v71rc1.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "import qancode as q"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "qa = q.QANCODE(rc_url=\"https://v71rc1-master.demo.encodedcc.org/\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Experiment\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=File\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Library\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=AntibodyLot\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Biosample\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Donor\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: search/?type=GeneticModification\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=FileSet\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Annotation\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Series\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=OrganismDevelopmentSeries\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=UcscBrowserComposite\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=ReferenceEpigenome\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Project\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=ReplicationTimingSeries\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=PublicationData\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=MatchedSet\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=TreatmentConcentrationSeries\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=TreatmentTimeSeries\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Target\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Pipeline\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Publication\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /search/?type=Software\n",
      "Search page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /matrix/?type=Experiment\n",
      "Matrix page detected\n",
      "Opening https://www.encodeproject.org in Chrome\n",
      "Getting type: /matrix/?type=Annotation\n",
      "Matrix page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Experiment\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=File\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Library\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=AntibodyLot\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Biosample\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Donor\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: search/?type=GeneticModification\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=FileSet\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Annotation\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Series\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=OrganismDevelopmentSeries\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=UcscBrowserComposite\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=ReferenceEpigenome\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Project\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=ReplicationTimingSeries\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=PublicationData\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=MatchedSet\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=TreatmentConcentrationSeries\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=TreatmentTimeSeries\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Target\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Pipeline\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Publication\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /search/?type=Software\n",
      "Search page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /matrix/?type=Experiment\n",
      "Matrix page detected\n",
      "Opening https://v71rc1-master.demo.encodedcc.org/ in Chrome\n",
      "Getting type: /matrix/?type=Annotation\n",
      "Matrix page detected\n",
      "\n",
      "---------------------------------- Experiment ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Experiment\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [(\"5' RLM RACE\", '2'), ('5C', '13'), ('ATAC-seq', '180'), ('CAGE', '121'), ('CRISPR RNA-seq', '50'), ('CRISPRi RNA-seq', '77'), ('ChIA-PET', '62'), ('ChIP-seq', '8911'), ('Circulome-seq', '1'), ('DNA-PET', '6'), ('DNAme array', '259'), ('DNase-seq', '873'), ('FAIRE-seq', '37'), ('Hi-C', '36'), ('MNase-seq', '2'), ('MRE-seq', '68'), ('MS-MS', '14'), ('MeDIP-seq', '55'), ('PAS-seq', '47'), ('RAMPAGE', '168'), ('RIP-chip', '32'), ('RIP-seq', '73'), ('RNA Bind-n-Seq', '161'), ('RNA microarray', '291'), ('RNA-PET', '31'), ('RRBS', '218'), ('Repli-chip', '63'), ('Repli-seq', '119'), ('Switchgear', '2'), ('TAB-seq', '8'), ('WGBS', '258'), ('eCLIP', '359'), ('genetic modification DNase-seq', '40'), ('genotyping HTS', '16'), ('genotyping array', '142'), ('iCLIP', '7'), ('microRNA counts', '115'), ('microRNA-seq', '185'), ('polyA RNA-seq', '817'), ('polyA depleted RNA-seq', '32'), ('shRNA RNA-seq', '533'), ('siRNA RNA-seq', '113'), ('single cell RNA-seq', '120'), ('small RNA-seq', '216'), ('total RNA-seq', '413'), ('whole genome sequencing assay', '21')]\u001b[0m\n",
      "ASSAY CATEGORY\n",
      "     \u001b[33mprod: [('3D chromatin structure', '111'), ('DNA accessibility', '1132'), ('DNA binding', '8911'), ('DNA methylation', '866'), ('DNA sequencing', '22'), ('Genotyping', '164'), ('Proteomics', '14'), ('RNA binding', '634'), ('Replication timing', '182'), ('Transcription', '3331')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('control extremely low read depth', '24'), ('extremely low coverage', '7'), ('extremely low read depth', '221'), ('extremely low read length', '10'), ('extremely low spot score', '49'), ('inconsistent control', '3'), ('inconsistent library biosample', '1'), ('inconsistent read count', '2'), ('missing antibody', '75'), ('missing control alignments', '418'), ('missing donor', '1'), ('missing nih_institutional_certification', '33'), ('missing possible_controls', '2')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('antibody not characterized to standard', '25'), ('control insufficient read depth', '952'), ('insufficient coverage', '4'), ('insufficient read depth', '1757'), ('insufficient read length', '511'), ('insufficient replicate concordance', '48'), ('missing RNA fragment size', '2'), ('missing controlled_by', '596'), ('missing documents', '30'), ('missing input control', '2'), ('missing possible_controls', '27'), ('missing spikeins', '173'), ('partially characterized antibody', '139'), ('poor library complexity', '283'), ('severe bottlenecking', '271'), ('uncharacterized antibody', '11'), ('unreplicated experiment', '341')]\u001b[0m\n",
      "AUDIT CATEGORY3\n",
      "     \u001b[33mprod: [('antibody characterized with exemption', '676'), ('borderline replicate concordance', '455'), ('control low read depth', '659'), ('file validation error', '40'), ('high lambda C methylation ratio', '3'), ('inconsistent assembly', '18'), ('inconsistent control read length', '907'), ('inconsistent control run_type', '158'), ('inconsistent platforms', '1032'), ('inconsistent target of control experiment', '217'), ('low coverage', '4'), ('low read depth', '2545'), ('low read length', '3292'), ('low replicate concordance', '89'), ('low spot score', '321'), ('mild to moderate bottlenecking', '2873'), ('missing external identifiers', '330'), ('missing genetic modification characterization', '2307'), ('missing genotype', '116'), ('missing spikeins', '28'), ('mixed read lengths', '482'), ('mixed run types', '101'), ('moderate library complexity', '1280')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('CEL', '4'), ('bam', '12757'), ('bed bed12', '43'), ('bed bed3', '7'), ('bed bed3+', '869'), ('bed bed6+', '115'), ('bed bed9', '18'), ('bed bedExonScore', '27'), ('bed bedGraph', '30'), ('bed bedLogR', '64'), ('bed bedMethyl', '278'), ('bed bedRnaElements', '288'), ('bed broadPeak', '2451'), ('bed idr_peak', '134'), ('bed modPepMap', '6'), ('bed narrowPeak', '7324'), ('bed pepMap', '6'), ('bed peptideMapping', '8'), ('bed tss_peak', '235'), ('bedpe', '5'), ('bigBed bed12', '43'), ('bigBed bed3', '7'), ('bigBed bed3+', '13'), ('bigBed bed6+', '115'), ('bigBed bed9', '18'), ('bigBed bedExonScore', '27'), ('bigBed bedLogR', '63'), ('bigBed bedMethyl', '278'), ('bigBed bedRnaElements', '288'), ('bigBed broadPeak', '1992'), ('bigBed idr_peak', '134'), ('bigBed modPepMap', '6'), ('bigBed narrowPeak', '7313'), ('bigBed pepMap', '6'), ('bigBed peptideMapping', '8'), ('bigBed tss_peak', '235'), ('bigWig', '11714'), ('csfasta', '25'), ('csqual', '13'), ('fasta', '3'), ('fastq', '13745'), ('gff gff3', '235'), ('gtf', '269'), ('hdf5', '20'), ('hic', '5'), ('idat', '277'), ('rcc', '115'), ('sam', '59'), ('sra', '672'), ('tagAlign', '1368'), ('tar', '110'), ('tsv', '2470'), ('vcf', '13'), ('wig', '59')]\u001b[0m\n",
      "BIOSAMPLE TREATMENT\n",
      "     \u001b[33mprod: [('17β-estradiol', '38'), ('17β-hydroxy-17-methylestra-4,9,11-trien-3-one', '4'), ('17β-hydroxy-5α-androstan-3-one', '3'), ('20-hydroxyecdysone', '16'), ('Lipopolysaccharide', '66'), ('Sendai virus', '1'), ('Sindbis virus', '4'), ('Transforming growth factor beta-1', '1'), ('UT189', '3'), ('afimoxifene', '16'), ('all-trans-retinoic acid', '21'), ('bisphenol A', '4'), ('cadmium dichloride', '4'), ('caffeine', '3'), ('calcium', '52'), ('cisplatin', '1'), ('cold shock treatment', '2'), ('copper(II) sulfate', '32'), ('dexamethasone', '293'), ('differentiation', '1'), ('dimethyl sulfoxide', '39'), ('doxycycline', '1'), ('doxycycline hyclate', '33'), ('erythropoietin', '9'), ('estradiol', '8'), ('ethanol', '57'), ('forskolin and pyruvate', '8'), ('genistein', '4'), ('heat shock treatment', '1'), ('hydrocortisone succinate', '9'), ('hydroxyurea', '1'), ('insulin and 22-hydroxycholesterol', '2'), ('interferon alpha', '19'), ('interferon gamma', '18'), ('interleukin-3', '9'), ('ionomycin', '14'), ('kit ligand', '9'), ('lactate', '3'), ('methyltrienolone', '1'), ('paraquat', '2'), ('phorbol 13-acetate 12-myristate', '14'), ('pravastatin', '4'), ('resveratrol', '1'), ('retinoic acid', '2'), ('rotenone', '3'), ('serum free', '2'), ('sodium butyrate', '3'), ('tamoxifen', '2'), ('tumor necrosis factor', '20'), ('vorinostat', '1'), ('zinc dichloride', '3')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '5779'), ('cell-free sample', '161'), ('in vitro differentiated cells', '679'), ('induced pluripotent stem cell line', '137'), ('primary cell', '1678'), ('stem cell', '506'), ('tissue', '4375'), ('whole organisms', '2052')]\u001b[0m\n",
      "DATE SUBMITTED\n",
