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commit 2292857672c25c797dbff70f935aa6fc9b56566a 1 parent 0c5eb69
Christopher L Plaisier, PhD authored

Showing 54 changed files with 15,069 additions and 1 deletion. Show diff stats Hide diff stats

  1. +3 1 README.md → README
  2. 0  __init__.py
  3. +14 0 manage.py
  4. 0  network/__init__.py
  5. +107 0 network/models.py
  6. BIN  network/static/Gnomes_plan.png
  7. BIN  network/static/cancerMiRNARegulatoryNetwork.gif
  8. BIN  network/static/cancerMiRNARegulatoryNetwork.jpg
  9. +434 0 network/static/cmrn.css
  10. +5,130 0 network/static/compendium_miRNA_target_genes.csv
  11. BIN  network/static/favicon.ico
  12. BIN  network/static/firm/FIRM.tgz
  13. BIN  network/static/hanahanWeinbergHallmarksOfCancer.gif
  14. BIN  network/static/hanahanWeinbergHallmarksOfCancer.jpg
  15. +18 0 network/static/jquery-1.6.1.min.js
  16. +4 0 network/static/jquery.tablesorter.min.js
  17. +1 0  network/static/js/cytoscape_web/AC_OETags.min.js
  18. +1 0  network/static/js/cytoscape_web/cytoscapeweb.min.js
  19. +1 0  network/static/js/cytoscape_web/json2.min.js
  20. +3,064 0 network/static/sig_overlap_network_0.05.gml
  21. +407 0 network/static/sig_overlap_network_0.05.sif
  22. +408 0 network/static/sig_overlap_network_0.05_type_edge.attr
  23. +176 0 network/static/sig_overlap_network_0.05_type_node.attr
  24. +86 0 network/static/sig_overlap_network_0.05_validated_edge.attr
  25. BIN  network/static/swf/CytoscapeWeb.swf
  26. BIN  network/static/swf/playerProductInstall.swf
  27. +16 0 network/tests.py
  28. +1,961 0 network/views.py
  29. +160 0 settings.py
  30. +77 0 templates/base.html
  31. +92 0 templates/cancer.html
  32. +52 0 templates/citation.html
  33. +141 0 templates/cluster.html
  34. +79 0 templates/compendium.html
  35. +30 0 templates/count_em.html
  36. +32 0 templates/count_em2.html
  37. +173 0 templates/cytoscape_web.html
  38. +67 0 templates/dataset.html
  39. +112 0 templates/firm.html
  40. +47 0 templates/go_term_list_genes.html
  41. +95 0 templates/hallmark.html
  42. +20 0 templates/help.html
  43. +1,429 0 templates/index.html
  44. +62 0 templates/inference.html
  45. +44 0 templates/list_go_terms.html
  46. +47 0 templates/miRNA.html
  47. +62 0 templates/miRNA_and_GO_term.html
  48. +62 0 templates/miRNA_list_genes.html
  49. +65 0 templates/overlap.html
  50. +98 0 templates/overlapping.html
  51. +33 0 templates/overlapping_mirna.html
  52. +56 0 templates/overlapping_mirna_go.html
  53. +45 0 templates/specific_miRNA.html
  54. +58 0 urls.py
4 README.md → README
... ... @@ -1,4 +1,6 @@
1 1 Cancer-miRNA-Regulatory-Network
2 2 ===============================
3 3
4   -A database containing the predictions for the Cancer miRNA-Regulatory Network.
  4 +A database containing the predictions for the Cancer miRNA-Regulatory Network.
  5 +
  6 +This application was developed using Django, Python and PosgreSQL.
0  __init__.py
No changes.
14 manage.py
... ... @@ -0,0 +1,14 @@
  1 +#!/usr/bin/env python
  2 +from django.core.management import execute_manager
  3 +import imp
  4 +try:
  5 + imp.find_module('settings') # Assumed to be in the same directory.
  6 +except ImportError:
  7 + import sys
  8 + sys.stderr.write("Error: Can't find the file 'settings.py' in the directory containing %r. It appears you've customized things.\nYou'll have to run django-admin.py, passing it your settings module.\n" % __file__)
  9 + sys.exit(1)
  10 +
  11 +import settings
  12 +
  13 +if __name__ == "__main__":
  14 + execute_manager(settings)
0  network/__init__.py
No changes.
