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1 parent 0c5eb69 commit 2292857672c25c797dbff70f935aa6fc9b56566a @cplaisier committed Jul 3, 2012
Showing with 15,069 additions and 1 deletion.
  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
@@ -1,4 +1,6 @@
Cancer-miRNA-Regulatory-Network
===============================
-A database containing the predictions for the Cancer miRNA-Regulatory Network.
+A database containing the predictions for the Cancer miRNA-Regulatory Network.
+
+This application was developed using Django, Python and PosgreSQL.
View
No changes.
View
@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+from django.core.management import execute_manager
+import imp
+try:
+ imp.find_module('settings') # Assumed to be in the same directory.
+except ImportError:
+ import sys
+ 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__)
+ sys.exit(1)
+
+import settings
+
+if __name__ == "__main__":
+ execute_manager(settings)
View
No changes.
View
@@ -0,0 +1,107 @@
+from django.db import models
+
+class Cancer(models.Model):
+ name = models.CharField(max_length=200)
+ short_name = models.CharField(max_length=100)
+ publication = models.CharField(max_length=200)
+ pmid = models.IntegerField()
+ tissue = models.CharField(max_length=100)
+
+ def __unicode__(self):
+ return self.short_name
+
+class Gene(models.Model):
+ entrez_id = models.IntegerField()
+
+ def __unicode__(self):
+ return str(self.entrez_id)
+
+class Coexpression_Cluster(models.Model):
+ cancer = models.ForeignKey(Cancer)
+ number = models.IntegerField()
+ cluster_membership = models.ManyToManyField(Gene)
+
+ def __unicode__(self):
+ return self.cancer.__unicode__()+'.'+str(self.number)
+
+class MiRNA(models.Model):
+ name = models.CharField(max_length=100)
+ mature_sequence_id = models.CharField(max_length=100)
+ mature_sequence = models.CharField(max_length=100)
+ pita_targets = models.ManyToManyField(Gene, related_name='MiRNAtoPITA')
+ targetscan_targets = models.ManyToManyField(Gene,related_name='MiRNAtoTargetScan')
+
+ def __unicode__(self):
+ return self.name
+
+class Validation(models.Model):
+ cancer = models.ForeignKey(Cancer)
+ mirna = models.ForeignKey(MiRNA)
+ method = models.CharField(max_length=100)
+
+ def __unicode__(self):
+ return self.method+'.'+self.cancer.__unicode__()+'.'+self.mirna.__unicode__()
+
+class Inferred_MiRNA(models.Model):
+ coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
+ mirna = models.ForeignKey(MiRNA)
+ method = models.CharField(max_length=100)
+ target_genes = models.ManyToManyField(Gene, through='Target_Gene')
+
+ def __unicode__(self):
+ return self.coexpression_cluster.__unicode__()+'-'+self.mirna.__unicode__()
+
+class Gene_Ontology(models.Model):
+ go_id = models.CharField(max_length=100)
+ term = models.CharField(max_length=500)
+ category = models.CharField(max_length=100)
+ annotated_genes = models.ManyToManyField(Gene)
+
+ def __unicode__(self):
+ return self.go_id
+
+class Functional_Enrichment(models.Model):
+ coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
+ gene_ontology = models.ForeignKey(Gene_Ontology)
+ annotated_genes = models.ManyToManyField(Gene)
+
+ def __unicode__(self):
+ return self.coexpression_cluster.__unicode__()+'-'+self.gene_ontology.__unicode__()
+
+class Target_Gene(models.Model):
+ inferred_mirna = models.ForeignKey(Inferred_MiRNA)
+ gene = models.ForeignKey(Gene)
+ strand = models.CharField(max_length=10)
+ site = models.CharField(max_length=10)
+ start = models.IntegerField()
+ match = models.FloatField()
+
+ def __unicode__(self):
+ return self.inferred_mirna.__unicode__()+' '+self.gene.__unicode__()
+
+class Gene_Annotation(models.Model):
+ gene = models.ForeignKey(Gene)
+ category = models.CharField(max_length=100)
+ annotation = models.CharField(max_length=1000)
+
+ def __unicode__(self):
+ return str(self.gene.entrez_id)+' = '+self.annotation
+
+class Hallmarks_Of_Cancer(models.Model):
+ coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
+ hallmark_of_cancer = models.CharField(max_length=1000)
+ semantic_similarity = models.FloatField()
+
+ def __unicode__(self):
+ return self.coexpression_cluster.__unicode__()+' '+self.hallmark_of_cancer+'='+str(self.semantic_similarity)
+
+class MiRNA_Target_GO_Term_Overlap(models.Model):
+ coexpression_cluster = models.ForeignKey(Coexpression_Cluster)
+ inferred_mirna = models.ForeignKey(Inferred_MiRNA)
+ functional_enrichment = models.ForeignKey(Functional_Enrichment)
+ p_value = models.FloatField()
+ genes_overlapping = models.ManyToManyField(Gene)
+
+ def __unicode__(self):
+ return self.coexpression_cluster.__unicode__()+' '+self.inferred_mirna.__unicode__()+' '+self.gene_ontology.__unicode__()
+
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