      "     \u001b[33mprod: [('2010-11-16', '12'), ('2011-01-11', '18'), ('2011-06-25', '14'), ('2011-07-13', '12'), ('2011-10-27', '10'), ('2011-12-23', '14'), ('2012-01-23', '29'), ('2013-05-09', '16'), ('2013-07-16', '15'), ('2013-07-18', '10'), ('2014-01-30', '23'), ('2014-02-25', '53'), ('2014-03-13', '24'), ('2014-03-15', '161'), ('2014-03-19', '69'), ('2014-03-20', '23'), ('2014-04-04', '15'), ('2014-04-29', '11'), ('2014-05-13', '39'), ('2014-05-14', '16'), ('2014-05-29', '36'), ('2014-06-10', '18'), ('2014-06-17', '20'), ('2014-06-30', '22'), ('2014-07-01', '22'), ('2014-07-03', '12'), ('2014-07-04', '71'), ('2014-07-06', '25'), ('2014-07-26', '35'), ('2014-07-30', '30'), ('2014-09-15', '26'), ('2014-09-17', '24'), ('2014-09-27', '32'), ('2014-09-29', '41'), ('2014-10-07', '21'), ('2014-10-24', '41'), ('2014-10-26', '25'), ('2014-10-29', '33'), ('2014-11-04', '31'), ('2014-11-21', '12'), ('2014-12-05', '13'), ('2014-12-08', '23'), ('2014-12-11', '53'), ('2014-12-13', '48'), ('2014-12-16', '21'), ('2014-12-17', '51'), ('2015-02-19', '24'), ('2015-02-21', '10'), ('2015-03-11', '13'), ('2015-03-13', '10'), ('2015-03-27', '29'), ('2015-03-31', '55'), ('2015-04-02', '19'), ('2015-05-22', '10'), ('2015-05-29', '16'), ('2015-06-18', '57'), ('2015-06-25', '19'), ('2015-06-28', '17'), ('2015-06-30', '30'), ('2015-07-16', '36'), ('2015-07-19', '96'), ('2015-07-23', '166'), ('2015-07-24', '123'), ('2015-07-29', '184'), ('2015-07-30', '54'), ('2015-08-05', '14'), ('2015-08-12', '18'), ('2015-08-13', '36'), ('2015-08-14', '43'), ('2015-08-24', '14'), ('2015-09-23', '12'), ('2015-09-24', '22'), ('2015-09-29', '27'), ('2015-09-30', '59'), ('2015-10-03', '27'), ('2015-10-21', '16'), ('2015-10-22', '12'), ('2015-10-30', '32'), ('2015-10-31', '27'), ('2015-12-07', '11'), ('2015-12-08', '13'), ('2015-12-10', '36'), ('2015-12-11', '38'), ('2015-12-14', '20'), ('2015-12-15', '20'), ('2015-12-16', '25'), ('2015-12-17', '16'), ('2015-12-22', '12'), ('2016-01-13', '20'), ('2016-01-22', '23'), ('2016-01-27', '22'), ('2016-02-01', '10'), ('2016-02-06', '20'), ('2016-02-10', '31'), ('2016-02-11', '25'), ('2016-02-16', '10'), ('2016-02-17', '10'), ('2016-02-26', '39'), ('2016-03-02', '17'), ('2016-03-03', '16'), ('2016-03-04', '45'), ('2016-03-07', '17'), ('2016-03-08', '11'), ('2016-03-09', '16'), ('2016-03-11', '62'), ('2016-03-13', '23'), ('2016-03-14', '35'), ('2016-03-15', '20'), ('2016-03-16', '56'), ('2016-03-17', '70'), ('2016-03-21', '155'), ('2016-03-22', '109'), ('2016-03-23', '29'), ('2016-03-25', '16'), ('2016-03-26', '21'), ('2016-03-30', '10'), ('2016-03-31', '98'), ('2016-04-09', '40'), ('2016-04-10', '16'), ('2016-04-11', '111'), ('2016-04-12', '14'), ('2016-04-13', '12'), ('2016-04-18', '11'), ('2016-04-19', '16'), ('2016-04-23', '43'), ('2016-04-24', '29'), ('2016-04-26', '20'), ('2016-04-27', '89'), ('2016-04-28', '51'), ('2016-04-29', '15'), ('2016-05-03', '17'), ('2016-05-09', '20'), ('2016-05-12', '19'), ('2016-05-13', '27'), ('2016-05-20', '20'), ('2016-05-26', '31'), ('2016-05-30', '83'), ('2016-06-22', '24'), ('2016-06-28', '45'), ('2016-06-29', '29'), ('2016-07-07', '19'), ('2016-07-20', '32'), ('2016-07-27', '12'), ('2016-07-29', '131'), ('2016-07-30', '156'), ('2016-07-31', '13'), ('2016-08-01', '57'), ('2016-08-02', '15'), ('2016-08-03', '66'), ('2016-08-04', '26'), ('2016-08-05', '18'), ('2016-08-23', '12'), ('2016-08-24', '40'), ('2016-09-16', '16'), ('2016-09-24', '14'), ('2016-09-25', '18'), ('2016-10-04', '26'), ('2016-10-11', '20'), ('2016-10-12', '21'), ('2016-10-14', '13'), ('2016-10-18', '13'), ('2016-10-19', '94'), ('2016-10-20', '68'), ('2016-10-21', '18'), ('2016-10-22', '27'), ('2016-10-24', '12'), ('2016-10-28', '23'), ('2016-10-31', '56'), ('2016-11-18', '39'), ('2016-12-05', '13'), ('2016-12-08', '14'), ('2016-12-09', '44'), ('2016-12-12', '25'), ('2016-12-15', '49'), ('2016-12-16', '12'), ('2016-12-20', '45'), ('2016-12-21', '48'), ('2016-12-31', '13'), ('2017-01-01', '11'), ('2017-01-12', '15'), ('2017-01-18', '25'), ('2017-01-23', '12'), ('2017-01-24', '29'), ('2017-01-25', '50'), ('2017-01-26', '26'), ('2017-01-27', '55'), ('2017-01-29', '25'), ('2017-01-30', '16'), ('2017-01-31', '118'), ('2017-02-10', '14'), ('2017-02-22', '11'), ('2017-03-08', '15'), ('2017-03-14', '65'), ('2017-03-17', '22'), ('2017-05-02', '14'), ('2017-06-30', '18'), ('2017-07-28', '27'), ('2017-09-11', '84'), ('2017-10-05', '41'), ('2018-02-21', '12')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2011', '149'), ('April, 2012', '77'), ('April, 2013', '6'), ('April, 2014', '2'), ('April, 2015', '28'), ('April, 2016', '170'), ('April, 2017', '52'), ('April, 2018', '48'), ('August, 2011', '88'), ('August, 2012', '257'), ('August, 2015', '180'), ('August, 2016', '265'), ('August, 2017', '71'), ('December, 2010', '68'), ('December, 2011', '87'), ('December, 2014', '247'), ('December, 2015', '40'), ('December, 2016', '174'), ('December, 2017', '139'), ('February, 2011', '255'), ('February, 2012', '264'), ('February, 2013', '1'), ('February, 2014', '7'), ('February, 2015', '3'), ('February, 2016', '183'), ('February, 2017', '138'), ('February, 2018', '177'), ('January, 2011', '6'), ('January, 2012', '59'), ('January, 2015', '8'), ('January, 2016', '110'), ('January, 2017', '399'), ('January, 2018', '156'), ('July, 2009', '22'), ('July, 2011', '263'), ('July, 2012', '128'), ('July, 2013', '2761'), ('July, 2014', '300'), ('July, 2015', '103'), ('July, 2016', '614'), ('July, 2017', '39'), ('June, 2011', '83'), ('June, 2012', '75'), ('June, 2014', '432'), ('June, 2015', '106'), ('June, 2016', '221'), ('June, 2017', '272'), ('March, 2011', '160'), ('March, 2012', '170'), ('March, 2013', '1'), ('March, 2014', '887'), ('March, 2015', '2'), ('March, 2016', '291'), ('March, 2017', '96'), ('March, 2018', '134'), ('May, 2011', '35'), ('May, 2012', '138'), ('May, 2013', '2'), ('May, 2014', '8'), ('May, 2015', '12'), ('May, 2016', '569'), ('May, 2017', '66'), ('May, 2018', '15'), ('November, 2010', '9'), ('November, 2011', '76'), ('November, 2012', '7'), ('November, 2014', '98'), ('November, 2015', '225'), ('November, 2016', '400'), ('November, 2017', '428'), ('October, 2009', '4'), ('October, 2010', '1'), ('October, 2011', '456'), ('October, 2014', '86'), ('October, 2015', '106'), ('October, 2016', '485'), ('October, 2017', '200'), ('September, 2011', '134'), ('September, 2012', '190'), ('September, 2014', '41'), ('September, 2015', '17'), ('September, 2016', '209'), ('September, 2017', '115')]\u001b[0m\n",
      "EXPERIMENT STATUS\n",
      "     \u001b[33mprod: [('archived', '1012'), ('released', '14124'), ('revoked', '231')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '7315'), ('ce10', '838'), ('ce11', '897'), ('dm3', '835'), ('dm6', '811'), ('hg19', '7492'), ('mm10', '1508'), ('mm9', '338')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Alexander Urban, Stanford', '3'), ('Ali Mortazavi, UCI', '231'), ('Andrew Z. Fire, Stanford', '4'), ('Barbara Wold, Caltech', '287'), ('Bing Ren, UCSD', '1379'), ('Bradley Bernstein, Broad', '1957'), ('Brenton Graveley, UConn', '789'), ('Brian Oliver, NIH', '27'), ('Chris Burge, MIT', '161'), ('Christina Leslie, MSKCC', '32'), ('David Gilbert, FSU', '77'), ('David MacAlpine, Duke', '39'), ('Eric Lécuyer, IRCM', '30'), ('Gene Yeo, UCSD', '366'), ('Gregory Crawford, Duke', '162'), ('Jason Lieb, UNC', '37'), ('Job Dekker, UMass', '26'), ('Joe Ecker, Salk', '193'), ('John Rinn, Broad', '35'), ('John Stamatoyannopoulos, UW', '1594'), ('Joseph Costello, UCSF', '595'), ('Kevin Struhl, HMS', '43'), ('Kevin White, UChicago', '1064'), ('Manuel Garber, UMass', '68'), ('Michael Snyder, Stanford', '2401'), ('Morgan Giddings, UNC', '14'), ('Paul Khavari, Stanford', '13'), ('Peggy Farnham, USC', '125'), ('Piero Carninci, RIKEN', '78'), ('Richard Myers, HAIB', '1423'), ('Ross Hardison, PennState', '128'), ('Scott Tenenbaum, SUNY-Albany', '42'), ('Sherman Weissman, Yale', '65'), ('Susan Celniker, LBNL', '239'), ('Terry Orr-Weaver, MIT', '2'), ('Thomas Gingeras, CSHL', '736'), ('Tim Reddy, Duke', '298'), ('Valerie Reinke, Yale', '361'), ('Vishwanath Iyer, UTA', '85'), ('Will Greenleaf, Stanford', '13'), ('Xiang-Dong Fu, UCSD', '97'), ('Yijun Ruan, JAX', '48')]\u001b[0m\n",
      "LIBRARY DEPLETED IN\n",
      "     \u001b[33mprod: [('polyadenylated mRNA', '57'), ('rRNA', '870')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('10-50', '2'), ('100-100', '3'), ('100-300', '24'), ('100-350', '17'), ('100-500', '17'), ('120-200', '128'), ('120-280', '1'), ('125-278', '1'), ('138-1000', '1'), ('149-512', '1'), ('150-1000', '13'), ('150-150', '35'), ('150-250', '47'), ('150-300', '4'), ('150-350', '537'), ('150-400', '15'), ('151-347', '1'), ('151-379', '1'), ('151-499', '1'), ('153-309', '1'), ('153-499', '1'), ('156-312', '1'), ('157-497', '1'), ('159-196', '1'), ('165-203', '1'), ('168-367', '1'), ('169-225', '1'), ('170-202', '1'), ('171-201', '1'), ('172-1452', '1'), ('172-200', '1'), ('175-196', '1'), ('175-250', '3'), ('175-275', '2'), ('175-300', '359'), ('175-500', '35'), ('177-207', '1'), ('180-500', '84'), ('184-224', '1'), ('185-234', '1'), ('186-747', '1'), ('187-1606', '1'), ('19-25', '66'), ('20-20', '132'), ('200-1000', '9'), ('200-1500', '6'), ('200-200', '6'), ('200-250', '48'), ('200-300', '3'), ('200-325', '1'), ('200-400', '97'), ('200-491', '1'), ('200-500', '183'), ('200-594', '1'), ('200-600', '734'), ('200-650', '2'), ('200-712', '1'), ('200-750', '74'), ('200-764', '1'), ('200-800', '802'), ('200-900', '1'), ('208-442', '1'), ('209-891', '1'), ('210-480', '1'), ('213-451', '1'), ('215-1000', '1'), ('217-475', '1'), ('221-1000', '1'), ('222-318', '1'), ('225-350', '1'), ('232-1000', '1'), ('240-420', '13'), ('250-430', '4'), ('250-470', '2'), ('266-470', '1'), ('267-400', '2'), ('268-478', '1'), ('270-500', '1'), ('275-470', '1'), ('280-509', '1'), ('285-477', '1'), ('287-478', '1'), ('289-481', '1'), ('2963-2963', '1'), ('299-300', '28'), ('300-1000', '43'), ('300-350', '4'), ('300-400', '1'), ('300-500', '644'), ('300-600', '79'), ('300-700', '1'), ('300-800', '19'), ('312-506', '1'), ('312-531', '1'), ('325-425', '1'), ('325-450', '1'), ('350-450', '26'), ('373-373', '1'), ('40-40', '27'), ('400-400', '3'), ('450-650', '1085'), ('50-300', '11'), ('<200', '216'), ('<30', '231'), ('>175', '17'), ('>200', '2660')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '11433'), ('RNA', '2112'), ('miRNA', '300'), ('polyadenylated mRNA', '1509')]\u001b[0m\n",
      "LIBRARY TREATMENT\n",
      "     \u001b[33mprod: [('Antarctic Phosphatase', '26'), ('Tobacco Acid Pyrophosphatase', '179'), ('duplex-specific nuclease (DSN) normalization', '29')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('L1 larva', '187'), ('L2 larva', '106'), ('L3 larva', '119'), ('L4 larva', '153'), ('L4/young adult', '6'), ('adult', '6601'), ('child', '1305'), ('dauer', '2'), ('early embryonic', '20'), ('embryonic', '3978'), ('first instar larva', '5'), ('larva', '3'), ('late embryonic', '137'), ('midembryonic', '4'), ('mixed stage (embryonic)', '70'), ('newborn', '333'), ('postnatal', '250'), ('prepupa', '129'), ('pupa', '21'), ('second instar larva', '4'), ('third instar larva', '78'), ('unknown', '1446'), ('wandering third instar larva', '109'), ('young adult', '162')]\u001b[0m\n",
      "MAPPED READ LENGTH (NT)\n",
      "     \u001b[33mprod: [('100', '832'), ('101', '262'), ('25', '16'), ('27', '42'), ('28', '83'), ('30', '57'), ('32', '55'), ('33', '5'), ('35', '9'), ('36', '3162'), ('37', '10'), ('38', '3'), ('40', '98'), ('41', '25'), ('45', '10'), ('47', '1'), ('48', '7'), ('50', '652'), ('51', '32'), ('72', '3'), ('74', '21'), ('75', '143'), ('76', '821'), ('83', '7')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '137'), ('adrenal gland', '105'), ('artery', '42'), ('blood', '2614'), ('blood vessel', '208'), ('bodily fluid', '2614'), ('bone element', '117'), ('bone marrow', '38'), ('brain', '937'), ('breast', '49'), ('bronchus', '20'), ('connective tissue', '571'), ('embryo', '984'), ('epithelium', '723'), ('esophagus', '117'), ('extraembryonic component', '203'), ('eye', '36'), ('gonad', '130'), ('heart', '340'), ('intestine', '559'), ('kidney', '571'), ('large intestine', '359'), ('limb', '356'), ('liver', '1184'), ('lung', '927'), ('lymph node', '169'), ('lymphatic vessel', '6'), ('lymphoid tissue', '41'), ('mammary gland', '427'), ('mouth', '25'), ('musculature of body', '553'), ('nerve', '39'), ('nose', '2'), ('ovary', '55'), ('pancreas', '146'), ('penis', '212'), ('pericardium', '4'), ('placenta', '65'), ('prostate gland', '118'), ('skeleton', '5'), ('skin of body', '565'), ('small intestine', '107'), ('spinal cord', '28'), ('spleen', '195'), ('stomach', '250'), ('testis', '69'), ('thymus', '53'), ('thyroid gland', '60'), ('tongue', '5'), ('trachea', '3'), ('ureter', '31'), ('urinary bladder', '21'), ('uterus', '230'), ('vagina', '29'), ('vasculature', '231'), ('vein', '69')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Caenorhabditis elegans', '975'), ('Drosophila ananassae', '1'), ('Drosophila melanogaster', '1435'), ('Drosophila mojavensis', '4'), ('Drosophila pseudoobscura', '12'), ('Drosophila simulans', '8'), ('Drosophila virilis', '1'), ('Drosophila yakuba', '1'), ('Homo sapiens', '10891'), ('Mus musculus', '1864')]\u001b[0m\n",