107 network/models.py
... ... @@ -0,0 +1,107 @@
  1 +from django.db import models
  2 +
  3 +class Cancer(models.Model):
  4 + name = models.CharField(max_length=200)
  5 + short_name = models.CharField(max_length=100)
  6 + publication = models.CharField(max_length=200)
  7 + pmid = models.IntegerField()
  8 + tissue = models.CharField(max_length=100)
  9 +
  10 + def __unicode__(self):
  11 + return self.short_name
  12 +
  13 +class Gene(models.Model):
  14 + entrez_id = models.IntegerField()
  15 +
  16 + def __unicode__(self):
  17 + return str(self.entrez_id)
  18 +
  19 +class Coexpression_Cluster(models.Model):
  20 + cancer = models.ForeignKey(Cancer)
  21 + number = models.IntegerField()
  22 + cluster_membership = models.ManyToManyField(Gene)
  23 +
  24 + def __unicode__(self):
  25 + return self.cancer.__unicode__()+'.'+str(self.number)
  26 +
  27 +class MiRNA(models.Model):
  28 + name = models.CharField(max_length=100)
  29 + mature_sequence_id = models.CharField(max_length=100)
  30 + mature_sequence = models.CharField(max_length=100)
  31 + pita_targets = models.ManyToManyField(Gene, related_name='MiRNAtoPITA')
  32 + targetscan_targets = models.ManyToManyField(Gene,related_name='MiRNAtoTargetScan')
  33 +
  34 + def __unicode__(self):
  35 + return self.name
  36 +
  37 +class Validation(models.Model):
  38 + cancer = models.ForeignKey(Cancer)
  39 + mirna = models.ForeignKey(MiRNA)
  40 + method = models.CharField(max_length=100)
  41 +
  42 + def __unicode__(self):
  43 + return self.method+'.'+self.cancer.__unicode__()+'.'+self.mirna.__unicode__()
  44 +
  45 +class Inferred_MiRNA(models.Model):
  46 + coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
  47 + mirna = models.ForeignKey(MiRNA)
  48 + method = models.CharField(max_length=100)
  49 + target_genes = models.ManyToManyField(Gene, through='Target_Gene')
  50 +
  51 + def __unicode__(self):
  52 + return self.coexpression_cluster.__unicode__()+'-'+self.mirna.__unicode__()
  53 +
  54 +class Gene_Ontology(models.Model):
  55 + go_id = models.CharField(max_length=100)
  56 + term = models.CharField(max_length=500)
  57 + category = models.CharField(max_length=100)
  58 + annotated_genes = models.ManyToManyField(Gene)
  59 +
  60 + def __unicode__(self):
  61 + return self.go_id
  62 +
  63 +class Functional_Enrichment(models.Model):
  64 + coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
  65 + gene_ontology = models.ForeignKey(Gene_Ontology)
  66 + annotated_genes = models.ManyToManyField(Gene)
  67 +
  68 + def __unicode__(self):
  69 + return self.coexpression_cluster.__unicode__()+'-'+self.gene_ontology.__unicode__()
  70 +
  71 +class Target_Gene(models.Model):
  72 + inferred_mirna = models.ForeignKey(Inferred_MiRNA)
  73 + gene = models.ForeignKey(Gene)
  74 + strand = models.CharField(max_length=10)
  75 + site = models.CharField(max_length=10)
  76 + start = models.IntegerField()
  77 + match = models.FloatField()
  78 +
  79 + def __unicode__(self):
  80 + return self.inferred_mirna.__unicode__()+' '+self.gene.__unicode__()
  81 +
  82 +class Gene_Annotation(models.Model):
  83 + gene = models.ForeignKey(Gene)
  84 + category = models.CharField(max_length=100)
  85 + annotation = models.CharField(max_length=1000)
  86 +
  87 + def __unicode__(self):
  88 + return str(self.gene.entrez_id)+' = '+self.annotation
  89 +
  90 +class Hallmarks_Of_Cancer(models.Model):
  91 + coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
  92 + hallmark_of_cancer = models.CharField(max_length=1000)
  93 + semantic_similarity = models.FloatField()
  94 +
  95 + def __unicode__(self):
  96 + return self.coexpression_cluster.__unicode__()+' '+self.hallmark_of_cancer+'='+str(self.semantic_similarity)
  97 +
  98 +class MiRNA_Target_GO_Term_Overlap(models.Model):
  99 + coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
  100 + inferred_mirna = models.ForeignKey(Inferred_MiRNA)
  101 + functional_enrichment = models.ForeignKey(Functional_Enrichment)
  102 + p_value = models.FloatField()
  103 + genes_overlapping = models.ManyToManyField(Gene)
  104 +
  105 + def __unicode__(self):
  106 + return self.coexpression_cluster.__unicode__()+' '+self.inferred_mirna.__unicode__()+' '+self.gene_ontology.__unicode__()
  107 +
BIN  network/static/Gnomes_plan.png
BIN  network/static/cancerMiRNARegulatoryNetwork.gif
BIN  network/static/cancerMiRNARegulatoryNetwork.jpg
434 network/static/cmrn.css
... ... @@ -0,0 +1,434 @@
  1 +body{
  2 + background-color: #ffffff;
  3 + font-family: Arial, Verdana, Helvetica, sans-serif;
  4 + color: #000000;
  5 + text-align: center;
  6 + /* min-width:600px; */
  7 + width: 100%;
  8 + margin: 0;
  9 + padding: 0;
  10 + border: 0;
  11 +}
  12 +.mc_ul {
  13 + width: 45em;
  14 +}
  15 +.mc_li {
  16 + float:left;
  17 + width:15em;
  18 +}
  19 +.cl_br {
  20 + clear: left;
  21 +}
  22 +ol_bold {
  23 + font-weight: bold;
  24 +}
  25 +ol span {
  26 + font-weight: normal;
  27 +}
  28 +.center {
  29 + align: center;
  30 + width: 100%;
  31 +}
  32 +.center1 {
  33 + text-align: center;
  34 + font-size: 120%;
  35 + font-weight: bold;
  36 +}
  37 +.center2 {
  38 + text-align: center;
  39 + font-size: 120%;
  40 + font-weight: bold;
  41 + width: 40%;
  42 +}
  43 +.tableft {
  44 + background-color: #225588;
  45 + color: #ffffff;
  46 + border-top-left-radius: 15px;
  47 + -moz-border-radius-topleft: 15px;
  48 + -webkit-border-radius-topleft: 15px;
