-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathbiofet-sim.html
executable file
·320 lines (315 loc) · 15.6 KB
/
biofet-sim.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
<head>
<title>BioFET-SIM Online</title>
<link rel="stylesheet" href="./bfs_jvs/baker.css" type="text/css">
<script type="text/javascript" src="./jmol_dir/jmol.js"></script>
<script type="text/javascript" src="./bfs_jvs/jq.js"></script>
<script type="text/javascript" src="./bfs_jvs/init.js"></script>
<script type="text/javascript" src="./bfs_jvs/num_lib.js"></script>
<script type="text/javascript" src="./bfs_jvs/engine.js"></script>
<script type="text/javascript">
/*
$(function() {
$('#fileupload').submit(function() {
var filename = $('input[type=file]').val().split('\\').pop();
if (filename == "") {
alert("You must select a file to upload.");
return false;
}
return true;
});
});
*/
</script>
</head>
<body>
<h2 name="top">BioFET-SIM 2.0</h2>
<div class="cite">
<a href="./ku_help.html" target="_blank">Recommended parameter values</a>
<br />
<br />
<a href="http://www.biofetsim.org/v0.1/biofet-sim-1.0-interface.cgi">BioFET-SIM 1.0</a> (Mobile friendly)
</div><br />
<fieldset>
<form id="uploadform" method="post" enctype="multipart/form-data" action="">
Upload a file: <input type="file" name="images[]" id="images" />
<button type="submit" id="btn">Upload</button><a class="cite" href="#reqs">File requirements</a>
</form>
</fieldset>
<p>OR</p>
<fieldset>
<form method="get" action="./bfs_cgi/bio_def.cgi" id="setup">
<label for="target">Download from PDB: </label>
<input value="1AVD" type="text" size="24" name="target" id="target">
<label for="pH">pH Value:</label>
<input value="7.4" type="text" size="6" name="pH" id="pH">
<input type="submit" value="Initialize">
<p>
<label for="uploaded">Use uploaded:</label>
<input type="checkbox" value="uploaded" id="uploaded" name="uploaded">
<label style="visibility:hidden" for="overwrite" id="overwriteLab">Reinitialize? </label>
<input style="visibility:hidden" type="checkbox" value="overwrite" id="overwrite" name="overwrite">
<label class="cite" style="visibility:hidden" id="overwriteLabExpl">
(Enable to overwrite previously uploaded structure)</label>
<br />
<label class="cite">
(Enable when using an uploaded structure)</label>
</p>
<div style="visibility:visible" id="status">Ready.</div>
<div style="visibility:hidden" id="loader">
<img src='./bfs_jvs/ajax-loader.gif' alt='Loading...'>
</div>
<!--
<input type="hidden" name="state" value="download">
-->
</form>
</fieldset>
<br />
<table>
<tr>
<td>
<script type="text/javascript">
jmolInitialize("./jmol_dir", true);
jmolSetCallback("UseCommandThread", "true");
jmolApplet([400,300]);
</script>
</td>
<td>
<img id="resPlot" src="./bfs_res/result_default.png" style="width:400px;height=300px">
</td>
</tr>
<tr>
<td>
<div class="inst">Use Alt-left (Alt-right on Linux) and drag the structure to adjust the orientation.</div>
<div id="imn"></div>
</td>
</tr>
</table>
<br />
<script type="text/javascript" src="./bfs_jvs/interface.js"></script>
<!--BFS Parameter definitions-->
<form id="form_bfs" action="./bfs_cgi/bio_sim.cgi">
<fieldset>
<table>
<tr>
<td id="targetLab">Structure:</td>
<td><input type="button" id="bfs_signal" value="BioFET-SIM"></td>
<td>Download <a id="bfs_response" href="">BioFET-SIM Signal</a><label class="cite"> (right-click, "Save as...")</label></td>
<td><input type="hidden" id="targetLabHid" name="targetLabHid" value="">
<td><input type="hidden" id="timestamp" name="timestamp" value=""></td>
</tr>
<tr>
<td id="QLab">Q<sub>tot</sub> at pH 0.0: 0.0 [e]</td>
<td><input type="button" id="pHresp" value="pH Response"></td>
<td>Download <a id="pH_response" href="">pH Response</a><label class="cite"> (right-click, "Save as...")</label></td>
</tr>
<tr>
<td id="base_conductance">Base conductance G<sub>0</sub>:</td>
</tr>
<tr>
<td id="sensitivity">Sensitivity:</td>
</tr>
</table>
<table>
<tr>