      "PLATFORM\n",
      "     \u001b[33mprod: [('Affymetrix - Human Exon 1.0 ST V2 tilling array', '4'), ('Applied Biosystems SOLiD System 3 Plus', '50'), ('Illumina - Methylation 450K BeadChip', '62'), ('Illumina Genome Analyzer', '976'), ('Illumina Genome Analyzer I', '138'), ('Illumina Genome Analyzer II', '765'), ('Illumina Genome Analyzer IIe', '97'), ('Illumina Genome Analyzer IIx', '2417'), ('Illumina HiSeq 1000', '8'), ('Illumina HiSeq 2000', '6401'), ('Illumina HiSeq 2500', '2495'), ('Illumina HiSeq 4000', '1509'), ('Illumina HiSeq X Ten', '37'), ('Illumina Infinium Methylation EPIC BeadChip', '156'), ('Illumina Infinium Omni5Exome-4 Kit', '59'), ('Illumina MiSeq', '4'), ('Illumina NextSeq 500', '246'), ('Mouse 385K Whole Genome CGH Tiling Array', '16'), ('Mouse 3x720K Whole Genome CGH Tiling Array', '2'), ('Nimbelgen - Human 3x720K Whole Genome CGH Tiling Array', '34'), ('Nimblegen - Human 2.1M Whole-Genome CGH Tiling Array v2.0', '8'), ('Nimblegen - Human 6x630K CGH Whole Genome tiling array', '12'), ('Roche 454 Genome Sequencer FLX', '2'), ('nCounter Human V2 miRNA Expression array', '38'), ('nCounter Mouse V1.2 miRNA Expression array', '5'), ('nCounter Mouse V1.3 miRNA Expression array', '58'), ('nCounter Mouse V1.5 miRNA Expression array', '14')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '9701'), ('GGR', '461'), ('Roadmap', '2761'), ('community', '7'), ('modENCODE', '1330'), ('modERN', '1107')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE2', '2805'), ('ENCODE2-Mouse', '564'), ('ENCODE3', '6291'), ('ENCODE4', '41'), ('GGR', '461'), ('Roadmap', '2761'), ('community', '7'), ('modENCODE', '1330'), ('modERN', '1107')]\u001b[0m\n",
      "READ LENGTH (NT)\n",
      "     \u001b[33mprod: [('100', '2090'), ('101', '1132'), ('108', '11'), ('113', '1'), ('117', '2'), ('125', '11'), ('130', '40'), ('132', '3'), ('133', '3'), ('136', '2'), ('139', '3'), ('150', '10'), ('151', '44'), ('152', '6'), ('176', '1'), ('18', '5'), ('191', '1'), ('20', '153'), ('202', '17'), ('25', '84'), ('250', '1'), ('27', '90'), ('28', '59'), ('29', '9'), ('30', '119'), ('300', '2'), ('31', '73'), ('32', '526'), ('33', '44'), ('34', '78'), ('35', '42'), ('36', '4574'), ('37', '44'), ('38', '7'), ('39', '33'), ('40', '191'), ('41', '23'), ('42', '15'), ('43', '66'), ('44', '87'), ('45', '249'), ('458', '1'), ('46', '46'), ('47', '2'), ('48', '35'), ('49', '15'), ('50', '2739'), ('51', '394'), ('52', '2'), ('53', '1'), ('55', '125'), ('56', '3'), ('58', '1'), ('59', '1'), ('61', '1'), ('62', '1'), ('70', '2'), ('71', '1'), ('72', '10'), ('73', '30'), ('74', '22'), ('75', '256'), ('76', '1471'), ('78', '42'), ('80', '27'), ('82', '2'), ('83', '10'), ('84', '1'), ('85', '6'), ('86', '2'), ('87', '4'), ('88', '1'), ('90', '1'), ('94', '1'), ('98', '1'), ('99', '9')]\u001b[0m\n",
      "REPLICATION TYPE\n",
      "     \u001b[33mprod: [('anisogenic', '430'), ('isogenic', '8730'), ('unreplicated', '6205')]\u001b[0m\n",
      "RUN TYPE\n",
      "     \u001b[33mprod: [('paired-ended', '4504'), ('single-ended', '9669')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '1466'), ('broad histone mark', '1727'), ('chromatin remodeller', '254'), ('control', '2568'), ('histone', '3102'), ('narrow histone mark', '1265'), ('nucleotide modification', '70'), ('other context', '58'), ('other post-translational modification', '76'), ('recombinant protein', '1271'), ('tag', '1'), ('transcription factor', '3971')]\u001b[0m\n",
      "\n",
      "------------------------------------- File -------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=File\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('control extremely low read depth', '67'), ('extremely low coverage', '551'), ('extremely low read depth', '653'), ('extremely low read length', '54'), ('extremely low spot score', '360'), ('inconsistent control', '7'), ('inconsistent library biosample', '4'), ('inconsistent read count', '4'), ('missing antibody', '208'), ('missing control alignments', '1470'), ('missing nih_institutional_certification', '88'), ('missing possible_controls', '24')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('antibody not characterized to standard', '81'), ('control insufficient read depth', '2546'), ('insufficient coverage', '54'), ('insufficient read depth', '5319'), ('insufficient read length', '2109'), ('insufficient replicate concordance', '267'), ('missing controlled_by', '1283'), ('missing documents', '110'), ('missing input control', '4'), ('missing possible_controls', '61'), ('missing spikeins', '780'), ('partially characterized antibody', '577'), ('poor library complexity', '1078'), ('severe bottlenecking', '1114'), ('uncharacterized antibody', '82'), ('unreplicated experiment', '948')]\u001b[0m\n",
      "AUDIT CATEGORY3\n",
      "     \u001b[33mprod: [('antibody characterized with exemption', '3199'), ('borderline replicate concordance', '1792'), ('control low read depth', '1853'), ('file validation error', '148'), ('high lambda C methylation ratio', '238'), ('inconsistent assembly', '93'), ('inconsistent control read length', '1586'), ('inconsistent control run_type', '320'), ('inconsistent platforms', '4179'), ('inconsistent target of control experiment', '880'), ('low coverage', '20'), ('low read depth', '8967'), ('low read length', '10417'), ('low replicate concordance', '657'), ('low spot score', '2075'), ('mild to moderate bottlenecking', '10435'), ('missing spikeins', '212'), ('mixed read lengths', '1973'), ('mixed run types', '573'), ('moderate library complexity', '4717')]\u001b[0m\n",
      "CONTENT CATEGORY\n",
      "     \u001b[33mprod: [('alignment', '83296'), ('annotation', '139643'), ('quantification', '22336'), ('raw data', '48346'), ('reference', '145'), ('signal', '130574'), ('validation', '56')]\u001b[0m\n",
      "CONTENT TYPE\n",
      "     \u001b[33mprod: [('HMM predicted chromatin state', '54'), ('RNA-binding protein associated mRNAs', '92'), ('alignments', '52579'), ('base overlap signal', '194'), ('blacklisted regions', '14'), ('candidate enhancers', '873'), ('candidate promoters', '570'), ('candidate regulatory elements', '2903'), ('chromatin interactions', '300'), ('clusters', '68'), ('conservative idr thresholded peaks', '7235'), ('contigs', '422'), ('control normalized signal', '5405'), ('copy number variation', '179'), ('distal peaks', '8'), ('enhancer validation', '21'), ('enrichment', '4081'), ('exon quantifications', '901'), ('female genome index', '14'), ('female genome reference', '3'), ('filtered SNPs', '5'), ('filtered indels', '6'), ('filtered modified peptide quantification', '12'), ('filtered peaks', '346'), ('filtered peptide quantification', '28'), ('filtered regions', '20'), ('filtered transcribed fragments', '52'), ('fold change over control', '25044'), ('gene quantifications', '8091'), ('genome compartments', '52'), ('genome index', '30'), ('genome reference', '39'), ('hotspots', '12519'), ('idat green channel', '279'), ('idat red channel', '275'), ('intensity values', '127'), ('library fraction', '301'), ('long range chromatin interactions', '93'), ('male genome index', '16'), ('male genome reference', '11'), ('methylation state at CHG', '544'), ('methylation state at CHH', '544'), ('methylation state at CpG', '979'), ('microRNA quantifications', '454'), ('minus strand signal', '515'), ('minus strand signal of all reads', '10343'), ('minus strand signal of unique reads', '11441'), ('nested topologically associated domains', '24'), ('normalized signal of all reads', '70'), ('open chromatin regions', '20'), ('optimal idr thresholded peaks', '14297'), ('peaks', '82553'), ('percentage normalized signal', '96'), ('plus strand signal', '515'), ('plus strand signal of all reads', '10344'), ('plus strand signal of unique reads', '11439'), ('predicted enhancers', '7'), ('predicted forebrain enhancers', '93'), ('predicted heart enhancers', '97'), ('predicted transcription start sites', '160'), ('predicted whole brain enhancers', '5'), ('primer sequence', '2'), ('proximal peaks', '8'), ('pseudoreplicated idr thresholded peaks', '1194'), ('rRNA reference', '2'), ('raw signal', '1507'), ('read-depth normalized signal', '9011'), ('reads', '47007'), ('redacted alignments', '1701'), ('redacted unfiltered alignments', '1702'), ('rejected reads', '431'), ('relative replication signal', '7'), ('replicated peaks', '7070'), ('replication timing profile', '70'), ('reporter code counts', '227'), ('representative dnase hypersensitivity sites', '4'), ('semi-automated genome annotation', '360'), ('sequence alignability', '20'), ('sequence uniqueness', '2'), ('signal', '2239'), ('signal of all reads', '2286'), ('signal of unique reads', '11871'), ('signal p-value', '28089'), ('spike-in alignments', '94'), ('spike-in sequence', '5'), ('splice junctions', '367'), ('stable peaks', '4700'), ('summed densities signal', '16'), ('topologically associated domains', '37'), ('transcribed fragments', '62'), ('transcript quantifications', '6291'), ('transcription start sites', '2729'), ('transcriptome alignments', '5824'), ('transcriptome reference', '1'), ('unfiltered alignments', '21396'), ('unfiltered modified peptide quantification', '12'), ('unfiltered peptide quantification', '28'), ('validation', '35'), ('valleys', '32'), ('variant calls', '13'), ('wavelet-smoothed signal', '142')]\u001b[0m\n",
      "FILE FORMAT\n",
      "     \u001b[33mprod: [('CEL', '8'), ('bam', '80877'), ('bed', '75479'), ('bedpe', '5'), ('bigBed', '69860'), ('bigWig', '130365'), ('csfasta', '49'), ('csqual', '38'), ('fasta', '26'), ('fastq', '46115'), ('gff', '720'), ('gtf', '1172'), ('hdf5', '280'), ('hic', '20'), ('idat', '554'), ('rcc', '227'), ('sam', '188'), ('sra', '1233'), ('tagAlign', '2278'), ('tar', '244'), ('tsv', '14446'), ('vcf', '24'), ('wig', '188')]\u001b[0m\n",
      "FILE STATUS\n",
      "     \u001b[33mprod: [('archived', '62785'), ('released', '337559'), ('revoked', '24052')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Alexander Urban, Stanford', '11'), ('Ali Mortazavi, UCI', '2262'), ('Andrew Z. Fire, Stanford', '8'), ('Anshul Kundaje, Stanford', '7802'), ('Barbara Wold, Caltech', '2781'), ('Bill Noble, UW', '3056'), ('Bing Ren, UCSD', '3434'), ('Bradley Bernstein, Broad', '6873'), ('Brenton Graveley, UConn', '10391'), ('Brian Oliver, NIH', '116'), ('Chris Burge, MIT', '1098'), ('Christina Leslie, MSKCC', '249'), ('David Gilbert, FSU', '350'), ('David MacAlpine, Duke', '10'), ('ENCODE Consortium', '1456'), ('ENCODE Consortium Analysis Working Group', '689'), ('ENCODE Processing Pipeline', '274085'), ('Erez Lieberman-Aiden, Baylor', '1'), ('Eric Lécuyer, IRCM', '120'), ('Ewan Birney, EBI', '2'), ('Gene Yeo, UCSD', '7322'), ('Gregory Crawford, Duke', '1106'), ('Guo-Cheng Yuan, Harvard', '23'), ('J. Michael Cherry, Stanford', '218'), ('Jason Lieb, UNC', '301'), ('Jennifer Harrow, Sanger', '12'), ('Job Dekker, UMass', '1655'), ('Joe Ecker, Salk', '1053'), ('John Rinn, Broad', '144'), ('John Stamatoyannopoulos, UW', '11157'), ('Joseph Costello, UCSF', '2101'), ('Kevin Struhl, HMS', '320'), ('Kevin White, UChicago', '43498'), ('Len Pennacchio, LBNL', '6'), ('Manolis Kellis, Broad', '10'), ('Manuel Garber, UMass', '283'), ('Mark Gerstein, Yale', '73'), ('Michael Beer, JHU', '26'), ('Michael Brent, WUSTL', '30'), ('Michael Snyder, Stanford', '10768'), ('Morgan Giddings, UNC', '40'), ('Peggy Farnham, USC', '758'), ('Piero Carninci, RIKEN', '663'), ('Richard Myers, HAIB', '6141'), ('Robert Waterston, UW', '11'), ('Roderic Guigo, CRG', '52'), ('Ross Hardison, PennState', '1283'), ('Scott Tenenbaum, SUNY-Albany', '152'), ('Sherman Weissman, Yale', '391'), ('Sunduz Keles, UW-M', '29'), ('Susan Celniker, LBNL', '534'), ('Thomas Gingeras, CSHL', '5635'), ('Thomas Tullius, BU', '2'), ('Tim Reddy, Duke', '4034'), ('Vishwanath Iyer, UTA', '535'), ('W. James Kent, UCSC', '34'), ('Wei Wang, UCSD', '7'), ('Will Greenleaf, Stanford', '2'), ('Xiang-Dong Fu, UCSD', '224'), ('Yijun Ruan, JAX', '436'), ('Zhiping Weng, UMass', '8533')]\u001b[0m\n",