  49 + vertical-align: middle;
  50 + text-align: center;
  51 +}
  52 +.tabmid {
  53 + background-color: #225588;
  54 + color: #ffffff;
  55 + vertical-align: middle;
  56 + text-align: center;
  57 +}
  58 +.tabright {
  59 + background-color: #225588;
  60 + color: #ffffff;
  61 + border-top-right-radius: 15px;
  62 + -moz-border-radius-topright: 15px;
  63 + -webkit-border-radius-topright: 15px;
  64 + vertical-align: middle;
  65 + text-align: center;
  66 +}
  67 +.tab {
  68 + /* background-color: #225588; */
  69 + background-color: #225588;
  70 + color: #ffffff;
  71 + border-top-left-radius: 15px;
  72 + border-top-right-radius: 15px;
  73 + -moz-border-radius-topleft: 15px;
  74 + -moz-border-radius-topright: 15px;
  75 + -webkit-border-radius-topleft: 15px;
  76 + -webkit-border-radius-topright: 15px;
  77 + vertical-align: middle;
  78 + text-align: center;
  79 +}
  80 +.bottomtab {
  81 + border-color: #225588;
  82 + margin-top: 0px;
  83 + margin-left: 0px;
  84 + margin-right: 0px;
  85 + margin-bottom: 0px;
  86 + padding-top: 0px;
  87 + padding-left: 0px;
  88 + padding-right: 0px;
  89 + padding-bottom: 0px;
  90 + border-top-width: 0;
  91 + border-left-width: 0;
  92 + border-right-width: 0;
  93 + border-bottom-width: 0;
  94 + border-spacing: 0;
  95 + border-collapse: collapse;
  96 + background-color: #225588;
  97 + color: #ffffff;
  98 + border-bottom-left-radius: 15px;
  99 + -moz-border-radius-bottomleft: 15px;
  100 + -webkit-border-radius-bottomleft: 15px;
  101 + border-bottom-right-radius: 15px;
  102 + -moz-border-radius-bottomright: 15px;
  103 + -webkit-border-radius-bottomright: 15px;
  104 + vertical-align: middle;
  105 + text-align: center;
  106 +}
  107 +.header {
  108 + background-color: #aa0000;
  109 + color: #ffffff;
  110 + border-radius: 15px;
  111 + -moz-border-radius: 15px;
  112 + -webkit-border-radius: 15px;
  113 + padding: 10px 10px 10px 10px;
  114 + vertical-align: middle;
  115 +}
  116 +
  117 +.header2 {
  118 + background-color: #225588;
  119 + color: #ffffff;
  120 + border-radius: 15px;
  121 + -moz-border-radius: 15px;
  122 + -webkit-border-radius: 15px;
  123 + padding: 10px 10px 10px 10px;
  124 + vertical-align: middle;
  125 + font-weight: bold;
  126 + text-align: center;
  127 + width: 250px;
  128 +}
  129 +.header3 {
  130 + background-color: #225588;
  131 + color: #ffffff;
  132 + border-radius: 15px;
  133 + -moz-border-radius: 15px;
  134 + -webkit-border-radius: 15px;
  135 + padding: 10px 10px 10px 10px;
  136 + vertical-align: middle;
  137 + font-weight: bold;
  138 + text-align: center;
  139 +}
  140 +.header_left {
  141 + background-color: #225588;
  142 + color: #ffffff;
  143 + border-top-left-radius: 15px;
  144 + border-bottom-left-radius: 15px;
  145 + -moz-border-radius-topleft: 15px;
  146 + -moz-border-radius-bottomleft: 15px;
  147 + -webkit-border-radius-topleft: 15px;
  148 + -webkit-border-radius-bottomleft: 15px;
  149 + vertical-align: middle;
  150 + text-align: center;
  151 +}
  152 +.header_middle {
  153 + background-color: #225588;
  154 + color: #ffffff;
  155 + vertical-align: middle;
  156 + text-align: center;
  157 +}
  158 +.header_right {
  159 + background-color: #225588;
  160 + color: #ffffff;
  161 + border-top-right-radius: 15px;
  162 + border-bottom-right-radius: 15px;
  163 + -moz-border-radius-topright: 15px;
  164 + -moz-border-radius-bottomright: 15px;
  165 + -webkit-border-radius-topright: 15px;
  166 + -webkit-border-radius-bottomright: 15px;
  167 + vertical-align: middle;
  168 + text-align: center;
  169 +}
  170 +.entry {
  171 + background-color: #cccccc;
  172 + color: #000000;
  173 + border-radius: 15px;
  174 + -moz-border-radius: 15px;
  175 + -webkit-border-radius: 15px;
  176 + vertical-align: middle;
  177 + text-align: center;
  178 +}
  179 +.entry_left {
  180 + background-color: #cccccc;
  181 + color: #000000;
  182 + border-top-left-radius: 15px;
  183 + border-bottom-left-radius: 15px;
  184 + -moz-border-radius-topleft: 15px;
  185 + -moz-border-radius-bottomleft: 15px;
  186 + -webkit-border-radius-topleft: 15px;
  187 + -webkit-border-radius-bottomleft: 15px;
  188 + vertical-align: middle;
  189 + text-align: center;
  190 +}
  191 +.entry_middle {
  192 + background-color: #cccccc;
  193 + color: #000000;
  194 + vertical-align: middle;
  195 + text-align: center;
  196 +}
  197 +.entry_right {
  198 + background-color: #cccccc;
  199 + color: #000000;
  200 + border-top-right-radius: 15px;
  201 + border-bottom-right-radius: 15px;
  202 + -moz-border-radius-topright: 15px;
  203 + -moz-border-radius-bottomright: 15px;
  204 + -webkit-border-radius-topright: 15px;
  205 + -webkit-border-radius-bottomright: 15px;
  206 + vertical-align: middle;
  207 + text-align: center;
  208 +}
  209 +.entry2 {
  210 + background-color: #cccccc;
  211 + color: #000000;
  212 + border-radius: 15px;
  213 + -moz-border-radius: 15px;
  214 + -webkit-border-radius: 15px;
  215 + vertical-align: middle;
  216 + text-align: center;
  217 + width: 100px;
  218 +}
  219 +td {
  220 + padding: 15px;
  221 +}
  222 +.fill {
  223 + width: 100%;
  224 +}
  225 +.matchBackground {
  226 + color: #cccccc;
  227 +}
  228 +.afooter_like {
  229 + color: #ffffff;
  230 + font-weight: bold;
  231 +}
  232 +img {
  233 + margin:10px 0 5px;
  234 + border-style: none;
  235 +}
  236 +a:link {
  237 + color: #990000;
  238 +}
  239 +a:hover {
  240 + color: #cc0000;
