cknoxrun

use strict;
package HyperGeometric;

use base 'Exporter';
our @EXPORT = qw( hypergeom );

####################################################################
## To calculate p-value using a hypergeometric test for compounds 
## matched to a particular pathway in a given pathway database
##

cknoxrun

require 'java'
require 'jchem_connection'

require 'lib/jchem/lib/jchem.jar'

java_package 'search.db'

java_import 'chemaxon.jchem.db.JChemSearch'
java_import 'chemaxon.sss.SearchConstants'
java_import 'chemaxon.sss.search.JChemSearchOptions'

cknoxrun

    def self.apply!(features, ca, oxy, hy, halo, s, ni, total_atom_nr, morphology, amino_acid_derivative, bile_acid_or_alcohol)
      # TODO: ca + oxy + hy == total_atom_nr does not always hold
      # for fatty acids, exple given CCCCCCCC(=O)O.NN.
      # Deal with this!

      if features.include?('fatty-ester-head') &&
          features.include_any?('pregnane-skeleton',
                                 'cholestane-skeleton',
                                 'androstane-skeleton',
                                 'estrane-skeleton',

cknoxrun

# Note that this action responds to fracked up datatable parameters.
  # If you need to use this for some other reason (HTML, etc), you
  # might want to consider moving it into it's own method 
  # (datatable or something).
  def index
    # These are the columns, in the correct order, used by datatables
    cols = [:gene_name, :gene_symbol, :gene_id, :interaction, :chromosome]

    @gene_regulations = 
      if params[:kind] == 'up_regulated'

cknoxrun

json.key_format! camelize: :lower
json.draw params[:draw].to_i + 1
json.records_total @total_count
json.records_filtered @filter_count
json.data do
  json.array! @gene_regulations.each do |gene_regulation|
    json.array! [ gene_regulation.gene_name,
                  bio_link_out(:genecard, gene_regulation.gene_symbol), 
                  bio_link_out(:ncbi_gene, gene_regulation.gene_id), 
                  gene_regulation.interaction,

cknoxrun

$ ->
  $('.gene-regulations').each ->
    table = $(this)
    source = table.data('source')
    table.dataTable
      processing: true
      serverSide: true
      ajax: source
      aoColumnDefs: [
        # Don't sort columns with class 'no-sort'

cknoxrun

Drug Groups

Vitamin D - Several individual compounds is_a vitamin D Often referred to as a single compound, even by DPD/FDA

Prodrug

cknoxrun

Fun times!

cknoxrun

namespace :redis do
  namespace :flush do
    desc "Flushes all redis cached moldbi views"
    task :moldbi do
      on roles(:db) do
        execute "redis-cli KEYS \"moldbi/*\" | xargs redis-cli DEL"
      end
    end

    desc "Flushes all redis cached moldbi resources"

cknoxrun

#
# This group is read both both by the client and the server
# use it for options that affect everything
#
[client-server]
max_allowed_packet=500M

#
# include all files from the config directory
#