      "MAPPING ASSEMBLY\n",
      "     \u001b[33mprod: [('GRCh38', '123627'), ('GRCh38-minimal', '7'), ('J02459.1', '2'), ('ce10', '10218'), ('ce11', '10881'), ('dm3', '10307'), ('dm6', '10652'), ('hg19', '162080'), ('mm10', '29449'), ('mm10-minimal', '14257'), ('mm9', '4137')]\u001b[0m\n",
      "PLATFORM\n",
      "     \u001b[33mprod: [('Affymetrix - Human Exon 1.0 ST V2 tilling array', '8'), ('Applied Biosystems SOLiD System 3 Plus', '292'), ('Illumina - Methylation 450K BeadChip', '126'), ('Illumina Genome Analyzer', '2388'), ('Illumina Genome Analyzer I', '329'), ('Illumina Genome Analyzer II', '2777'), ('Illumina Genome Analyzer IIe', '139'), ('Illumina Genome Analyzer IIx', '5477'), ('Illumina HiSeq 1000', '8'), ('Illumina HiSeq 2000', '22324'), ('Illumina HiSeq 2500', '8912'), ('Illumina HiSeq 4000', '4589'), ('Illumina HiSeq X Ten', '100'), ('Illumina Infinium Methylation EPIC BeadChip', '314'), ('Illumina Infinium Omni5Exome-4 Kit', '114'), ('Illumina MiSeq', '8'), ('Illumina NextSeq 500', '787'), ('Mouse 385K Whole Genome CGH Tiling Array', '29'), ('Mouse 3x720K Whole Genome CGH Tiling Array', '4'), ('Nimbelgen - Human 3x720K Whole Genome CGH Tiling Array', '136'), ('Nimblegen - Human 2.1M Whole-Genome CGH Tiling Array v2.0', '21'), ('Nimblegen - Human 6x630K CGH Whole Genome tiling array', '69'), ('Roche 454 Genome Sequencer FLX', '18'), ('nCounter Human V2 miRNA Expression array', '73'), ('nCounter Mouse V1.2 miRNA Expression array', '10'), ('nCounter Mouse V1.3 miRNA Expression array', '116'), ('nCounter Mouse V1.5 miRNA Expression array', '28')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '357965'), ('GGR', '5010'), ('Roadmap', '14548'), ('community', '12'), ('modENCODE', '18385'), ('modERN', '28476')]\u001b[0m\n",
      "SPECIFIC FILE FORMAT TYPE\n",
      "     \u001b[33mprod: [('bed12', '106'), ('bed3', '52'), ('bed3+', '8377'), ('bed6', '6'), ('bed6+', '454'), ('bed9', '543'), ('bedExonScore', '120'), ('bedGraph', '78'), ('bedLogR', '176'), ('bedMethyl', '2067'), ('bedRnaElements', '834'), ('broadPeak', '16503'), ('candidate enhancer predictions', '90'), ('enhancer predictions', '77'), ('enhancerAssay', '4'), ('gappedPeak', '162'), ('gff3', '720'), ('idr_peak', '512'), ('modPepMap', '24'), ('narrowPeak', '113602'), ('openChromCombinedPeaks', '34'), ('pepMap', '24'), ('peptideMapping', '32'), ('shortFrags', '10'), ('tss_peak', '1428'), ('unknown', '25')]\u001b[0m\n",
      "\n",
      "----------------------------------- Library ------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Library\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('missing donor', '3')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('missing external identifiers', '484'), ('missing genotype', '173')]\u001b[0m\n",
      "LIBRARY STATUS\n",
      "     \u001b[33mprod: [('released', '27070'), ('revoked', '182')]\u001b[0m\n",
      "\n",
      "--------------------------------- AntibodyLot ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=AntibodyLot\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('inconsistent ontology term', '5')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('need compliant primaries', '1465'), ('need compliant secondary', '87'), ('no characterizations submitted', '534'), ('no primary characterizations', '80'), ('no secondary characterizations', '1290')]\u001b[0m\n",
      "CHARACTERIZATION METHOD\n",
      "     \u001b[33mprod: [('ChIP-seq comparison', '166'), ('ChIP-string comparison', '26'), ('dot blot assay', '97'), ('immunoblot', '726'), ('immunofluorescence', '4'), ('immunoprecipitation', '1793'), ('immunoprecipitation followed by mass spectrometry', '335'), ('knockdown or knockout', '303'), ('motif enrichment', '79'), ('peptide ELISA assay', '3'), ('peptide competition assay', '1')]\u001b[0m\n",
      "CLONALITY\n",
      "     \u001b[33mprod: [('monoclonal', '653'), ('polyclonal', '2642')]\u001b[0m\n",
      "ELIGIBILITY STATUS\n",
      "     \u001b[33mprod: [('awaiting characterization', '1235'), ('characterized to standards', '562'), ('characterized to standards with exemption', '180'), ('not characterized to standards', '236'), ('not pursued', '1091'), ('partially characterized', '605')]\u001b[0m\n",
      "HOST ORGANISM\n",
      "     \u001b[33mprod: [('chicken', '1'), ('goat', '81'), ('guineapig', '9'), ('mouse', '556'), ('rabbit', '2677'), ('rat', '14'), ('savidinii', '1'), ('sheep', '1')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Abby Dernburg, Berkeley', '1'), ('Bing Ren, UCSD', '24'), ('Bradley Bernstein, Broad', '179'), ('Brenton Graveley, UConn', '261'), ('Gary Karpen, LBNL', '5'), ('Gene Yeo, UCSD', '717'), ('Gregory Crawford, Duke', '1'), ('J. Michael Cherry, Stanford', '4'), ('Jason Lieb, UNC', '6'), ('John Stamatoyannopoulos, UW', '1'), ('Julie Ahringer, Cambridge', '9'), ('Kevin White, UChicago', '4'), ('Michael Snyder, Stanford', '1044'), ('Peggy Farnham, USC', '4'), ('Richard Myers, HAIB', '219'), ('Ross Hardison, PennState', '16'), ('Sarah Elgin, WashU', '4'), ('Scott Tenenbaum, SUNY-Albany', '7'), ('Susan Strome, UCSC', '18'), ('Vincenzo Pirrotta, Rutgers', '1'), ('Xiang-Dong Fu, UCSD', '102'), ('Yijun Ruan, JAX', '3')]\u001b[0m\n",
      "SOURCE\n",
      "     \u001b[33mprod: [('ABclonal', '5'), ('Abcam', '255'), ('Abnova', '3'), ('Active Motif', '195'), ('Andrew Dingwall', '3'), ('Anthony Hyman', '1'), ('Anthony Schwacha', '1'), ('Arno Greenleaf', '1'), ('Arshad Desai', '2'), ('Assay Biotech', '28'), ('Aviva', '68'), ('Axxora', '1'), ('BD Biosciences', '6'), ('Bethyl Labs', '725'), ('BioLegend', '3'), ('Bioss', '30'), ('CDI', '112'), ('Callaini Guiliano', '1'), ('Carl Wu', '1'), ('Cayman', '1'), ('Cell Signaling', '75'), ('Claude Desplan', '2'), ('Covance', '14'), ('David Anderson', '1'), ('Diagenode', '23'), ('Dmitry Fyodorov', '1'), ('Donna Arndt-Jovin', '1'), ('Emery Bresnick', '2'), ('Epitomics', '1'), ('Eric Lai', '1'), ('Erika Bach', '2'), ('Eurogentec', '4'), ('Everest Biotech', '25'), ('Florence Maschat', '2'), ('Francesca Palladino', '1'), ('Francis Stewart', '2'), ('GeneTex', '419'), ('Giacomo Cavalli', '1'), ('Harald Saumweber', '2'), ('Haruhiko Siomi', '1'), ('Hiroshi Kimura', '6'), ('Huabing Li and Vincenzo Pirrotta', '1'), ('Hugo Bellen', '1'), ('Invitrogen', '1'), ('James Engel', '1'), ('James Kadonaga', '2'), ('Jan Larsson', '1'), ('Jean-Antoine Lepseant', '1'), ('Jianhong Wu and Tao Shi Hsieh', '1'), ('John Reinitz', '1'), ('Julie Ahringer', '2'), ('Karen Schulze and Hugo Bellen', '1'), ('Ken Cadigan', '1'), ('Kenneth Irvine', '1'), ('Kevin White', '35'), ('Kirsten Hagstrom', '1'), ('Kyoko Yokomori', '1'), ('LSBio', '4'), ('Lake Placid Biologicals', '8'), ('Laszlo Tora', '3'), ('MBLI', '113'), ('Marek Bartkuhn', '1'), ('Mattias Mannervik', '3'), ('Max Reuter', '1'), ('Medimabs', '1'), ('Millipore', '113'), ('Novus', '22'), ('Nuria Paricio', '1'), ('Origene', '29'), ('Pacific Immunology', '2'), ('Pamela Geyer', '1'), ('Paul Schedl, Jason Blanton and Greg Shanowe', '1'), ('Paul Yaswen', '1'), ('Peggy Farnham', '1'), ('Proteintech', '6'), ('RAN', '1'), ('RD Systems', '1'), ('Rainer Renkawitz', '2'), ('ReproCELL', '1'), ('Richard Mann', '1'), ('Robert Horvitz', '5'), ('Robert White', '5'), ('Roberto Mantovani', '2'), ('Roche', '1'), ('Rockland', '16'), ('SDIX, LLC', '109'), ('Santa Cruz Biotech', '281'), ('Sarah Elgin', '4'), ('Scott Hawley', '1'), ('Sigma', '426'), ('Stephen Bell', '1'), ('Stephen Crews', '2'), ('Stephen Smale', '1'), ('Steven Henikoff', '2'), ('Susan Strome', '1'), ('Thermo Fisher', '41'), ('Thomas Jenuwein', '2'), ('Tirtha Das and Ross Cagan', '1'), ('Tom Williams and Sean Carroll', '2'), ('Ulrich Laemmli', '1'), ('Unknown Source', '3'), ('Victor Corces', '6'), ('Victor Lobanenkov', '1'), ('Vincenzo Pirrotta', '8'), ('Wako Chemicals', '7'), ('William Kelly', '1'), ('Yang Shi', '2'), ('Zen Bioscience', '11')]\u001b[0m\n",
      "TARGET ORGANISM\n",
      "     \u001b[33mprod: [('Aequorea victoria', '8'), ('Caenorhabditis elegans', '143'), ('Drosophila melanogaster', '231'), ('Homo sapiens', '2920'), ('Mus musculus', '123'), ('influenzavirus', '3'), ('synthetic', '3')]\u001b[0m\n",
      "TARGET OF ANTIBODY\n",
      "     \u001b[33mprod: [('RNA binding protein', '1039'), ('broad histone mark', '144'), ('chromatin remodeller', '136'), ('control', '13'), ('histone', '334'), ('narrow histone mark', '105'), ('nucleotide modification', '6'), ('other context', '5'), ('other post-translational modification', '6'), ('recombinant protein', '1'), ('tag', '14'), ('transcription factor', '2190')]\u001b[0m\n",
      "\n",
      "---------------------------------- Biosample -----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Biosample\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('missing donor', '4')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('missing external identifiers', '424'), ('missing genetic modification characterization', '3637'), ('missing genotype', '186')]\u001b[0m\n",
      "BIOSAMPLE STATUS\n",
      "     \u001b[33mprod: [('released', '12913'), ('revoked', '24')]\u001b[0m\n",
      "BIOSAMPLE TREATMENT\n",
      "     \u001b[33mprod: [('17β-estradiol', '17'), ('17β-hydroxy-17-methylestra-4,9,11-trien-3-one', '1'), ('17β-hydroxy-5α-androstan-3-one', '4'), ('20-hydroxyecdysone', '16'), ('Diphtheria Toxin', '10'), ('LCMV', '4'), ('Lipopolysaccharide', '56'), ('Sendai virus', '2'), ('Sindbis virus', '8'), ('Tamoxifen', '15'), ('Transforming growth factor beta-1', '1'), ('UT189', '1'), ('activated CD4-positive, alpha-beta T cell', '1'), ('activated regulatory T-cells', '2'), ('afimoxifene', '10'), ('all-trans-retinoic acid', '8'), ('bisphenol A', '5'), ('bone marrow hematopoietic cell', '2'), ('cadmium dichloride', '8'), ('caffeine', '6'), ('calcium', '24'), ('cisplatin', '1'), ('cold shock treatment', '4'), ('copper(II) sulfate', '72'), ('dexamethasone', '786'), ('differentiation', '1'), ('dimethyl sulfoxide', '14'), ('doxycycline', '1'), ('doxycycline hyclate', '6'), ('effector memory CD4-positive, alpha-beta T cell', '1'), ('erythropoietin', '18'), ('estradiol', '13'), ('ethanol', '16'), ('forskolin and pyruvate', '1'), ('genistein', '5'), ('heat shock treatment', '2'), ('hydrocortisone succinate', '18'), ('hydroxyurea', '1'), ('inflammation-experienced regulatory T-cells', '1'), ('insulin and 22-hydroxycholesterol', '1'), ('interferon alpha', '3'), ('interferon gamma', '4'), ('interleukin-3', '18'), ('ionomycin', '4'), ('irradiation', '2'), ('kit ligand', '18'), ('lactate', '2'), ('methyltrienolone', '2'), ('paraquat', '4'), ('phorbol 13-acetate 12-myristate', '4'), ('pravastatin', '1'), ('regulatory T cell', '1'), ('resveratrol', '2'), ('retinoic acid', '2'), ('rotenone', '6'), ('serum free', '1'), ('sodium butyrate', '1'), ('tamoxifen', '2'), ('tumor necrosis factor', '10'), ('vorinostat', '1'), ('zinc dichloride', '6')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '5449'), ('in vitro differentiated cells', '311'), ('induced pluripotent stem cell line', '55'), ('primary cell', '1045'), ('stem cell', '301'), ('tissue', '2757'), ('whole organisms', '3019')]\u001b[0m\n",
      "CELL CYCLE PHASE\n",
      "     \u001b[33mprod: [('G1', '6'), ('G1b', '21'), ('G2', '20'), ('S1', '18'), ('S2', '16'), ('S3', '16'), ('S4', '16'), ('early S', '7'), ('late S', '7')]\u001b[0m\n",
      "HAS NIH INSTITUTIONAL CERTIFICATION\n",