  241 +}
  242 +a:visited {
  243 + color: #cc0000;
  244 +}
  245 +a:active {
  246 + color: #cc0000;
  247 +}
  248 +a.cite:link {
  249 + color: #000000;
  250 + text-decoration:none;
  251 +}
  252 +a.cite:hover {
  253 + color: #000000;
  254 + text-decoration:underline;
  255 +}
  256 +a.cite:visited {
  257 + color: #000000;
  258 + text-decoration:none;
  259 +}
  260 +a.cite:active {
  261 + color: #000000;
  262 + text-decoration:underline;
  263 +}
  264 +a.cite:link {
  265 + color: #000000;
  266 + text-decoration:none;
  267 +}
  268 +a.cite:hover {
  269 + color: #000000;
  270 + text-decoration:underline;
  271 +}
  272 +a.cite:visited {
  273 + color: #000000;
  274 + text-decoration:none;
  275 +}
  276 +a.cite:active {
  277 + color: #000000;
  278 + text-decoration:underline;
  279 +}
  280 +.nospacing {
  281 + border-color: #225588;
  282 + background-color: #225588;
  283 + margin-top: 0px;
  284 + margin-left: 0px;
  285 + margin-right: 0px;
  286 + margin-bottom: 0px;
  287 + padding-top: 0px;
  288 + padding-left: 0px;
  289 + padding-right: 0px;
  290 + padding-bottom: 0px;
  291 + border-style: solid;
  292 + border-top-width: 4;
  293 + border-left-width: 4;
  294 + border-right-width: 4;
  295 + border-bottom-width: 4;
  296 + border-spacing: 0;
  297 + border-collapse: collapse;
  298 +}
  299 +.tdtab {
  300 + background-color: #ffffff;
  301 + border-top-left-radius: 15px;
  302 + border-top-right-radius: 15px;
  303 + -moz-border-radius-topleft: 15px;
  304 + -moz-border-radius-topright: 15px;
  305 + -webkit-border-radius-topleft: 15px;
  306 + -webkit-border-radius-topright: 15px;
  307 + border-bottom-left-radius: 15px;
  308 + border-bottom-right-radius: 15px;
  309 + -moz-border-radius-bottomleft: 15px;
  310 + -moz-border-radius-bottomright: 15px;
  311 + -webkit-border-radius-bottomleft: 15px;
  312 + -webkit-border-radius-bottomright: 15px;
  313 + vertical-align: middle;
  314 + text-align: center;
  315 +}
  316 +.nobottomspacing {
  317 + border-collapse: collapse;
  318 +}
  319 +.spacer {
  320 + width: 2px;
  321 + background-color: #ffffff;
  322 + margin-top: 0px;
  323 + margin-left: 0px;
  324 + margin-right: 0px;
  325 + margin-bottom: 0px;
  326 + padding-top: 0px;
  327 + padding-left: 0px;
  328 + padding-right: 0px;
  329 + padding-bottom: 0px;
  330 + border-top-width: 0;
  331 + border-left-width: 0;
  332 + border-right-width: 0;
  333 + border-bottom-width: 0;
  334 + border-spacing: 0;
  335 + border-collapse: collapse;
  336 +}
  337 +a.tab:link {
  338 + color: #ffffff;
  339 + font-weight:bold;
  340 + font-size:110%;
  341 + text-decoration:none;
  342 +}
  343 +a.tab:hover {
  344 + color: #ffffff;
  345 + font-weight:bold;
  346 + font-size:110%;
  347 + text-decoration:underline;
  348 +}
  349 +a.tab:visited {
  350 + color: #ffffff;
  351 + font-weight:bold;
  352 + font-size:110%;
  353 + text-decoration:none;
  354 +}
  355 +a.tab:active {
  356 + color: #ffffff;
  357 + font-weight:bold;
  358 + font-size:110%;
  359 + text-decoration:underline;
  360 +}
  361 +a.footer:link {
  362 + font-weight:bold;
  363 + color: #ffffff;
  364 +}
  365 +a.footer:hover {
  366 + font-weight:bold;
  367 + color: #ffffff;
  368 +}
  369 +a.footer:visited {
  370 + font-weight:bold;
  371 + color: #ffffff;
  372 +}
  373 +a.footer:active {
  374 + font-weight:bold;
  375 + color: #ffffff;
  376 +}
  377 +#header {
  378 + clear:both;
  379 + float:left;
  380 + width:100%;
  381 +}
  382 +/* column container */
  383 +.colmask {
  384 + position:relative; /* This fixes the IE7 overflow hidden bug */
  385 + clear:both;
  386 + float:left;
  387 + width:100%; /* width of whole page */
  388 + overflow:hidden; /* This chops off any overhanging divs */
  389 +}
  390 +/* common column settings */
  391 +.colright,
  392 +.colmid,
  393 +.colleft {
  394 + float:left;
  395 + width:100%; /* width of page */
  396 + position:relative;
  397 +}
  398 +.col1,
  399 +.col2,
  400 +.col3 {
  401 + float:left;
  402 + position:relative;
  403 + padding:0 0 1em 0; /* no left and right padding on columns, we just make them narrower instead
  404 + only padding top and bottom is included here, make it whatever value you need */
  405 + overflow:hidden;
  406 +}
  407 +/* 3 Column settings */
  408 +.threecol .colmid {
  409 + right:8%;
  410 + background:#ffffff;
  411 +}
  412 +.threecol .colleft {
  413 + right:84%;
  414 + /* background:#ffffff; */
  415 +}
  416 +.threecol .col1 {
  417 + width:80%; /* width of center column content (column width minus padding on either side) */
  418 + left:102%; /* 100% plus left padding of center column */
  419 +}
  420 +.threecol .col2 {
  421 + width:4%; /* Width of left column content (column width minus padding on either side) */
  422 + left:18%; /* width of (right column) plus (center column left and right padding) plus (left column left padding) */
  423 +}
  424 +.threecol .col3 {
  425 + width:4%; /* Width of right column content (column width minus padding on either side) */
  426 + left:102%; /* Please make note of the brackets here:
  427 + (100% - left column width) plus (center column left and right padding) plus (left column left and right padding) plus (right column left padding) */
  428 +}
  429 +/* Footer styles */
  430 +#footer {
  431 + clear:both;
  432 + float:left;
  433 + width:100%;
  434 +}
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  1 +/*!
