-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathindex.html
More file actions
559 lines (510 loc) · 25.5 KB
/
index.html
File metadata and controls
559 lines (510 loc) · 25.5 KB
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
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="description" content="foarlab homepage">
<title>FOA Research Lab</title>
<!-- Bootstrap Core CSS -->
<link href="css/bootstrap.min.css" rel="stylesheet">
<!-- Custom CSS -->
<link href="css/agency.css" rel="stylesheet">
<!-- Custom Fonts -->
<link href="font-awesome/css/font-awesome.min.css" rel="stylesheet" type="text/css">
<link href="https://fonts.googleapis.com/css?family=Montserrat:400,700" rel="stylesheet" type="text/css">
<link href='https://fonts.googleapis.com/css?family=Kaushan+Script' rel='stylesheet' type='text/css'>
<link href='https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic,700italic' rel='stylesheet'
type='text/css'>
<link href='https://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700' rel='stylesheet' type='text/css'>
<!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!-- WARNING: Respond.js doesn't work if you view the page via file:// -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
<script src="https://oss.maxcdn.com/libs/respond.js/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body id="page-top" class="index">
<!-- Navigation -->
<nav class="navbar navbar-default navbar-fixed-top">
<div class="container">
<!-- Brand and toggle get grouped for better mobile display -->
<div class="navbar-header page-scroll">
<button type="button" class="navbar-toggle" data-toggle="collapse"
data-target="#bs-example-navbar-collapse-1">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand page-scroll" href="#page-top">FOA Research Lab</a>
</div>
<!-- Collect the nav links, forms, and other content for toggling -->
<div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1">
<ul class="nav navbar-nav navbar-right">
<li class="hidden">
<a href="#page-top"></a>
</li>
<li>
<a class="page-scroll" href="#foa">What we do?</a>
</li>
<li>
<a class="page-scroll" href="#fields_application">Application</a>
</li>
<li>
<a class="page-scroll" href="#publications">Publications</a>
</li>
<li>
<a class="page-scroll" href="#software">Software</a>
</li>
<li>
<a class="page-scroll" href="#team">Team</a>
</li>
<li>
<a class="page-scroll" href="#contact">Contact</a>
</li>
</ul>
</div>
<!-- /.navbar-collapse -->
</div>
<!-- /.container-fluid -->
</nav>
<!-- Header -->
<header>
<div class="container">
<div class="intro-text">
<div class="row">
<div class="col-lg-12 text-center">
<h1 class="intro-heading">FOA Research Lab</h1>
<div class="intro-lead-in">
studies a structure of the symbol sequences
</div>
<div class="intro-lead-in">
determines the symbol sequence as the alphabet and the order
</div>
<div class="intro-lead-in">
explores the order as a special and the most important property of the sequence
</div>
</div>
</div>
<div class="row text-center">
<div class="col-md-4">
<span class="fa-stack fa-4x">
<i class="fa fa-circle fa-stack-2x text-primary"></i>
<i class="fa fa-stack-1x fa-icon fa-foa fa-inverse"></i>
</span>
<h4 class="service-heading">Formal Order Analysis</h4>
<p class="text-muted">
The mathematical tool provides the characteristics to measure different
properties of the order.
</p>
<a href="#foa" class="page-scroll btn btn-xl">Tell Me More</a>
</div>
<div class="col-md-4">
<span class="fa-stack fa-4x">
<i class="fa fa-circle fa-stack-2x text-primary"></i>
<i class="fa fa-stack-1x fa-icon fa-fields-application fa-inverse"></i>
</span>
<h4 class="service-heading">Fields of Application</h4>
<p class="text-muted">
Symbol sequences as an object of study are found in a variety of fields of
knowledge - from music to biology.
</p>
<a href="#fields_application" class="page-scroll btn btn-xl">Tell me more</a>
</div>
<div class="col-md-4">
<span class="fa-stack fa-4x">
<i class="fa fa-circle fa-stack-2x text-primary"></i>
<i class="fa fa-stack-1x fa-icon fa-publications fa-inverse"></i>
</span>
<h4 class="service-heading">Publications</h4>
<p class="text-muted">
The results of studies the order of symbol sequences of different nature and
the FOA as a math tool.
</p>
<a href="#publications" class="page-scroll btn btn-xl">Tell Me More</a>
</div>
</div>
</div>
</div>
</header>
<!-- FOA Section -->
<section id="foa">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">Formal Order Analysis </h2>
<h3 class="section-subheading text-muted">
The mathematical tool provides the characteristics to measure
different properties of the order.