      "     \u001b[33mprod: [('no', '12937')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Alexander Urban, Stanford', '1'), ('Ali Mortazavi, UCI', '6'), ('Andrew Z. Fire, Stanford', '3'), ('Barbara Wold, Caltech', '850'), ('Bing Ren, UCSD', '229'), ('Bradley Bernstein, Broad', '593'), ('Brenton Graveley, UConn', '1348'), ('Brian Oliver, NIH', '48'), ('Christina Leslie, MSKCC', '79'), ('David Gilbert, FSU', '100'), ('David MacAlpine, Duke', '13'), ('ENCODE Consortium', '101'), ('Eric Lécuyer, IRCM', '60'), ('Gene Yeo, UCSD', '110'), ('Gregory Crawford, Duke', '170'), ('Job Dekker, UMass', '6'), ('John Stamatoyannopoulos, UW', '1427'), ('Joseph Costello, UCSF', '224'), ('Kevin Struhl, HMS', '9'), ('Kevin White, UChicago', '1652'), ('Len Pennacchio, LBNL', '335'), ('Manuel Garber, UMass', '60'), ('Michael Snyder, Stanford', '1713'), ('Morgan Giddings, UNC', '20'), ('Paul Khavari, Stanford', '26'), ('Peggy Farnham, USC', '73'), ('Peter Cherbas, IndianaU', '298'), ('Piero Carninci, RIKEN', '56'), ('Richard Myers, HAIB', '583'), ('Ross Hardison, PennState', '160'), ('Scott Tenenbaum, SUNY-Albany', '6'), ('Sherman Weissman, Yale', '231'), ('Susan Celniker, LBNL', '32'), ('Thomas Gingeras, CSHL', '524'), ('Tim Reddy, Duke', '873'), ('Unknown Lab', '15'), ('Valerie Reinke, Yale', '651'), ('Vishwanath Iyer, UTA', '10'), ('Xiang-Dong Fu, UCSD', '202'), ('Yijun Ruan, JAX', '40')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('L1 larva', '254'), ('L2 larva', '140'), ('L3 larva', '173'), ('L4 larva', '232'), ('L4/young adult', '7'), ('adult', '5195'), ('child', '1175'), ('dauer', '4'), ('early embryonic', '30'), ('embryonic', '3499'), ('first instar larva', '2'), ('larva', '3'), ('late embryonic', '200'), ('midembryonic', '6'), ('mixed stage (embryonic)', '84'), ('newborn', '156'), ('postnatal', '181'), ('prepupa', '210'), ('pupa', '27'), ('second instar larva', '2'), ('third instar larva', '63'), ('unknown', '912'), ('wandering third instar larva', '132'), ('young adult', '250')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '81'), ('adrenal gland', '53'), ('artery', '43'), ('blood', '2125'), ('blood vessel', '154'), ('bodily fluid', '2125'), ('bone element', '112'), ('bone marrow', '83'), ('brain', '498'), ('breast', '27'), ('bronchus', '16'), ('connective tissue', '277'), ('embryo', '679'), ('epithelium', '389'), ('esophagus', '56'), ('extraembryonic component', '92'), ('eye', '31'), ('gonad', '76'), ('heart', '191'), ('intestine', '230'), ('kidney', '644'), ('large intestine', '141'), ('limb', '648'), ('liver', '1189'), ('lung', '1152'), ('lymph node', '77'), ('lymphatic vessel', '8'), ('lymphoid tissue', '26'), ('mammary gland', '227'), ('mouth', '15'), ('musculature of body', '249'), ('nerve', '26'), ('nose', '5'), ('ovary', '30'), ('pancreas', '60'), ('penis', '81'), ('pericardium', '3'), ('placenta', '38'), ('prostate gland', '77'), ('skeleton', '5'), ('skin of body', '287'), ('small intestine', '38'), ('spinal cord', '18'), ('spleen', '73'), ('stomach', '118'), ('testis', '38'), ('thymus', '30'), ('thyroid gland', '33'), ('tongue', '5'), ('trachea', '5'), ('ureter', '18'), ('urinary bladder', '14'), ('uterus', '118'), ('vagina', '16'), ('vasculature', '172'), ('vein', '46')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Caenorhabditis elegans', '1387'), ('Drosophila ananassae', '2'), ('Drosophila melanogaster', '1927'), ('Drosophila mojavensis', '6'), ('Drosophila pseudoobscura', '16'), ('Drosophila simulans', '16'), ('Drosophila virilis', '2'), ('Drosophila yakuba', '2'), ('Homo sapiens', '7814'), ('Mus musculus', '1765')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '7472'), ('GGR', '1038'), ('Roadmap', '1028'), ('community', '4'), ('modENCODE', '1510'), ('modERN', '1885')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '386'), ('ENCODE2', '1279'), ('ENCODE2-Mouse', '316'), ('ENCODE3', '5027'), ('ENCODE4', '464'), ('GGR', '1038'), ('Roadmap', '1028'), ('community', '4'), ('modENCODE', '1510'), ('modERN', '1885')]\u001b[0m\n",
      "SEX\n",
      "     \u001b[33mprod: [('female', '4042'), ('hermaphrodite', '416'), ('male', '3998'), ('mixed', '2767'), ('unknown', '1714')]\u001b[0m\n",
      "SOURCE\n",
      "     \u001b[33mprod: [('A. Thomas Look', '4'), ('ATCC', '3465'), ('Agilent', '3'), ('Alan Mackay-Sim', '3'), ('Albert La Spada', '4'), ('Alex Meissner', '97'), ('Ambion', '5'), ('Amy Murtha', '1'), ('Andrew Z. Fire', '2'), ('Ari Melnick', '2'), ('Arthur Skoultchi', '4'), ('Arthur Weiss', '32'), ('ArunA Biomedical', '11'), ('Asterand', '1'), ('Austin Smith', '2'), ('BDRL', '70'), ('Barbara Wold', '275'), ('Beverly Torok-Storb', '9'), ('Bing Ren', '78'), ('BioChain', '70'), ('Bloomington Drosophila Stock Center at Indiana University', '3'), ('Bradley Bernstein', '8'), ('Brenton Graveley', '186'), ('BresaGen', '1'), ('Brian Oliver', '16'), ('CDI', '11'), ('CGC', '410'), ('Calvin Cotton', '1'), ('Carl Mann', '8'), ('Carol Ware', '2'), ('Cellular Dynamics', '47'), ('Charles Graham', '1'), ('Chordoma', '1'), ('Christina Leslie', '79'), ('Christine Disteche', '3'), ('Coriell', '292'), ('DSMZ', '7'), ('Dana Levasseur', '8'), ('Darrell Bigner', '3'), ('David Bodine', '121'), ('David Gilbert', '9'), ('David Herrmann', '1'), ('David Randolph', '5'), ('Dharmacon', '5'), ('Donald Sens', '2'), ('Drosophila Genomics Resource Center', '122'), ('Drosophila Species Stock Center', '32'), ('ECACC', '15'), ('Emery Bresnick', '1'), ('Eric Bouhassira', '1'), ('Evan Rosen', '3'), ('Genetically Engineered Mouse Services, California Institute of Technology', '453'), ('Genhong Cheng', '4'), ('Gerd Blobel', '6'), ('Gordon Hager', '2'), ('Gregory Crawford', '2'), ('Haplogen Genomics', '4'), ('Harvard iPSC', '2'), ('Hugo Bellen', '78'), ('Huntington Willard', '5'), ('ICRC', '1'), ('Ian Glass', '287'), ('Invitrogen', '1'), ('James Thomson', '71'), ('Jan Brinchmann', '8'), ('Jefferey Marks', '1'), ('Jeffrey Engelman', '2'), ('Jennifer Brown', '1'), ('Jennifer Condon-Jeyasuria', '1'), ('Jerrold Olefsky', '2'), ('John Stamatoyannopoulos', '202'), ('Jonathan Weissman', '33'), ('Joseph Costello', '15'), ('Josh Chenoweth', '4'), ('KPBBB', '2'), ('Keith Ligon', '31'), ('Kevin Struhl', '14'), ('Kevin White', '1574'), ('Kristin Ardlie', '585'), ('LEIDOS', '101'), ('Len Pennacchio', '335'), ('Licia Selleri', '9'), ('Lonza', '173'), ('Lurdes Queimado', '2'), ('MMRRC', '2'), ('Manuel Garber', '4'), ('Marella deBruijn', '2'), ('Maria Roubelakis', '5'), ('Mark Groudine', '24'), ('Mark Minden', '12'), ('Max Planck Institute', '3'), ('Melanie Ehrlich and Koji Tsumagari', '4'), ('Michael Bender', '8'), ('Michael Bender and Rachel Byron', '1'), ('Michael Mannstadt', '2'), ('Michael Snyder', '335'), ('Miguel Ramalho-Santos', '3'), ('Ming-Sound Tsao', '1'), ('Mitchell Weiss', '3'), ('NCTC', '7'), ('NDRI', '7'), ('NICHD', '25'), ('NICHD BTB', '36'), ('PGP', '2'), ('Paul Khavari', '26'), ('Paul Tesar', '2'), ('Pedro Caballero-Campo', '6'), ('Peggy Farnham', '1'), ('Peter Cherbas', '206'), ('Progeria Research', '1'), ('PromoCell', '82'), ('Rajinder Kaul', '9'), ('Ravi Jhaveri', '2'), ('Richard Myers', '25'), ('Robert Paulson', '4'), ('Rush University', '20'), ('SESCC', '53'), ('ScienCell', '88'), ('Shelly Heimfeld', '99'), ('Sherman Weissman', '218'), ('Shin Lin', '45'), ('Sigma', '19'), ('Stephen Dalton', '24'), ('Stephen Hauschka', '1'), ('Steve Choi', '1'), ('Steven Young', '4'), ('Stuart Schreiber', '2'), ('Susan Celniker', '32'), ('Susan Fisher', '59'), ('TCESC', '4'), ('Takemi Ohtsuki', '2'), ('The Jackson Laboratory', '13'), ('Thea Tlsty', '47'), ('Thermo Fisher', '3'), ('Thomas Gingeras', '76'), ('Thomas Montine', '20'), ('Thomas Reh', '10'), ('Timothy Hughes', '432'), ('Todd Golub', '15'), ('UNC CF Center', '2'), ('Unknown Source', '560'), ('Valerie Reinke', '651'), ('ViroMed Laboratories', '10'), ('WiCell', '12'), ('Woodring Wright', '7'), ('Yardena Samuels', '1'), ('Yoichi Shinkai', '3'), ('ZenBio', '1')]\u001b[0m\n",
      "SUBCELLULAR FRACTION\n",
      "     \u001b[33mprod: [('chromatin', '9'), ('cytosol', '83'), ('insoluble cytoplasmic fraction', '12'), ('membrane', '14'), ('mitochondria', '2'), ('nucleolus', '16'), ('nucleoplasm', '7'), ('nucleus', '83'), ('polysome', '5')]\u001b[0m\n",
      "\n",
      "------------------------------------ Donor -------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Donor\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('missing external identifiers', '120'), ('missing genetic modification characterization', '657'), ('missing genotype', '83')]\u001b[0m\n",
      "DATA TYPE\n",
      "     \u001b[33mprod: [('Donor', '1586'), ('FlyDonor', '451'), ('HumanDonor', '780'), ('MouseDonor', '40'), ('WormDonor', '315')]\u001b[0m\n",
      "\n",
      "----------------------------- GeneticModification ------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32msearch/?type=GeneticModification\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('missing genetic modification characterization', '1128')]\u001b[0m\n",
      "CATEGORY\n",
      "     \u001b[33mprod: [('deletion', '80'), ('insertion', '1128'), ('interference', '481')]\u001b[0m\n",
      "GENETIC MODIFICATION STATUS\n",
      "     \u001b[33mprod: [('released', '1688'), ('revoked', '1')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Bradley Bernstein, Broad', '1'), ('Brenton Graveley, UConn', '401'), ('Gregory Crawford, Duke', '2'), ('John Stamatoyannopoulos, UW', '48'), ('Kevin Struhl, HMS', '1'), ('Kevin White, UChicago', '460'), ('Michael Snyder, Stanford', '230'), ('Peggy Farnham, USC', '4'), ('Richard Myers, HAIB', '108'), ('Robert Waterston, UW', '278'), ('Sherman Weissman, Yale', '108'), ('Susan Celniker, LBNL', '33'), ('Valerie Reinke, Yale', '15')]\u001b[0m\n",
      "METHOD\n",
      "     \u001b[33mprod: [('CRISPR', '255'), ('RNAi', '406'), ('TALEN', '44'), ('bombardment', '302'), ('microinjection', '1'), ('site-specific recombination', '558'), ('stable transfection', '122'), ('transduction', '1')]\u001b[0m\n",
      "PURPOSE\n",
      "     \u001b[33mprod: [('repression', '517'), ('tagging', '1128'), ('validation', '44')]\u001b[0m\n",
      "\n",
      "----------------------------------- FileSet ------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=FileSet\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('inconsistent assembly', '32'), ('inconsistent control read length', '1')]\u001b[0m\n",
      "DATA TYPE\n",
      "     \u001b[33mprod: [('Annotation', '5735'), ('Dataset', '5880'), ('FileSet', '5880'), ('Project', '18'), ('PublicationData', '7'), ('Reference', '52'), ('UcscBrowserComposite', '68')]\u001b[0m\n",
      "\n",
      "---------------------------------- Annotation ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Annotation\u001b[0m\n",
      "ANNOTATION TYPE\n",
      "     \u001b[33mprod: [('binding sites', '2'), ('blacklist', '3'), ('candidate regulatory elements', '2178'), ('chromatin state', '330'), ('enhancer predictions', '111'), ('gene expression', '14'), ('other', '3048'), ('overlap', '17'), ('representative DNase hypersensitivity sites', '6'), ('transcript expression', '14'), ('validated enhancers', '6')]\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ChIP-seq', '20')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('inconsistent assembly', '28')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '3'), ('bed bed3', '4'), ('bed bed3+', '2164'), ('bed bed6', '2'), ('bed bed9', '91'), ('bed candidate enhancer predictions', '46'), ('bed enhancer predictions', '50'), ('bed enhancerAssay', '2'), ('bed narrowPeak', '2'), ('bed openChromCombinedPeaks', '17'), ('bigBed bed3+', '2154'), ('bigBed bed6', '2'), ('bigBed bed9', '218'), ('bigBed broadPeak', '1'), ('bigBed enhancerAssay', '2'), ('bigBed openChromCombinedPeaks', '17'), ('bigBed unknown', '9'), ('bigWig', '3049'), ('fasta', '1'), ('fastq', '20'), ('tsv', '39')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '393'), ('in vitro differentiated cells', '124'), ('induced pluripotent stem cell line', '44'), ('primary cell', '603'), ('stem cell', '101'), ('tissue', '1362'), ('whole organisms', '6')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2014', '3'), ('April, 2017', '3'), ('April, 2018', '3048'), ('August, 2015', '92'), ('August, 2016', '452'), ('August, 2017', '779'), ('December, 2011', '1'), ('February, 2012', '10'), ('February, 2015', '2'), ('July, 2013', '225'), ('July, 2016', '3'), ('June, 2011', '16'), ('June, 2015', '2'), ('June, 2016', '276'), ('March, 2014', '9'), ('March, 2016', '1'), ('November, 2016', '17'), ('October, 2011', '2'), ('October, 2015', '10'), ('September, 2012', '2'), ('September, 2014', '22'), ('September, 2015', '2'), ('September, 2017', '758')]\u001b[0m\n",