  2 + * jQuery JavaScript Library v1.6.1
  3 + * http://jquery.com/
  4 + *
  5 + * Copyright 2011, John Resig
  6 + * Dual licensed under the MIT or GPL Version 2 licenses.
  7 + * http://jquery.org/license
  8 + *
  9 + * Includes Sizzle.js
  10 + * http://sizzlejs.com/
  11 + * Copyright 2011, The Dojo Foundation
  12 + * Released under the MIT, BSD, and GPL Licenses.
  13 + *
  14 + * Date: Thu May 12 15:04:36 2011 -0400
  15 + */
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e.animatedProperties)e.animatedProperties[g]!==!0&&(c=!1);if(c){e.overflow!=null&&!f.support.shrinkWrapBlocks&&f.each(["","X","Y"],function(a,b){d.style["overflow"+b]=e.overflow[a]}),e.hide&&f(d).hide();if(e.hide||e.show)for(var i in e.animatedProperties)f.style(d,i,e.orig[i]);e.complete.call(d)}return!1}e.duration==Infinity?this.now=b:(h=b-this.startTime,this.state=h/e.duration,this.pos=f.easing[e.animatedProperties[this.prop]](this.state,h,0,1,e.duration),this.now=this.start+(this.end-this.start)*this.pos),this.update();return!0}},f.extend(f.fx,{tick:function(){for(var 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h=e.body,i=cy(e),j=g.clientTop||h.clientTop||0,k=g.clientLeft||h.clientLeft||0,l=i.pageYOffset||f.support.boxModel&&g.scrollTop||h.scrollTop,m=i.pageXOffset||f.support.boxModel&&g.scrollLeft||h.scrollLeft,n=c.top+l-j,o=c.left+m-k;return{top:n,left:o}}:f.fn.offset=function(a){var b=this[0];if(a)return this.each(function(b){f.offset.setOffset(this,a,b)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return f.offset.bodyOffset(b);f.offset.initialize();var c,d=b.offsetParent,e=b,g=b.ownerDocument,h=g.documentElement,i=g.body,j=g.defaultView,k=j?j.getComputedStyle(b,null):b.currentStyle,l=b.offsetTop,m=b.offsetLeft;while((b=b.parentNode)&&b!==i&&b!==h){if(f.offset.supportsFixedPosition&&k.position==="fixed")break;c=j?j.getComputedStyle(b,null):b.currentStyle,l-=b.scrollTop,m-=b.scrollLeft,b===d&&(l+=b.offsetTop,m+=b.offsetLeft,f.offset.doesNotAddBorder&&(!f.offset.doesAddBorderForTableAndCells||!cw.test(b.nodeName))&&(l+=parseFloat(c.borderTopWidth)||0,m+=parseFloat(c.borderLeftWidth)||0),e=d,d=b.offsetParent),f.offset.subtractsBorderForOverflowNotVisible&&c.overflow!=="visible"&&(l+=parseFloat(c.borderTopWidth)||0,m+=parseFloat(c.borderLeftWidth)||0),k=c}if(k.position==="relative"||k.position==="static")l+=i.offsetTop,m+=i.offsetLeft;f.offset.supportsFixedPosition&&k.position==="fixed"&&(l+=Math.max(h.scrollTop,i.scrollTop),m+=Math.max(h.scrollLeft,i.scrollLeft));return{top:l,left:m}},f.offset={initialize:function(){var a=c.body,b=c.createElement("div"),d,e,g,h,i=parseFloat(f.css(a,"marginTop"))||0,j="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";f.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"}),b.innerHTML=j,a.insertBefore(b,a.firstChild),d=b.firstChild,e=d.firstChild,h=d.nextSibling.firstChild.firstChild,this.doesNotAddBorder=e.offsetTop!==5,this.doesAddBorderForTableAndCells=h.offsetTop===5,e.style.position="fixed",e.style.top="20px",this.supportsFixedPosition=e.offsetTop===20||e.offsetTop===15,e.style.position=e.style.top="",d.style.overflow="hidden",d.style.position="relative",this.subtractsBorderForOverflowNotVisible=e.offsetTop===-5,this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==i,a.removeChild(b),f.offset.initialize=f.noop},bodyOffset:function(a){var b=a.offsetTop,c=a.offsetLeft;f.offset.initialize(),f.offset.doesNotIncludeMarginInBodyOffset&&(b+=parseFloat(f.css(a,"marginTop"))||0,c+=parseFloat(f.css(a,"marginLeft"))||0);return{top:b,left:c}},setOffset:function(a,b,c){var d=f.css(a,"position");d==="static"&&(a.style.position="relative");var e=f(a),g=e.offset(),h=f.css(a,"top"),i=f.css(a,"left"),j=(d==="absolute"||d==="fixed")&&f.inArray("auto",[h,i])>-1,k={},l={},m,n;j?(l=e.position(),m=l.top,n=l.left):(m=parseFloat(h)||0,n=parseFloat(i)||0),f.isFunction(b)&&(b=b.call(a,c,g)),b.top!=null&&(k.top=b.top-g.top+m),b.left!=null&&(k.left=b.left-g.left+n),"using"in b?b.using.call(a,k):e.css(k)}},f.fn.extend({position:function(){if(!this[0])return null;var a=this[0],b=this.offsetParent(),c=this.offset(),d=cx.test(b[0].nodeName)?{top:0,left:0}:b.offset();c.top-=parseFloat(f.css(a,"marginTop"))||0,c.left-=parseFloat(f.css(a,"marginLeft"))||0,d.top+=parseFloat(f.css(b[0],"borderTopWidth"))||0,d.left+=parseFloat(f.css(b[0],"borderLeftWidth"))||0;return{top:c.top-d.top,left:c.left-d.left}},offsetParent:function(){return this.map(function(){var a=this.offsetParent||c.body;while(a&&!cx.test(a.nodeName)&&f.css(a,"position")==="static")a=a.offsetParent;return 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4 network/static/jquery.tablesorter.min.js