<td class="prop_title"><strong>NW Properties</strong></td>
<td class="tab_head">Value</td>
<td class="low">Lower Limit</td>
<td class="tab_head">Upper Limit</td>
<td class="tab_head">Plot</td>
</tr>
<tr>
<td><label for="nw_len">NW Length [nm]:</label></td>
<td><input class="val" type="text" id="nw_len" name="nw_len" value="2000.0"></td>
<td><input class="low" type="text" id="nw_len_x_min" name="nw_len_x_min" value="1500.0" onfocus="xLabel('nw_len')"></td>
<td><input class="high" type="text" id="nw_len_x_max" name="nw_len_x_max" value="2500.0" onfocus="xLabel('nw_len')"></td>
<td><input type="radio" name="abs" value="nw_len" onclick="xLabel('nw_len')"></td>
</tr>
<tr>
<td><label for="nw_rad">NW Radius [nm]:</label></td>
<td><input class="val" type="text" id="nw_rad" name="nw_rad" value="10.0"></td>
<td><input class="low" type="text" id="nw_rad_x_min" name="nw_rad_x_min" value="8.0" onfocus="xLabel('nw_rad')"></td>
<td><input class="high" type="text" id="nw_rad_x_max" name="nw_rad_x_max" value="12.0" onfocus="xLabel('nw_rad')"></td>
<td><input type="radio" name="abs" value="nw_rad" onclick="xLabel('nw_rad')"></td>
</tr>
<tr>
<td><label for="L_tf">Thomas-Fermi Length [nm]:</label></td>
<td><input class="val" type="text" id="L_tf" name="L_tf" value="2.04"></td>
<!--
<td><input class="low" type="text" id="L_tf_x_min" name="L_tf_x_min" value="1.54" onfocus="xLabel('L_tf')"></td>
<td><input class="high" type="text" id="L_tf_x_max" name="L_tf_x_max" value="2.54" onfocus="xLabel('L_tf')"></td>
<td><input type="radio" name="abs" value="L_tf" onclick="xLabel('L_tf')"></td>
-->
</tr>
<tr>
<td><label for="eps_1">NW Permittivity [ε<sub>0</sub>]:</label></td>
<td><input class="val" type="text" id="eps_1" name="eps_1" value="12.0"></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="mu">Charge Carrier Mobility [m<sup>2</sup>V<sup>-1</sup>s<sup>-1</sup>]:</label></td>
<td><input class="val" type="text" id="mu" name="mu" value="0.01"></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="n_0">Charge Carrier Density [m<sup>-3</sup>]:</label></td>
<td><input class="val" type="text" id="n_0" name="n_0" value="1.11e+24"></td>
</tr>
<tr>
<td><label for="nw_type">NW Type:</label></td>
<td><input type="radio" name="nw_type" id="p_type" value="P" checked="true">
<label for="p_type">p-type</label></td>
<td><input type="radio" name="nw_type" id="n_type" value="N">
<label for="n_type">n-type</label></td>
<td></td>
<td></td>
</tr>
<tr>
<td colspan="5" class="prop_title"><strong>Oxide and Biofunctionalization Layer Properties</strong></th>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="lay_ox">Oxide Layer Thickness [nm]:</label></td>
<td><input class="val" type="text" id="lay_ox" name="lay_ox" value="2.0"></td>
<td><input class="low" type="text" id="lay_ox_x_min" name="lay_ox_x_min" value="1.0" onfocus="xLabel('lay_ox')"></td>
<td><input class="high" type="text" id="lay_ox_x_max" name="lay_ox_x_max" value="3.0" onfocus="xLabel('lay_ox')"></td>
<td><input type="radio" name="abs" value="lay_ox" onclick="xLabel('lay_ox')"></td>
</tr>
<tr>
<td><label for="eps_2">Oxide Layer Permittivity [ε<sub>0</sub>]:</td></label>
<td><input class="val" type="text" id="eps_2" name="eps_2" value="3.9"></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="lay_bf">Biofunctionalization Thickness [nm]:</label></td>
<td><input class="val" type="text" id="lay_bf" name="lay_bf" value="1.0"></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td class="prop_title"><strong>Solvent Properties</strong></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="L_d">Debye Length [nm]:</label></td>
<td><input class="val" type="text" id="L_d" name="L_d" value="2.0"></td>
<td><input class="low" type="text" id="L_d_x_min" name="L_d_x_min" value="1.0" onfocus="xLabel('L_d')"></td>
<td><input class="high" type="text" id="L_d_x_max" name="L_d_x_max" value="3.0" onfocus="xLabel('L_d')"></td>
<td><input type="radio" name="abs" value="L_d" checked="true" onclick="xLabel('L_d')">