      "ENCYCLOPEDIA VERSION\n",
      "     \u001b[33mprod: [('1', '3'), ('2', '141'), ('3', '847'), ('4', '4587'), ('Blacklists', '2'), ('ENCODE2', '27'), ('ROADMAP', '127')]\u001b[0m\n",
      "FILE SET STATUS\n",
      "     \u001b[33mprod: [('archived', '968'), ('released', '4767')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '4166'), ('mm10', '455'), ('mm9', '17')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Bill Noble, UW', '3057'), ('Bing Ren, UCSD', '1'), ('Bradley Bernstein, Broad', '9'), ('Ewan Birney, EBI', '1'), ('Gregory Crawford, Duke', '18'), ('Guo-Cheng Yuan, Harvard', '10'), ('John Stamatoyannopoulos, UW', '3'), ('Len Pennacchio, LBNL', '4'), ('Manolis Kellis, Broad', '231'), ('Mark Gerstein, Yale', '39'), ('Michael Beer, JHU', '13'), ('Richard Myers, HAIB', '1'), ('Roderic Guigo, CRG', '28'), ('Ross Hardison, PennState', '22'), ('Sunduz Keles, UW-M', '18'), ('Wei Wang, UCSD', '3'), ('Zhiping Weng, UMass', '2277')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '435'), ('embryonic', '795'), ('postnatal', '100'), ('unknown', '235'), ('young adult', '58')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '9'), ('adrenal gland', '21'), ('artery', '10'), ('blood', '228'), ('blood vessel', '52'), ('bodily fluid', '228'), ('bone element', '33'), ('bone marrow', '15'), ('brain', '331'), ('breast', '1'), ('bronchus', '8'), ('connective tissue', '200'), ('embryo', '217'), ('epithelium', '174'), ('esophagus', '17'), ('extraembryonic component', '52'), ('eye', '30'), ('gonad', '26'), ('heart', '109'), ('intestine', '156'), ('kidney', '123'), ('large intestine', '90'), ('limb', '108'), ('liver', '89'), ('lung', '162'), ('lymph node', '50'), ('lymphatic vessel', '2'), ('lymphoid tissue', '2'), ('mammary gland', '44'), ('mouth', '17'), ('musculature of body', '155'), ('ovary', '12'), ('pancreas', '33'), ('penis', '54'), ('placenta', '27'), ('prostate gland', '15'), ('skin of body', '129'), ('small intestine', '41'), ('spinal cord', '15'), ('spleen', '29'), ('stomach', '70'), ('testis', '13'), ('thymus', '34'), ('thyroid gland', '8'), ('tongue', '4'), ('ureter', '14'), ('urinary bladder', '2'), ('uterus', '22'), ('vagina', '3'), ('vasculature', '64'), ('vein', '15')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '4951'), ('Mus musculus', '784')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '5510'), ('Roadmap', '225')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '3276'), ('ENCODE2', '50'), ('ENCODE3', '2184'), ('Roadmap', '225')]\u001b[0m\n",
      "READ LENGTH (NT)\n",
      "     \u001b[33mprod: [('30', '2'), ('32', '1'), ('36', '17'), ('45', '1'), ('48', '2'), ('50', '2'), ('51', '2'), ('55', '5')]\u001b[0m\n",
      "RUN TYPE\n",
      "     \u001b[33mprod: [('single-ended', '20')]\u001b[0m\n",
      "SOFTWARE USED\n",
      "     \u001b[33mprod: [('chromhmm', '225'), ('predictd', '3048'), ('segway', '9')]\u001b[0m\n",
      "TARGET(S) OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '172'), ('broad histone mark', '1'), ('histone', '1328'), ('narrow histone mark', '1327'), ('transcription factor', '235')]\u001b[0m\n",
      "TARGET(S) OF ASSAY2\n",
      "     \u001b[33mprod: [('CTCF', '235'), ('H3K27ac', '684'), ('H3K4me1', '1'), ('H3K4me3', '860'), ('H3K9ac', '1')]\u001b[0m\n",
      "\n",
      "------------------------------------ Series ------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Series\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('multiple biosample term names in reference epigenome', '2'), ('multiple biosample treatments in reference epigenome', '1'), ('partial reference epigenome', '95')]\u001b[0m\n",
      "DATA TYPE\n",
      "     \u001b[33mprod: [('Dataset', '387'), ('MatchedSet', '5'), ('OrganismDevelopmentSeries', '73'), ('ReferenceEpigenome', '248'), ('ReplicationTimingSeries', '22'), ('Series', '387'), ('TreatmentConcentrationSeries', '2'), ('TreatmentTimeSeries', '37')]\u001b[0m\n",
      "\n",
      "-------------------------- OrganismDevelopmentSeries ---------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=OrganismDevelopmentSeries\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('CAGE', '1'), ('ChIP-seq', '49'), ('DNase-seq', '1'), ('MRE-seq', '1'), ('RNA-seq', '12'), ('single cell isolation followed by RNA-seq', '7'), ('transcription profiling by array assay', '1'), ('whole-genome shotgun bisulfite sequencing', '8')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '71'), ('bed bed3+', '1'), ('bed bedExonScore', '1'), ('bed bedMethyl', '8'), ('bed bedRnaElements', '3'), ('bed broadPeak', '19'), ('bed idr_peak', '1'), ('bed narrowPeak', '50'), ('bed tss_peak', '1'), ('bigBed bedExonScore', '1'), ('bigBed bedMethyl', '8'), ('bigBed bedRnaElements', '3'), ('bigBed broadPeak', '19'), ('bigBed idr_peak', '1'), ('bigBed narrowPeak', '50'), ('bigBed tss_peak', '1'), ('bigWig', '71'), ('fastq', '71'), ('gff gff3', '1'), ('gtf', '2'), ('tar', '1'), ('tsv', '13')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '2'), ('primary cell', '2'), ('tissue', '69')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('January, 2016', '73')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '3'), ('hg19', '4'), ('mm10', '68'), ('mm9', '18')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Barbara Wold, Caltech', '10'), ('Bing Ren, UCSD', '49'), ('Gregory Crawford, Duke', '2'), ('Joe Ecker, Salk', '8'), ('Piero Carninci, RIKEN', '1'), ('Richard Myers, HAIB', '1'), ('Thomas Gingeras, CSHL', '2')]\u001b[0m\n",
      "LIBRARY DEPLETED IN\n",
      "     \u001b[33mprod: [('rRNA', '2')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('180-500', '8'), ('200-500', '18'), ('300-500', '49'), ('<200', '1'), ('>200', '12')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '59'), ('RNA', '9'), ('polyadenylated mRNA', '12')]\u001b[0m\n",
      "LIBRARY TREATMENT\n",
      "     \u001b[33mprod: [('Tobacco Acid Pyrophosphatase', '1')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '23'), ('child', '4'), ('embryonic', '67'), ('postnatal', '67'), ('unknown', '1')]\u001b[0m\n",
      "MAPPED READ LENGTH\n",
      "     \u001b[33mprod: [('36', '49'), ('50', '49')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('brain', '24'), ('heart', '8'), ('kidney', '8'), ('liver', '11'), ('lung', '8'), ('musculature of body', '1'), ('skin of body', '2'), ('stomach', '8'), ('thymus', '1')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '73')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('100', '18'), ('101', '12'), ('108', '1'), ('117', '2'), ('125', '1'), ('130', '7'), ('132', '3'), ('133', '1'), ('136', '1'), ('139', '3'), ('36', '50'), ('50', '50'), ('51', '1'), ('76', '1')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('released', '73')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('broad histone mark', '33'), ('control', '7'), ('histone', '49'), ('narrow histone mark', '16')]\u001b[0m\n",
      "\n",
      "----------------------------- UcscBrowserComposite -----------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=UcscBrowserComposite\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bed bed9', '1'), ('bigBed bed9', '1'), ('bigWig', '2')]\u001b[0m\n",
      "COMPOSITE STATUS\n",
      "     \u001b[33mprod: [('archived', '68')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2011', '1'), ('April, 2012', '7'), ('August, 2011', '2'), ('August, 2012', '14'), ('December, 2011', '1'), ('February, 2011', '1'), ('February, 2012', '2'), ('February, 2016', '1'), ('January, 2012', '1'), ('January, 2014', '2'), ('July, 2012', '10'), ('June, 2011', '1'), ('June, 2012', '3'), ('March, 2006', '1'), ('March, 2012', '2'), ('May, 2011', '1'), ('May, 2012', '2'), ('November, 2009', '1'), ('October, 2011', '1'), ('October, 2012', '1'), ('September, 2010', '1'), ('September, 2011', '1'), ('September, 2012', '10')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '2')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Barbara Wold, Caltech', '4'), ('Bing Ren, UCSD', '3'), ('Bradley Bernstein, Broad', '2'), ('David Gilbert, FSU', '2'), ('ENCODE Consortium Analysis Working Group', '1'), ('Gregory Crawford, Duke', '5'), ('Job Dekker, UMass', '1'), ('John Stamatoyannopoulos, UW', '10'), ('Kevin White, UChicago', '1'), ('Michael Snyder, Stanford', '6'), ('Morgan Giddings, UNC', '2'), ('Peggy Farnham, USC', '1'), ('Piero Carninci, RIKEN', '1'), ('Richard Myers, HAIB', '9'), ('Roderic Guigo, CRG', '2'), ('Ross Hardison, PennState', '4'), ('Scott Tenenbaum, SUNY-Albany', '4'), ('Thomas Gingeras, CSHL', '4'), ('Thomas Tullius, BU', '1'), ('Timothy Hubbard, Sanger', '1'), ('Yijun Ruan, JAX', '4')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '68')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '5'), ('ENCODE2', '45'), ('ENCODE2-Mouse', '16'), ('ENCODE3', '2')]\u001b[0m\n",
      "\n",
      "------------------------------ ReferenceEpigenome ------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=ReferenceEpigenome\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ATAC-seq', '66'), ('ChIP-seq', '248'), ('DNase-seq', '117'), ('MRE-seq', '16'), ('MeDIP-seq', '16'), ('RNA-seq', '164'), ('RRBS', '61'), ('microRNA counts', '10'), ('microRNA-seq', '98'), ('transcription profiling by array assay', '24'), ('whole-genome shotgun bisulfite sequencing', '118')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('multiple biosample term names in reference epigenome', '2'), ('multiple biosample treatments in reference epigenome', '1'), ('partial reference epigenome', '95')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '246'), ('bed bed3+', '115'), ('bed bed6+', '10'), ('bed bed9', '1'), ('bed bedExonScore', '1'), ('bed bedMethyl', '131'), ('bed bedRnaElements', '26'), ('bed broadPeak', '180'), ('bed narrowPeak', '246'), ('bigBed bed6+', '10'), ('bigBed bed9', '1'), ('bigBed bedExonScore', '1'), ('bigBed bedMethyl', '131'), ('bigBed bedRnaElements', '26'), ('bigBed broadPeak', '123'), ('bigBed narrowPeak', '246'), ('bigWig', '246'), ('fasta', '1'), ('fastq', '246'), ('gtf', '29'), ('rcc', '10'), ('sra', '27'), ('tagAlign', '142'), ('tar', '2'), ('tsv', '162')]\u001b[0m\n",
      "BIOSAMPLE TREATMENT\n",
      "     \u001b[33mprod: [('dimethyl sulfoxide', '1'), ('doxycycline hyclate', '1'), ('ethanol', '2'), ('ionomycin', '2'), ('phorbol 13-acetate 12-myristate', '2')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '27'), ('in vitro differentiated cells', '19'), ('induced pluripotent stem cell line', '6'), ('primary cell', '55'), ('stem cell', '12'), ('tissue', '131')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2016', '1'), ('August, 2016', '25'), ('August, 2017', '3'), ('February, 2016', '61'), ('January, 2016', '10'), ('July, 2013', '127'), ('July, 2016', '5'), ('May, 2016', '16')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '161'), ('hg19', '161'), ('mm10', '85'), ('mm9', '14')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Anshul Kundaje, Stanford', '127'), ('ENCODE Consortium', '121')]\u001b[0m\n",
      "LIBRARY DEPLETED IN\n",