... ... @@ -0,0 +1,4 @@
  1 +
  2 +(function($){$.extend({tablesorter:new
  3 +function(){var parsers=[],widgets=[];this.defaults={cssHeader:"header",cssAsc:"headerSortUp",cssDesc:"headerSortDown",cssChildRow:"expand-child",sortInitialOrder:"asc",sortMultiSortKey:"shiftKey",sortForce:null,sortAppend:null,sortLocaleCompare:true,textExtraction:"simple",parsers:{},widgets:[],widgetZebra:{css:["even","odd"]},headers:{},widthFixed:false,cancelSelection:true,sortList:[],headerList:[],dateFormat:"us",decimal:'/\.|\,/g',onRenderHeader:null,selectorHeaders:'thead th',debug:false};function benchmark(s,d){log(s+","+(new Date().getTime()-d.getTime())+"ms");}this.benchmark=benchmark;function log(s){if(typeof console!="undefined"&&typeof console.debug!="undefined"){console.log(s);}else{alert(s);}}function buildParserCache(table,$headers){if(table.config.debug){var parsersDebug="";}if(table.tBodies.length==0)return;var rows=table.tBodies[0].rows;if(rows[0]){var list=[],cells=rows[0].cells,l=cells.length;for(var i=0;i<l;i++){var p=false;if($.metadata&&($($headers[i]).metadata()&&$($headers[i]).metadata().sorter)){p=getParserById($($headers[i]).metadata().sorter);}else if((table.config.headers[i]&&table.config.headers[i].sorter)){p=getParserById(table.config.headers[i].sorter);}if(!p){p=detectParserForColumn(table,rows,-1,i);}if(table.config.debug){parsersDebug+="column:"+i+" parser:"+p.id+"\n";}list.push(p);}}if(table.config.debug){log(parsersDebug);}return list;};function detectParserForColumn(table,rows,rowIndex,cellIndex){var l=parsers.length,node=false,nodeValue=false,keepLooking=true;while(nodeValue==''&&keepLooking){rowIndex++;if(rows[rowIndex]){node=getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex);nodeValue=trimAndGetNodeText(table.config,node);if(table.config.debug){log('Checking if value was empty on row:'+rowIndex);}}else{keepLooking=false;}}for(var i=1;i<l;i++){if(parsers[i].is(nodeValue,table,node)){return parsers[i];}}return parsers[0];}function getNodeFromRowAndCellIndex(rows,rowIndex,cellIndex){return rows[rowIndex].cells[cellIndex];}function trimAndGetNodeText(config,node){return $.trim(getElementText(config,node));}function getParserById(name){var l=parsers.length;for(var i=0;i<l;i++){if(parsers[i].id.toLowerCase()==name.toLowerCase()){return parsers[i];}}return false;}function buildCache(table){if(table.config.debug){var cacheTime=new Date();}var totalRows=(table.tBodies[0]&&table.tBodies[0].rows.length)||0,totalCells=(table.tBodies[0].rows[0]&&table.tBodies[0].rows[0].cells.length)||0,parsers=table.config.parsers,cache={row:[],normalized:[]};for(var i=0;i<totalRows;++i){var c=$(table.tBodies[0].rows[i]),cols=[];if(c.hasClass(table.config.cssChildRow)){cache.row[cache.row.length-1]=cache.row[cache.row.length-1].add(c);continue;}cache.row.push(c);for(var j=0;j<totalCells;++j){cols.push(parsers[j].format(getElementText(table.config,c[0].cells[j]),table,c[0].cells[j]));}cols.push(cache.normalized.length);cache.normalized.push(cols);cols=null;};if(table.config.debug){benchmark("Building cache for "+totalRows+" rows:",cacheTime);}return cache;};function getElementText(config,node){var text="";if(!node)return"";if(!config.supportsTextContent)config.supportsTextContent=node.textContent||false;if(config.textExtraction=="simple"){if(config.supportsTextContent){text=node.textContent;}else{if(node.childNodes[0]&&node.childNodes[0].hasChildNodes()){text=node.childNodes[0].innerHTML;}else{text=node.innerHTML;}}}else{if(typeof(config.textExtraction)=="function"){text=config.textExtraction(node);}else{text=$(node).text();}}return text;}function appendToTable(table,cache){if(table.config.debug){var appendTime=new Date()}var c=cache,r=c.row,n=c.normalized,totalRows=n.length,checkCell=(n[0].length-1),tableBody=$(table.tBodies[0]),rows=[];for(var i=0;i<totalRows;i++){var pos=n[i][checkCell];rows.push(r[pos]);if(!table.config.appender){var l=r[pos].length;for(var