</h3>
</div>
</div>
<div class="row text-center">
FOA METHOD DESCRIPTION:
<p>
Known means and model of mathematics (statistics, correlation, spectral and fractal analysis, Markov chains, methods of mathematical linguistics, weighted graphs, etc) don’t take directly into account the order of the components in the studied objects. This situation is to some extent explained by the lack of formalism for an abstract object that represents the order of the elements in the symbolic sequence. In FOA that object called an "order" or "arrangement of the components".
</p>
<p>
The object of study in FOA can be: texts, nucleotide sequences, musical entries, time series and data sets in general.
</p>
<p>
FOA is based on the concept of order – specific representation of the original sequence, in which all the information is discarded except for the location of the elements. Intervals between nearest identical elements are then extracted from the order. Such interval can be called inter-element interval or distance (or internucleotide distance in case of nucleotide sequences). All characteristics of order are based on the multiplication of these intervals.
</p>
<p>
Despite the resemblance characteristic of order are not statistical. As a rule, the statistical characteristics calculated by summing the values and dividing by the number of summands (arithmetic mean). Therefore arrays with different arrangement of elements can give the same values of statistical characteristics. On the contrary, all the characteristics of order are based on a multiplication of inter-element intervals, followed by extraction of the root of degree of the factors (geometric mean interval). If the order of elements in sequence is changed it is almost always changing the factors. Therefore numerical characteristics order directly takes into account the location of elements in the array. In the logarithmic scale order characteristics are based on a simple summation of the logarithms of the intervals.
</p>
</div>
</div>
</section>
<!-- Fields of applications Section -->
<section id="fields_application" class="bg-light-gray">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">Fields of Application</h2>
<h3 class="section-subheading text-muted">
Symbol sequences as an object of study are found in a variety
of fields of knowledge.
</h3>
</div>
</div>
<div class="row">
<div class="col-md-4 col-sm-6 portfolio-item">
<div class="portfolio-hover">
<div class="portfolio-hover-content">
<!--<i class="fa fa-plus fa-3x"></i>-->
</div>
</div>
<img src="img/dna.png" class="img-responsive" alt="">
<div class="portfolio-caption">
<h4>Bioinformatics</h4>
<p class="text-muted">DNA and Proteins analysis</p>
</div>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<div class="portfolio-hover">
<div class="portfolio-hover-content">
<!--<i class="fa fa-plus fa-3x"></i>-->
</div>
</div>
<img src="img/music.png" class="img-responsive" alt="">
<div class="portfolio-caption">
<h4>Music</h4>
<p class="text-muted">Music analysis</p>
</div>
</div>
<div class="col-md-4 col-sm-6 portfolio-item">
<div class="portfolio-hover">
<div class="portfolio-hover-content">
<!--<i class="fa fa-plus fa-3x"></i>-->
</div>
</div>
<img src="img/books.png" class="img-responsive" alt="">
<div class="portfolio-caption">
<h4>Texts</h4>
<p class="text-muted">Linguistics analysis</p>
</div>
</div>
</div>
</div>
</section>
<!-- Publictions Section -->
<section id="publications">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">Publications</h2>
<h3 class="section-subheading text-muted">
The results of studies the order of symbol sequences of
different nature and the FOA as a math tool.
</h3>
</div>
</div>
<div class="row text-left section-text">
<ul>
<li>
<a href="http://www.matbio.org/article_ref.php?lang=eng&id=290">
Shpynov S.N., Gumenuk A.S., Pozdnichenko N.N.
<em>
Application of the Numerical Characteristic of Formal Order Analysis of the Prokaryotic Genomes for Reclassification within the Genus Rickettsia.
</em>
Mathematical Biology and Bioinformatics, 2016, vol. 11, no. 2, pp. 336-350. (In Russian).
</a><span class="label label-info">Bioinformatics</span>
</li>
<li>
<a href="http://authors.elsevier.com/a/1S6L~4aWRJ2inh">
S. Shpynov, N. Pozdnichenko, A. Gumenuk
<em>
Approach for classification and taxonomy within family Rickettsiaceae based on the Formal Order Analysis.
</em>
Microbes and Infection, Volume 17, Issues 11–12, November–December 2015, Pages 839–844.
</a> <span class="label label-info">Bioinformatics</span>
</li>
<li>
<a href="http://journals.tsu.ru/informatics/en/&journal_page=archive&id=1119&article_id=17725">
Gumenyuk A.S., Pozdnichenko N.N.
<em>
Formal analysis of order in the local structure of the nucleotide sequences.
</em>
Tomsk State University Journal of Control and Computer Science, 2014, no. 4(29), pp. 23-30. (In Russian).