      "     \u001b[33mprod: [('rRNA', '46')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('10-50', '1'), ('100-300', '1'), ('120-200', '3'), ('120-280', '1'), ('150-250', '1'), ('150-350', '2'), ('180-500', '72'), ('19-25', '18'), ('200-200', '1'), ('200-250', '19'), ('200-500', '13'), ('200-600', '39'), ('200-750', '66'), ('240-420', '2'), ('270-500', '1'), ('275-470', '1'), ('299-300', '16'), ('300-1000', '1'), ('300-350', '2'), ('300-400', '1'), ('300-500', '72'), ('300-600', '3'), ('300-700', '1'), ('300-800', '3'), ('400-400', '1'), ('450-650', '1'), ('50-300', '4'), ('<200', '26'), ('<30', '80'), ('>175', '2'), ('>200', '116')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '248'), ('RNA', '59'), ('miRNA', '99'), ('polyadenylated mRNA', '148')]\u001b[0m\n",
      "LIBRARY TREATMENT\n",
      "     \u001b[33mprod: [('Tobacco Acid Pyrophosphatase', '21')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '89'), ('child', '15'), ('embryonic', '106'), ('newborn', '11'), ('postnatal', '9'), ('unknown', '41')]\u001b[0m\n",
      "MAPPED READ LENGTH\n",
      "     \u001b[33mprod: [('100', '1'), ('28', '1'), ('30', '7'), ('32', '3'), ('33', '2'), ('36', '188'), ('37', '2'), ('45', '1'), ('47', '2'), ('50', '52'), ('51', '3'), ('74', '2'), ('75', '8'), ('76', '27')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '1'), ('adrenal gland', '1'), ('blood', '26'), ('blood vessel', '3'), ('bodily fluid', '26'), ('brain', '37'), ('connective tissue', '15'), ('embryo', '27'), ('epithelium', '16'), ('esophagus', '1'), ('extraembryonic component', '3'), ('gonad', '2'), ('heart', '14'), ('intestine', '17'), ('kidney', '6'), ('large intestine', '8'), ('limb', '8'), ('liver', '12'), ('lung', '12'), ('lymph node', '4'), ('mammary gland', '5'), ('musculature of body', '14'), ('ovary', '1'), ('pancreas', '3'), ('penis', '7'), ('placenta', '1'), ('prostate gland', '1'), ('skin of body', '15'), ('small intestine', '5'), ('spleen', '3'), ('stomach', '8'), ('testis', '1'), ('thymus', '3'), ('uterus', '2'), ('vasculature', '3'), ('vein', '2')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '163'), ('Mus musculus', '85')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '121'), ('Roadmap', '127')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE3', '121'), ('Roadmap', '127')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('100', '102'), ('101', '62'), ('108', '5'), ('113', '1'), ('117', '2'), ('125', '6'), ('130', '28'), ('132', '3'), ('133', '3'), ('136', '2'), ('139', '3'), ('150', '5'), ('151', '1'), ('20', '1'), ('25', '12'), ('27', '1'), ('28', '2'), ('29', '6'), ('30', '13'), ('31', '13'), ('32', '3'), ('33', '2'), ('35', '1'), ('36', '203'), ('37', '3'), ('38', '2'), ('41', '3'), ('42', '1'), ('43', '2'), ('45', '4'), ('47', '2'), ('48', '1'), ('50', '102'), ('51', '11'), ('52', '1'), ('53', '1'), ('55', '1'), ('72', '1'), ('73', '11'), ('74', '2'), ('75', '11'), ('76', '69'), ('82', '2'), ('83', '1'), ('84', '1'), ('85', '5'), ('86', '2'), ('87', '2'), ('88', '1'), ('94', '1')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('archived', '16'), ('released', '232')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '25'), ('broad histone mark', '248'), ('chromatin remodeller', '13'), ('control', '248'), ('histone', '248'), ('narrow histone mark', '248'), ('nucleotide modification', '16'), ('other context', '6'), ('other post-translational modification', '6'), ('transcription factor', '50')]\u001b[0m\n",
      "\n",
      "----------------------------------- Project ------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Project\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ChIP-seq', '8'), ('DNase-seq', '2'), ('RAMPAGE', '1'), ('RNA-seq', '5'), ('single cell isolation followed by RNA-seq', '2')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('inconsistent control read length', '1')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '5'), ('bed bed3', '1'), ('bed idr_peak', '1'), ('bed narrowPeak', '1'), ('bed tss_peak', '1'), ('bigBed idr_peak', '1'), ('bigBed narrowPeak', '1'), ('bigBed tss_peak', '1'), ('bigWig', '5'), ('fasta', '1'), ('fastq', '16'), ('gff gff3', '1'), ('tsv', '4')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '9'), ('in vitro differentiated cells', '6'), ('induced pluripotent stem cell line', '1'), ('primary cell', '4'), ('stem cell', '4'), ('tissue', '12')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('June, 2014', '1'), ('June, 2015', '1'), ('November, 2013', '1'), ('October, 2015', '15')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '5')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Anshul Kundaje, Stanford', '1'), ('Mark Gerstein, Yale', '2'), ('Zhiping Weng, UMass', '15')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adrenal gland', '1'), ('artery', '1'), ('blood', '9'), ('blood vessel', '2'), ('bodily fluid', '9'), ('bone element', '3'), ('bone marrow', '1'), ('brain', '13'), ('breast', '2'), ('bronchus', '2'), ('connective tissue', '5'), ('embryo', '9'), ('epithelium', '10'), ('extraembryonic component', '1'), ('eye', '4'), ('heart', '11'), ('intestine', '7'), ('kidney', '9'), ('large intestine', '2'), ('limb', '7'), ('liver', '11'), ('lung', '11'), ('lymph node', '1'), ('lymphatic vessel', '1'), ('mouth', '3'), ('musculature of body', '5'), ('nose', '1'), ('penis', '1'), ('pericardium', '2'), ('prostate gland', '2'), ('skin of body', '4'), ('spinal cord', '3'), ('spleen', '1'), ('stomach', '7'), ('thymus', '2'), ('thyroid gland', '3'), ('tongue', '3'), ('trachea', '1'), ('urinary bladder', '5'), ('uterus', '4'), ('vasculature', '2')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '8'), ('Mus musculus', '8')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '18')]\u001b[0m\n",
      "PROJECT STATUS\n",
      "     \u001b[33mprod: [('released', '18')]\u001b[0m\n",
      "PROJECT TYPE\n",
      "     \u001b[33mprod: [('evaluation', '17'), ('validation', '1')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '1'), ('ENCODE3', '17')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('100', '4'), ('101', '6'), ('28', '1'), ('36', '8'), ('37', '1'), ('50', '7'), ('75', '1')]\u001b[0m\n",
      "RUN TYPE\n",
      "     \u001b[33mprod: [('paired-ended', '7'), ('single-ended', '13')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '1'), ('broad histone mark', '7'), ('control', '3'), ('histone', '7'), ('narrow histone mark', '7'), ('other context', '1'), ('other post-translational modification', '1'), ('transcription factor', '1')]\u001b[0m\n",
      "\n",
      "--------------------------- ReplicationTimingSeries ----------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=ReplicationTimingSeries\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('Repli-seq', '22')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '20'), ('bigWig', '13'), ('fastq', '20')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '19'), ('primary cell', '2'), ('stem cell', '1')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('December, 2015', '15'), ('July, 2017', '6'), ('September, 2017', '1')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '20')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('David Gilbert, FSU', '7'), ('David MacAlpine, Duke', '2'), ('John Stamatoyannopoulos, UW', '13')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('200-500', '7')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '22')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '8'), ('child', '3'), ('embryonic', '2'), ('newborn', '2'), ('third instar larva', '1'), ('unknown', '6')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('blood', '4'), ('blood vessel', '1'), ('bodily fluid', '4'), ('brain', '2'), ('connective tissue', '1'), ('embryo', '2'), ('epithelium', '2'), ('kidney', '2'), ('lung', '3'), ('lymph node', '1'), ('mammary gland', '2'), ('penis', '1'), ('prostate gland', '1'), ('skin of body', '2'), ('uterus', '1'), ('vasculature', '1'), ('vein', '1')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Drosophila melanogaster', '2'), ('Homo sapiens', '20')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '20'), ('modENCODE', '2')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '2'), ('ENCODE2', '11'), ('ENCODE3', '7'), ('modENCODE', '2')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('100', '1'), ('27', '3'), ('36', '13'), ('49', '1'), ('50', '6')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('released', '22')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('nucleotide modification', '2')]\u001b[0m\n",
      "\n",
      "------------------------------- PublicationData --------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=PublicationData\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('CAGE', '1'), ('ChIA-PET', '2'), ('RNA-seq', '2'), ('Repli-chip', '1'), ('shRNA knockdown followed by RNA-seq', '1')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '6'), ('in vitro differentiated cells', '2'), ('primary cell', '2'), ('stem cell', '2'), ('tissue', '2'), ('whole organisms', '2')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2014', '1'), ('August, 2014', '1'), ('February, 2016', '3'), ('May, 2015', '1'), ('September, 2017', '1')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '2')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Brenton Graveley, UConn', '1'), ('David Gilbert, FSU', '1'), ('Mark Gerstein, Yale', '1'), ('Michael Snyder, Stanford', '2'), ('Susan Celniker, LBNL', '2')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '3'), ('artery', '1'), ('blood', '5'), ('blood vessel', '1'), ('bodily fluid', '5'), ('bone element', '1'), ('bone marrow', '1'), ('brain', '1'), ('connective tissue', '4'), ('embryo', '3'), ('epithelium', '4'), ('extraembryonic component', '1'), ('gonad', '2'), ('limb', '2'), ('liver', '2'), ('lung', '1'), ('mammary gland', '1'), ('mouth', '1'), ('musculature of body', '2'), ('ovary', '2'), ('penis', '1'), ('placenta', '1'), ('skin of body', '1'), ('testis', '2'), ('uterus', '1'), ('vasculature', '1'), ('vein', '1')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Drosophila melanogaster', '2'), ('Drosophila pseudoobscura', '1'), ('Homo sapiens', '5')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '5'), ('modENCODE', '2')]\u001b[0m\n",
      "PUBLICATION DATA STATUS\n",
      "     \u001b[33mprod: [('released', '7')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE', '1'), ('ENCODE3', '4'), ('modENCODE', '2')]\u001b[0m\n",
      "\n",
      "---------------------------------- MatchedSet ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=MatchedSet\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ChIP-seq', '2'), ('DNase-seq', '3')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '5'), ('bed bed3+', '3'), ('bed broadPeak', '3'), ('bed narrowPeak', '3'), ('bigBed broadPeak', '3'), ('bigBed narrowPeak', '3'), ('bigWig', '3'), ('fastq', '5')]\u001b[0m\n",
      "BIOSAMPLE TERM NAME\n",
      "     \u001b[33mprod: [('AG08395', '1'), ('AG08396', '1'), ('AG20443', '1'), ('HEK293', '2'), ('eye', '1'), ('tongue', '1')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '3'), ('tissue', '2')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2011', '1'), ('August, 2015', '2'), ('October, 2016', '2')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '3'), ('hg19', '3')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Gregory Crawford, Duke', '1'), ('J. Michael Cherry, Stanford', '2'), ('John Stamatoyannopoulos, UW', '2')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('450-650', '2')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '5')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '1'), ('embryonic', '4')]\u001b[0m\n",
      "MAPPED READ LENGTH\n",
      "     \u001b[33mprod: [('101', '2')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('eye', '1'), ('kidney', '2'), ('mouth', '1'), ('tongue', '1')]\u001b[0m\n",
      "ORGAN3\n",