j=0;j<l;j++){tableBody[0].appendChild(r[pos][j]);}}}if(table.config.appender){table.config.appender(table,rows);}rows=null;if(table.config.debug){benchmark("Rebuilt table:",appendTime);}applyWidget(table);setTimeout(function(){$(table).trigger("sortEnd");},0);};function buildHeaders(table){if(table.config.debug){var time=new Date();}var meta=($.metadata)?true:false;var header_index=computeTableHeaderCellIndexes(table);$tableHeaders=$(table.config.selectorHeaders,table).each(function(index){this.column=header_index[this.parentNode.rowIndex+"-"+this.cellIndex];this.order=formatSortingOrder(table.config.sortInitialOrder);this.count=this.order;if(checkHeaderMetadata(this)||checkHeaderOptions(table,index))this.sortDisabled=true;if(checkHeaderOptionsSortingLocked(table,index))this.order=this.lockedOrder=checkHeaderOptionsSortingLocked(table,index);if(!this.sortDisabled){var 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1  network/static/js/cytoscape_web/AC_OETags.min.js
... ... @@ -0,0 +1 @@
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1  network/static/js/cytoscape_web/cytoscapeweb.min.js
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1  network/static/js/cytoscape_web/json2.min.js
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3,064 network/static/sig_overlap_network_0.05.gml
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  1 +graph [
  2 + node [
  3 + id 0
  4 + label "GLB Brain Sun.36"
  5 + type "cluster"
  6 + ]
  7 + node [
  8 + id 1
  9 + label "SMCL Lung Bhattacharjee.36"
  10 + type "cluster"
  11 + ]
  12 + node [
  13 + id 2
  14 + label "hsa-mir-29b_hsa-mir-29c_hsa-mir-29a"
  15 + miRBase_id "MIMAT0000100_MIMAT0000681_MIMAT0000086"
  16 + type "mirna"
  17 + ]
  18 + node [
  19 + id 3
  20 + label "hsa-mir-920"
  21 + miRBase_id "MIMAT0004970"
  22 + type "mirna"
  23 + ]
  24 + node [
  25 + id 4
  26 + label "SQ Lung Bhattacharjee.44"
  27 + type "cluster"
  28 + ]
  29 + node [
  30 + id 5
  31 + label "SQ Lung Bhattacharjee.45"
  32 + type "cluster"
  33 + ]
  34 + node [
  35 + id 6
  36 + label "hsa-mir-526b"
  37 + miRBase_id "MIMAT0002835"
  38 + type "mirna"
  39 + ]
  40 + node [
  41 + id 7
  42 + label "HSCC Head-Neck Chung.1"
  43 + type "cluster"
  44 + ]
  45 + node [
  46 + id 8
  47 + label "hsa-mir-370"
  48 + miRBase_id "MIMAT0000722"
  49 + type "mirna"
  50 + ]
  51 + node [
  52 + id 9
  53 + label "CA Colon Graudens.35"
  54 + type "cluster"
  55 + ]
  56 + node [
  57 + id 10
  58 + label "TU Prostate Lapointe.23"
  59 + type "cluster"
  60 + ]
  61 + node [
  62 + id 11
  63 + label "hsa-mir-548c-3p"
  64 + miRBase_id "MIMAT0003285"
  65 + type "mirna"
  66 + ]
  67 + node [
  68 + id 12
  69 + label "ODGL Brain Sun.2"
  70 + type "cluster"
  71 + ]
  72 + node [
  73 + id 13
  74 + label "ODGL Brain Sun.32"
  75 + type "cluster"
  76 + ]
  77 + node [
  78 + id 14
  79 + label "GCT Seminoma Korkola.75"
  80 + type "cluster"
  81 + ]
  82 + node [
  83 + id 15
  84 + label "hsa-let-7e_hsa-let-7f_hsa-let-7g_hsa-let-7a_hsa-let-7b_hsa-let-7d_hsa-let-7i_hsa-mir-98_hsa-let-7c"
  85 + miRBase_id "MIMAT0000066_MIMAT0000067_MIMAT0000414_MIMAT0000062_MIMAT0000063_MIMAT0000065_MIMAT0000415_MIMAT0000096_MIMAT0000064"
  86 + type "mirna"
  87 + ]
  88 + node [
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  90 + label "Bladder"
  91 + type "tissue"
  92 + ]
  93 + node [
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  96 + type "cluster"
  97 + ]
  98 + node [
  99 + id 18
  100 + label "AD Lung Bhattacharjee.59"
  101 + type "cluster"
  102 + ]
  103 + node [
  104 + id 19
  105 + label "GBM Brain Liang.18"
  106 + type "cluster"
  107 + ]
  108 + node [
  109 + id 20
  110 + label "hsa-mir-34a"
  111 + miRBase_id "MIMAT0000255"
  112 + type "mirna"
  113 + ]
  114 + node [
  115 + id 21
  116 + label "hsa-mir-640"
  117 + miRBase_id "MIMAT0003310"
  118 + type "mirna"
  119 + ]
  120 + node [
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  122 + label "END Ovarian Hendrix.58"
  123 + type "cluster"
  124 + ]
  125 + node [
  126 + id 23
  127 + label "hsa-mir-760"
  128 + miRBase_id "MIMAT0004957"
  129 + type "mirna"
  130 + ]
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  134 + type "cluster"
  135 + ]
  136 + node [
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  139 + miRBase_id "MIMAT0003945"
