>
380<option value="mNeonGreen (Dickinson lab)">mNeonGreen (Dickinson lab)</option></select>
381                      
381<script type="application/json" data-for="FluoInput" data-nonempty="">{}</script>
381
382                    </div>
383                  </div>
384                  
385                     <p align="justify"><div class="explain" style="display: none" id="explain_n_fluo">
386            We have designed sg-piRNAs that specifically target common fluorophores used in <i>C. elegans</i> labs. Please see the Download tab for primary DNA sequences. 
387                                     </div></p>
388                     
389                  <button id="ActionFluoSearch" type="button" class="btn btn-default action-button">Show piRNAs</button>
390                  <hr/>
391                  <div id="AdvDesignControls" class="shiny-html-output"></div>
392                  <hr/>
393                  <div id="AllPiTab" style="width:100%; height:auto; " class="datatables html-widget html-widget-output"></div>
394                </div>
395              </div>
396            </div>
397          </div>
398        </div>
399        <div class="tab-pane" data-value="Downloads" id="tab-3152-2">
400          <div class="col-sm-8">
401            <h3>Tracks</h3>
402            <br>Bed tracks with <i>C. elegans</i>  (WS270) guide-piRNAs for each specifity criteria.
403                              
404                              <p align="justify">
405                         <a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/piRNAi_Cel_WS270.tar.gz">Download (307 MB)</a><br>
406                         <br><h3>Sequences</h3>
407                         <table>
408  <tr>
409    <th>Name</th>
410    <th>Lab</th>
411    <th>GenBank file (ApE annotations)</th>
412  </tr>
413  <tr>
414    <td>ce-GFP</td>
415    <td>Froekjaer-Jensen lab</td>
416    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/ce-GFP_AlJohani.ape">ce-gfp.gb</a></td>
417  </tr>
418    <tr>
419    <td>ce-tagRFP</td>
420    <td>Froekjaer-Jensen lab</td>
421    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/ce-TagRFP-T_AlJohani.ape">ce-tagRFP-T.gb</a></td>
422  </tr>
423    <tr>
424    <td>GFP</td>
425    <td>Fire lab</td>
426    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/gfp(S65C_Fire).ape">gfp(S65C).gb</a></td>
427  </tr>
428    <tr>
429    <td>mCherry</td>
430    <td>Oegema lab</td>
431    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mCherry_Oegema.ape">mCherry(Oegema).gb</a></td>
432  </tr>
433    <tr>
434    <td>mCherry</td>
435    <td>Seydoux lab</td>
436    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mCherry_Seydoux.ape">mCherry(Seydoux).gb</a></td>
437  </tr>
438    <tr>
439    <td>mKate2</td>
440    <td>Dickinson lab</td>
441    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mKate2_Dickinson.ape">mKate2.gb</a></td>
442  </tr>
443    <tr>
444    <td>mNeonGreen</td>
445    <td>Dickinson lab</td>
446    <td><a href="https://s3.eu-central-1.amazonaws.com/wormbuilder.dev/Downloads/piRNAi_dev/Apes/mNeonGreen_Dickinson.ape">mNeonGreen.gb</a></td>
447  </tr>
448</table>
449                      </p>
450          </div>
451        </div>
452        <div class="tab-pane" data-value="About" id="tab-3152-3">
453          <div class="col-sm-8">
454            <h3>The piRNA-based RNA interference app ("piRNAi")</h3>
455            <p align="justify">
456                      This website was generated via custom modified css/html code running in R via the shiny library.
457                 <br>All the templates, libraries, and programs used to produce this site are under the MIT and GNU licenses.
458                    <br>While the rationale behind the app is described in the background section, its implementation can be found at <a href="https://www.researchgate.net/profile/Amhed_Vargas_Velazquez">Amhed Missael Vargas Velazquez</a> | <a href="https://github.com/AmhedVargas">Github account</a></p>
459            <h3>The Laboratory of Synthetic Genome Biology</h3>
460            <p align="justify">
461                 The Laboratory of Synthetic Genome Biology is located in building 2 - level 3 (Ibn Al-Haytham – Above Spine) at King Abdullah University of Science and Technology (KAUST).
462                 <br><i>Contact info</i>:<br>Christian-Froekjaer Jensen, Ph.D. 
463                 <br>Assistant Professor of Bioscience
464                 <br>Laboratory of Synthetic Genome Biology
465                 <br>
465Email: <a href="mailto:[email protected]">[email protected]</a>
466                      </p>
467          </div>
468        </div>
469      </div>
470    </div>
471    <hr/>
472    <a href="http://www.wormbuilder.org/">Wormbuilder</a><br>
473    <a href="mailto:[email protected]">Contact us!</a>
474  </div>
475</body>
476</html>

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