</tr>
<tr>
<td><label for="eps_3">Solvent Permittivity [ε<sub>0</sub>]:</label></td>
<td><input class="val" type="text" id="eps_3" name="eps_3" value=78.0></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label for="start"><strong>Calculation</strong></label></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td><label>Charge Model</label></td>
<td><input type="radio" name="model" id="singl" value="singl">
<label for="singl">Single</label></td>
<td><input type="radio" name="model" id="multi" value="multi" checked="true">
<label for="multi">Multiple</label></td>
</tr>
<tr>
<td><label for="num_prot_inp">Number of Proteins on NW:</label></td>
<td><input class="val" type="text" id="num_prot_inp" name="num_prot_inp" value="4000"></td>
<td><label for="overwrite_num_prot">Constant?</label><input type="checkbox" id="overwrite_num_prot" name="overwrite_num_prot" checked="checked"></td>
<td></td>
</tr>
<!--
<tr>
<td><label for="fileName">BioFET-SIM input file name:</label></td>
<td><input class="val" type="text" id="fileName" name="fileName" value=""></td>
<td></td>
<td></td>
<td></td>
</tr>
-->
<tr>
<td><label for="comment">Add comment to BFS input file:</label></td>
<td><textarea name="comment" rows="5" style="width:300px" id="comment">
</textarea></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td colspan="6">Download <a id="bfsInput" href="">BioFET-SIM input</a> <label class="cite"> (right-click, "Save as...")</label></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
</table>
<input type="hidden" id="pqr" value="$pqr" name="pqr">
<input type="hidden" value="$16.59" name="Q_tot">
<input type="hidden" value="" id="tmp_pqr" name="tmp_pqr">
</fieldset>
</form>
<br />
<div class="cite">
Interface <a href="https://github.com/mzhKU/BioFET-SIM-WEB" target="_blank">repository</a>,
command line version <a href="https://github.com/mzhKU/BioFET-SIM-CMD" target="_blank">repository</a>.<br />
Notifications of observed errors are welcomed at: biofetsim at gmail dot com.<br />
Instruction <a href="http://proteinsandwavefunctions.blogspot.dk/2012/07/biofet-sim-instruction-videos.html" target="_blank">videos</a> demonstrating interface operation are available.<br />
<p>Please cite these references in publications:</p>
De Vico et al., <a href="http://dx.doi.org/10.1039/C0NR00442A" target="_blank"><I>Nanoscale</I></a>, 2011.<br />
De Vico et al., <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2011/NR/c1nr10316d" target="_blank"><I>Nanoscale</I></a>, 2011.<br />
Hediger et al., <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045379" target="_blank">PLoS ONE</a>, 2012.<br />
Hediger et al., <a href="http://dx.doi.org/10.1007/978-3-319-02772-2_3" target="_blank">Nanoscale Sensors</a>, 2014.<br />
<p>
Interface requirements:
<a name="reqs"></a>
<ul name="reqs">
<li>First line of uploaded file must be "MODEL 1"</li>
<li>Last line of uploaded file must be "END"</li>
<li>NMR solution structures are not supported at the moment</li>
<li>We recommend to use SUN Java</li>
<li>Saving of state file requires "Allow" of signed applet</li>
<li>Filenames of uploaded files should not contain white spaces.</li>
</ul>
<a href="#top">Top</a>
<P CLASS="western" ALIGN=CENTER STYLE="margin-bottom: 0in; widows: 0; orphans: 0">
The BioFET method is developed by the<br>
<font COLOR="#0000ff"><U><A HREF="http://propka.ki.ku.dk/~jhjensen">Jensen
Research Group</A></U></font><br>
Department of Chemistry<br>
University of Copenhagen</P>
</p>
<p align=center>
<!-- Copyright (c)2009 Site Meter -->
<!-- Site Meter -->
<script type="text/javascript" src="http://s47.sitemeter.com/js/counter.js?site=s47biofet-sim">
</script>
<noscript>
<a href="http://s47.sitemeter.com/stats.asp?site=s47biofet-sim" target="_top">
<img src="http://s47.sitemeter.com/meter.asp?site=s47biofet-sim" alt="Site Meter" border="0"></a>
</noscript>
</p>
</div>
<div id="debug">
</div>
</body>
</html>