</a>
<span class="label label-info">Bioinformatics</span>
</li>
<li>
<a href="http://dx.doi.org/10.17537/2013.8.373">
Gumenyuk A.S., Pozdnichenko N.N., Shpynov S.N., Rodionov I.N.
<em>
Formal Analysis of Structures of Nucleotide Chains.
</em>
Mathematical Biology and Bioinformatics, 2013, vol. 8, no. 1, pp. 373-397. (In Russian).
</a><span class="label label-info">Bioinformatics</span>
</li>
<li>
Gumenyuk A.S., Pozdnichenko N.N.
<em>
Analysis of order of the nucleotide sequences.
</em>
The 4th All-Russian Conference “Knowledge – Ontology – Theory” (KONT-13). Novosibirsk, 2013, vol. 2, pp. 58-68. (In Russian).
<span class="label label-info">Bioinformatics</span>
</li>
<li>
<a href="http://journals.tsu.ru/informatics/en/&journal_page=archive&id=922&article_id=2373">
Verkhovin A., Gumenyuk A.
<em>
On means of formal analysis of the structure of musical text.
</em>
Tomsk State University Journal of Control and Computer Science, 2013, no. 3(24), pp. 47-56. (In Russian).
</a> <span class="label label-warning">Music</span>
</li>
<li>
Tsymbal V.S., Pozdnichenko N.N.
<em>
About the development of the module for the calculation of local characteristics of order of the nucleotide sequences.
</em>
Proc. of 12th All-Russian research conference “Information technologies and mathematical modeling” (ITMM-2013). Tomsk: Tomsk State University Publ., 2013, pp. 61-65. (In Russian).
<span class="label label-info">Bioinformatics</span>
</li>
<li>
Gumenyuk A.S., Morozenko E.V., Rodionov I.N.
<em>
Formalization of analysis of order of sign chains.
</em>
Tomsk State University Journal of Control and Computer Science, 2011, no. 2(15), pp. 15-23. (In Russian).
<span class="label label-default">Math</span>
</li>
<li>
Gumeniuk A., Klikushin I., Kobenko V., Tsiganenko V.
<em>
Algorithms for the analysis of signal and data structure.
</em>
Omsk; 2010. 272 p. (In Russian). <span class="label label-default">Math</span>
</li>
<li>
Gumenyuk A.S.
<em>
On the formalism of constructing abstract objects in the inner physical space of information system (Elements of the algebra of mental events).
</em>
The system analysis in the design and management. Procs. of the 10th International Scientific and Practical Conference. St. Petersburg: Polytechnic University Publ., 2006, pt. 2, pp. 172-181. (In Russian).
<span class="label label-default">Math</span>
</li>
<li>
Gumenyuk A.S.
<em>
On the means of analysis of mutual arrangement of the components of the sign sequence.
</em>
Military equipment, arms and double purpose technologies. Procs. of the 3rd International Congress of Technology. Omsk: OmSTU Publ., 2005, pt. 2, pp. 48-52. (In Russian).
<span class="label label-default">Math</span>
</li>
<li>
Gumenjuk A., Kostyshin A., Borisov K., Salnikova O.
<em>
On the acoustic elements of a poem and the formal procedures of their segmentation.
</em>
Glottometrics. Lüdenscheid: RAM-Verl., 2004. No 8. P. 42–67.
<span class="label label-warning">Music</span>
</li>
<li>
Gumenyuk A., Kostyshin A., Simonova S.
<em>
An approach to the research of the structure of linguistic and musical texts.
</em>
Glottometrics, 2002, no. 3, pp. 61-69.
<span class="label label-warning">Music</span> <span class="label label-success">Texts</span>
</li>
</ul>
</div>
</div>
</section>
<!-- Software Section -->
<section id="software" class="bg-light-gray">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">Software</h2>
<h3 class="section-subheading text-muted">
We provide online tool for calculation of FOA metrics for symbol
sequences. <br/> Beta version currently supports only DNA sequences analysis.