  140 + type "mirna"
  141 + ]
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  145 + miRBase_id "MIMAT0000269"
  146 + type "mirna"
  147 + ]
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  150 + label "AD Ovarian Welsh.1"
  151 + type "cluster"
  152 + ]
  153 + node [
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  156 + miRBase_id "MIMAT0000267"
  157 + type "mirna"
  158 + ]
  159 + node [
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  161 + label "Evading Apoptosis"
  162 + type "hallmark_of_cancer"
  163 + ]
  164 + node [
  165 + id 30
  166 + label "hsa-mir-369-5p"
  167 + miRBase_id "MIMAT0001621"
  168 + type "mirna"
  169 + ]
  170 + node [
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  172 + label "ME Melanoma Hoek.50"
  173 + type "cluster"
  174 + ]
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  178 + miRBase_id "MIMAT0004694"
  179 + type "mirna"
  180 + ]
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  183 + label "HSCC Head-Neck Cromer.25"
  184 + type "cluster"
  185 + ]
  186 + node [
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  188 + label "hsa-mir-9"
  189 + miRBase_id "MIMAT0000441"
  190 + type "mirna"
  191 + ]
  192 + node [
  193 + id 35
  194 + label "hsa-mir-548n_hsa-mir-607"
  195 + miRBase_id "MIMAT0005916_MIMAT0003275"
  196 + type "mirna"
  197 + ]
  198 + node [
  199 + id 36
  200 + label "GCT Seminoma Korkola.102"
  201 + type "cluster"
  202 + ]
  203 + node [
  204 + id 37
  205 + label "hsa-mir-1275"
  206 + miRBase_id "MIMAT0005929"
  207 + type "mirna"
  208 + ]
  209 + node [
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  211 + label "hsa-mir-423-5p"
  212 + miRBase_id "MIMAT0004748"
  213 + type "mirna"
  214 + ]
  215 + node [
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  217 + label "AD Lung Bhattacharjee.49"
  218 + type "cluster"
  219 + ]
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  222 + label "GLB Brain Sun.29"
  223 + type "cluster"
  224 + ]
  225 + node [
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  228 + miRBase_id "MIMAT0000691_MIMAT0000688_MIMAT0004958_MIMAT0000425_MIMAT0003885"
  229 + type "mirna"
  230 + ]
  231 + node [
  232 + id 42
  233 + label "AD Lung Bhattacharjee.41"
  234 + type "cluster"
  235 + ]
  236 + node [
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  238 + label "AD Lung Bhattacharjee.42"
  239 + type "cluster"
  240 + ]
  241 + node [
  242 + id 44
  243 + label "hsa-mir-656"
  244 + miRBase_id "MIMAT0003332"
  245 + type "mirna"
  246 + ]
  247 + node [
  248 + id 45
  249 + label "hsa-mir-548l"
  250 + miRBase_id "MIMAT0005889"
  251 + type "mirna"
  252 + ]
  253 + node [
  254 + id 46
  255 + label "hsa-mir-548k"
  256 + miRBase_id "MIMAT0005882"
  257 + type "mirna"
  258 + ]
  259 + node [
  260 + id 47
  261 + label "TU Prostate Lapointe.37"
  262 + type "cluster"
  263 + ]
  264 + node [
  265 + id 48
  266 + label "hsa-mir-718"
  267 + miRBase_id "MIMAT0012735"
  268 + type "mirna"
  269 + ]
  270 + node [
  271 + id 49
  272 + label "GCT Seminoma Korkola.4"
  273 + type "cluster"
  274 + ]
  275 + node [
  276 + id 50
  277 + label "SMCL Lung Bhattacharjee.25"
  278 + type "cluster"
  279 + ]
  280 + node [
  281 + id 51
  282 + label "hsa-mir-125a-3p"
  283 + miRBase_id "MIMAT0004602"
  284 + type "mirna"
  285 + ]
  286 + node [
  287 + id 52
  288 + label "hsa-mir-567"
  289 + miRBase_id "MIMAT0003231"
  290 + type "mirna"
  291 + ]
  292 + node [
  293 + id 53
  294 + label "B-CLL Leukemia Haslinger.27"
  295 + type "cluster"
  296 + ]
  297 + node [
  298 + id 54
  299 + label "SRS Ovarian Hendrix.72"
  300 + type "cluster"
  301 + ]
  302 + node [
  303 + id 55
  304 + label "hsa-mir-28-5p"
  305 + miRBase_id "MIMAT0000085"
  306 + type "mirna"
  307 + ]
  308 + node [
  309 + id 56
  310 + label "Head-neck"
  311 + type "tissue"
  312 + ]
  313 + node [
  314 + id 57
  315 + label "AD Lung Bhattacharjee.30"
  316 + type "cluster"
  317 + ]
  318 + node [
  319 + id 58
  320 + label "Mesothelioma"
  321 + type "tissue"
  322 + ]
  323 + node [
  324 + id 59
  325 + label "AD Lung Beer.31"
  326 + type "cluster"
  327 + ]
  328 + node [
  329 + id 60
  330 + label "AD Ovarian Welsh.16"
  331 + type "cluster"
  332 + ]