</h3>
<a href="http://libiada.foarlab.org" class="btn btn-xl">Try Libiada - beta</a>
</div>
</div>
</div>
</section>
<!-- Team Section -->
<section id="team">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">Our Team</h2>
<h3 class="section-subheading text-muted"></h3>
</div>
</div>
<div class="row">
<div class="col-sm-6">
<div class="team-member">
<img src="img/team/gumenuk.jpg" class="img-responsive img-circle" alt="">
<h4>Aleksandr Gumenuk</h4>
<p class="text-muted">Chief science officer</p>
<p class="text-muted">PhD, Docent</p>
</div>
</div>
<div class="col-sm-6">
<div class="team-member">
<img src="img/team/shpynov.jpg" class="img-responsive img-circle" alt="">
<h4>Stanislav Shpynov</h4>
<p class="text-muted">Lead biology researcher</p>
<p class="text-muted">PhD, MD</p>
</div>
</div>
<div class="col-sm-6">
<div class="team-member">
<img src="img/team/pozdnichenko.jpg" class="img-responsive img-circle" alt="">
<h4>Nikolay Pozdnichenko</h4>
<p class="text-muted">CTO</p>
<p class="text-muted">PhD student</p>
</div>
</div>
<div class="col-sm-6">
<div class="team-member">
<img src="img/team/rodionov.jpg" class="img-responsive img-circle" alt="">
<h4>Igor Rodionov</h4>
<p class="text-muted">Lead Developer</p>
<p class="text-muted">Master of Computer Science</p>
</div>
</div>
<!--
<div class="col-sm-4">
<div class="team-member">
<img src="img/team/skiba.jpg" class="img-responsive img-circle" alt="">
<h4>Artemiy Skiba</h4>
<p class="text-muted">Developer</p>
<p class="text-muted">Master of Computer Science</p>
</div>
</div>
-->
</div>
</div>
</section>
<!-- Contacts Section -->
<section id="contact">
<div class="container">
<div class="row">
<div class="col-lg-12 text-center">
<h2 class="section-heading">We are open for collaboration</h2>
<h3 class="section-subheading text-muted">questions are welcome</h3>
<a href="mailto:info@foarlab.org" class="btn btn-xl">Contact us</a>
</div>
</div>
</div>
</section>
<footer>
<div class="container">
<div class="row">
<div class="col-md-4">
<span class="copyright">Copyright © foarLab.org 2019</span>
</div>
<!--<div class="col-md-4">
<ul class="list-inline social-buttons">
<li><a href="#"><i class="fa fa-twitter"></i></a>
</li>
<li><a href="#"><i class="fa fa-facebook"></i></a>
</li>
<li><a href="#"><i class="fa fa-linkedin"></i></a>
</li>
</ul>
</div>
<div class="col-md-4">
<ul class="list-inline quicklinks">
<li><a href="#">Privacy Policy</a>
</li>
<li><a href="#">Terms of Use</a>
</li>
</ul>
</div>-->
</div>
</div>
</footer>
<!-- jQuery -->
<script src="js/jquery.js"></script>
<!-- Bootstrap Core JavaScript -->
<script src="js/bootstrap.min.js"></script>
<!-- Plugin JavaScript -->
<script src="http://cdnjs.cloudflare.com/ajax/libs/jquery-easing/1.3/jquery.easing.min.js"></script>
<script src="js/classie.js"></script>
<script src="js/cbpAnimatedHeader.js"></script>
<!-- Contact Form JavaScript -->
<script src="js/jqBootstrapValidation.js"></script>
<script src="js/contact_me.js"></script>
<!-- Custom Theme JavaScript -->
<script src="js/agency.js"></script>
<script>
(function (i, s, o, g, r, a, m) {
i['GoogleAnalyticsObject'] = r;
i[r] = i[r] || function () {
(i[r].q = i[r].q || []).push(arguments)
}, i[r].l = 1 * new Date();
a = s.createElement(o),
m = s.getElementsByTagName(o)[0];
a.async = 1;
a.src = g;
m.parentNode.insertBefore(a, m)
})(window, document, 'script', '//www.google-analytics.com/analytics.js', 'ga');
ga('create', 'UA-68413267-1', 'auto');
ga('send', 'pageview');
</script>
<!-- Yandex.Metrika counter -->
<script type="text/javascript">
(function (d, w, c) {
(w[c] = w[c] || []).push(function () {
try {
w.yaCounter32838312 = new Ya.Metrika({
id: 32838312,
clickmap: true,
trackLinks: true,
accurateTrackBounce: true,
webvisor: true,
trackHash: true
});
} catch (e) {
}
});
var n = d.getElementsByTagName("script")[0], s = d.createElement("script"), f = function () {
n.parentNode.insertBefore(s, n);
};
s.type = "text/javascript";
s.async = true;
s.src = "https://mc.yandex.ru/metrika/watch.js";
if (w.opera == "[object Opera]") {
d.addEventListener("DOMContentLoaded", f, false);
} else {
f();
}
})(document, window, "yandex_metrika_callbacks");
</script>
<noscript>
<div><img src="https://mc.yandex.ru/watch/32838312" style="position:absolute; left:-9999px;" alt="" /></div>
</noscript>
<!-- /Yandex.Metrika counter -->
</body>
</html>