      "     \u001b[33mprod: [('eye', '1'), ('kidney', '2'), ('mouth', '1'), ('tongue', '1')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '5')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '5')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE2', '1'), ('ENCODE3', '4')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('101', '2'), ('36', '3'), ('50', '1')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('released', '5')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('control', '2')]\u001b[0m\n",
      "\n",
      "------------------------- TreatmentConcentrationSeries -------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=TreatmentConcentrationSeries\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ChIP-seq', '1'), ('RNA-seq', '1')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '2'), ('bed broadPeak', '1'), ('bed narrowPeak', '1'), ('bigBed broadPeak', '1'), ('bigBed narrowPeak', '1'), ('bigWig', '2'), ('fastq', '2'), ('gtf', '1'), ('tsv', '1')]\u001b[0m\n",
      "BIOSAMPLE TREATMENT\n",
      "     \u001b[33mprod: [('dexamethasone', '2')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('December, 2015', '2')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '2'), ('hg19', '2')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Richard Myers, HAIB', '2')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('>200', '1')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '1'), ('polyadenylated mRNA', '1')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '2')]\u001b[0m\n",
      "MAPPED READ LENGTH\n",
      "     \u001b[33mprod: [('36', '1')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('lung', '2')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '2')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '2')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE2', '2')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('36', '2'), ('76', '1')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('released', '2')]\u001b[0m\n",
      "TARGET\n",
      "     \u001b[33mprod: [('NR3C1', '1')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('transcription factor', '1')]\u001b[0m\n",
      "\n",
      "----------------------------- TreatmentTimeSeries ------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=TreatmentTimeSeries\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ATAC-seq', '2'), ('CRISPR genome editing followed by RNA-seq', '1'), ('ChIP-seq', '26'), ('DNase-seq', '1'), ('HiC', '2'), ('PAS-seq', '1'), ('RAMPAGE', '1'), ('RNA-seq', '3')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '35'), ('bed broadPeak', '1'), ('bed idr_peak', '1'), ('bed narrowPeak', '22'), ('bed tss_peak', '1'), ('bedpe', '2'), ('bigBed broadPeak', '1'), ('bigBed idr_peak', '1'), ('bigBed narrowPeak', '21'), ('bigBed tss_peak', '1'), ('bigWig', '29'), ('fastq', '37'), ('gff gff3', '1'), ('hic', '2'), ('tsv', '8')]\u001b[0m\n",
      "BIOSAMPLE TREATMENT\n",
      "     \u001b[33mprod: [('afimoxifene', '1'), ('calcium', '11'), ('dexamethasone', '24')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '26'), ('primary cell', '11')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2018', '11'), ('December, 2015', '1'), ('December, 2016', '1'), ('January, 2017', '4'), ('July, 2016', '2'), ('March, 2016', '1'), ('March, 2018', '3'), ('May, 2016', '2'), ('May, 2018', '1'), ('November, 2016', '11')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '30'), ('hg19', '6')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Brenton Graveley, UConn', '1'), ('Kevin Struhl, HMS', '1'), ('Michael Snyder, Stanford', '9'), ('Paul Khavari, Stanford', '1'), ('Tim Reddy, Duke', '24'), ('Will Greenleaf, Stanford', '1')]\u001b[0m\n",
      "LIBRARY DEPLETED IN\n",
      "     \u001b[33mprod: [('rRNA', '1')]\u001b[0m\n",
      "LIBRARY INSERT SIZE (NT)\n",
      "     \u001b[33mprod: [('150-1000', '1'), ('300-1000', '1'), ('>200', '26')]\u001b[0m\n",
      "LIBRARY MADE FROM\n",
      "     \u001b[33mprod: [('DNA', '31'), ('RNA', '3'), ('polyadenylated mRNA', '3')]\u001b[0m\n",
      "LIFE STAGE\n",
      "     \u001b[33mprod: [('adult', '26'), ('newborn', '11')]\u001b[0m\n",
      "MAPPED READ LENGTH\n",
      "     \u001b[33mprod: [('101', '6'), ('36', '1')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('blood', '1'), ('bodily fluid', '1'), ('epithelium', '11'), ('lung', '24'), ('mammary gland', '1'), ('penis', '11'), ('skin of body', '11')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '37')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '2'), ('GGR', '35')]\u001b[0m\n",
      "RFA\n",
      "     \u001b[33mprod: [('ENCODE2', '1'), ('ENCODE3', '1'), ('GGR', '35')]\u001b[0m\n",
      "READ LENGTH\n",
      "     \u001b[33mprod: [('100', '1'), ('101', '10'), ('151', '2'), ('36', '1'), ('50', '1'), ('51', '22'), ('76', '1')]\u001b[0m\n",
      "SERIES STATUS\n",
      "     \u001b[33mprod: [('released', '37')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '3'), ('broad histone mark', '4'), ('control', '7'), ('histone', '8'), ('narrow histone mark', '4'), ('transcription factor', '13')]\u001b[0m\n",
      "\n",
      "------------------------------------ Target ------------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Target\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Aequorea victoria', '2'), ('Caenorhabditis elegans', '1968'), ('Discosoma striata', '1'), ('Drosophila melanogaster', '1595'), ('Homo sapiens', '5935'), ('Mus musculus', '75'), ('enterobacteria phage t7', '1'), ('influenzavirus', '1'), ('synthetic', '2')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '1126'), ('broad histone mark', '28'), ('chromatin remodeller', '80'), ('control', '183'), ('histone', '101'), ('narrow histone mark', '17'), ('nucleotide modification', '4'), ('other context', '8'), ('other post-translational modification', '6'), ('recombinant protein', '4303'), ('tag', '10'), ('transcription factor', '8236')]\u001b[0m\n",
      "\n",
      "----------------------------------- Pipeline -----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Pipeline\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [('ATAC-seq', '5'), ('CAGE', '1'), ('CRISPR genome editing followed by RNA-seq', '2'), ('CRISPRi followed by RNA-seq', '1'), ('ChIP-seq', '12'), ('DNase-seq', '7'), ('HiC', '1'), ('PAS-seq', '1'), ('RAMPAGE', '1'), ('RIP-seq', '1'), ('RNA-seq', '5'), ('Repli-seq', '1'), ('eCLIP', '1'), ('genetic modification followed by DNase-seq', '4'), ('genotyping by high throughput sequencing assay', '3'), ('microRNA counts', '1'), ('microRNA-seq', '2'), ('shRNA knockdown followed by RNA-seq', '2'), ('siRNA knockdown followed by RNA-seq', '1'), ('single cell isolation followed by RNA-seq', '1'), ('whole-genome shotgun bisulfite sequencing', '3')]\u001b[0m\n",
      "DEVELOPED BY\n",
      "     \u001b[33mprod: [('Ali Mortazavi, UCI', '2'), ('Brenton Graveley, UConn', '1'), ('Christina Leslie, MSKCC', '2'), ('David Gilbert, FSU', '1'), ('ENCODE Consortium Analysis Working Group', '2'), ('ENCODE Processing Pipeline', '18'), ('Erez Lieberman-Aiden, Baylor', '1'), ('Gene Yeo, UCSD', '1'), ('John Rinn, Broad', '1'), ('John Stamatoyannopoulos, UW', '1'), ('Kevin White, UChicago', '1'), ('Manuel Garber, UMass', '1'), ('Ross Hardison, PennState', '1'), ('Thomas Gingeras, CSHL', '3'), ('Tim Reddy, Duke', '4'), ('Zhiping Weng, UMass', '3')]\u001b[0m\n",
      "PIPELINE GROUPS\n",
      "     \u001b[33mprod: [('Candidate Regulatory Elements (cREs)', '1'), ('ChIP-seq read mapping', '1'), ('DNase-HS pipeline (paired-end)', '1'), ('DNase-HS pipeline (single-end)', '1'), ('DNase-HS pipeline paired-end - Version 2', '1'), ('DNase-HS pipeline single-end - Version 2', '1'), ('DNase-seq pipeline', '1'), ('DNase-seq pipeline (Reddy GGR)', '1'), ('ENCODE Encyclopedia', '1'), ('GGR ATAC-seq pipeline VERSION CL.1', '1'), ('GGR ATAC-seq pipeline VERSION TR.1', '1'), ('GGR ChIP-seq pipeline VERSION CL.1', '1'), ('GGR ChIP-seq pipeline VERSION TR.1', '1'), ('GGR RNA-seq pipeline VERSION LG.1', '1'), ('Gilbert Repli-seq Pipeline', '1'), ('Graveley shRNA-seq', '1'), ('Hardison ATAC-seq pipeline', '1'), ('HiC pipeline VERSION TR.1', '1'), ('Histone ChIP-seq', '1'), ('Histone ChIP-seq (unreplicated)', '1'), ('Kundaje lab ATAC-seq pipeline', '1'), ('Kundaje lab ATAC-seq pipeline (single replicate)', '1'), ('Pool and subsample alignments', '1'), ('RAMPAGE or CAGE (paired-end)', '1'), ('RIP-seq pipeline', '1'), ('RNA-seq of long RNAs (paired-end, stranded)', '1'), ('RNA-seq of long RNAs (single-end, unstranded)', '1'), ('RNA-seq pipeline (Reddy GGR)', '1'), ('Raw mapping with no filtration', '1'), ('Schatz lab variant calling pipeline', '1'), ('Schatz lab variant calling pipeline for 10X libraries using Long Ranger 2.1.2: Version 2', '1'), ('Schatz lab variant calling pipeline for 10X libraries: Version 1', '1'), ('Small RNA-seq single-end pipeline', '1'), ('Transcription factor ChIP-seq', '1'), ('Transcription factor ChIP-seq (unreplicated)', '1'), ('Transcription factor ChIP-seq pipeline (modERN)', '1'), ('WGBS paired-end pipeline', '1'), ('WGBS single-end pipeline', '2'), ('Weng Lab ChromHMM', '1'), ('eCLIP pipeline', '1'), ('microRNA counts pipeline', '1'), ('microRNA-seq pipeline', '1')]\u001b[0m\n",
      "PIPELINE STATUS\n",
      "     \u001b[33mprod: [('archived', '4'), ('released', '39')]\u001b[0m\n",
      "SOFTWARE\n",
      "     \u001b[33mprod: [('ANNOVAR', '1'), ('ATAC-seq software tools', '1'), ('BEDOPS', '5'), ('BEDTools', '24'), ('BWA', '11'), ('Bismark', '3'), ('Bowtie', '6'), ('Bowtie 2', '11'), ('CLIPper', '1'), ('ChromHMM', '1'), ('Concat-fastq', '3'), ('CpG methylation correlation', '2'), ('Cufflinks', '1'), ('DNA-me pipeline', '3'), ('DNase Pipeline', '4'), ('F-seq', '1'), ('FastQC', '3'), ('GATK', '1'), ('GRIT', '1'), ('Genomic Alignments', '1'), ('HOMER', '1'), ('Hotspot', '3'), ('Irreproducible Discovery Rate (IDR)', '6'), ('Java', '1'), ('Juicebox', '1'), ('Juicer', '1'), ('LongRanger', '2'), ('MACS', '10'), ('MATS', '1'), ('Median Absolute Deviation', '4'), ('Mott Trimmer', '2'), ('NextGenMap', '1'), ('Peak Input Normalization Wrapper', '1'), ('Phantompeakqualtools', '11'), ('Picard', '12'), ('Preseq', '2'), ('Pysam', '1'), ('R', '1'), ('RNA pipelines', '4'), ('RSEM', '3'), ('SPP', '12'), ('STAR', '7'), ('Samtools', '22'), ('Scalpel', '1'), ('SeparateReadpairs', '1'), ('StamPipes', '2'), ('Subread', '1'), ('TopHat', '5'), ('Tophat BAM Repair', '2'), ('Trim Galore', '1'), ('Trimmomatic', '5'), ('WGBS output processor', '3'), ('barcode_collapse_pe.py', '1'), ('bedGraphToBigWig', '13'), ('bedToBigBed', '22'), ('bigWigAverageOverBed', '1'), ('bigWigToWig', '4'), ('caTools', '4'), ('chromCor.Rscript', '4'), ('cutadapt', '6'), ('deepTools', '2'), ('dme-align-pe', '1'), ('dme-align-se-parallel', '2'), ('dme-bg-to-signal', '2'), ('dme-cx-to-bed', '2'), ('dme-extract-pe', '1'), ('dme-extract-se', '1'), ('dme-index-bismark', '2'), ('dme-index-bismark-bowtie2', '1'), ('dme-rep-corr', '2'), ('dnase-align-bwa-pe', '2'), ('dnase-align-bwa-se', '2'), ('dnase-call-hotspots', '4'), ('dnase-density', '2'), ('dnase-eval-bam', '2'), ('dnase-filter-pe', '2'), ('dnase-filter-se', '2'), ('dnase-index-bwa', '4'), ('dnase-qc-bam', '2'), ('dnase-rep-corr', '4'), ('edwBamFilter', '4'), ('edwBamStats', '4'), ('hictools', '1'), ('hotspot2', '4'), ('lrna-align-star-pe', '1'), ('lrna-align-star-se', '1'), ('lrna-align-tophat-pe', '1'), ('lrna-align-tophat-se', '1'), ('lrna-index-rsem', '2'), ('lrna-index-star', '3'), ('lrna-index-tophat', '2'), ('lrna-mad-qc', '2'), ('lrna-quantification', '2'), ('lrna-signals', '2'), ('lrna-signals-stranded', '1'), ('lrna-signals-unstranded', '1'), ('make_bigwig_files.py', '1'), ('makewigglefromBAM-NH', '1'), ('modwt', '4'), ('nanostringToBed', '1'), ('nsolver', '1'), ('overlap_peaks.py', '4'), ('rampage-align', '1'), ('rampage-idr', '1'), ('rampage-mad-qc', '1'), ('rampage-peaks', '1'), ('rampage-signals', '1'), ('rtracklayer', '1'), ('snow', '4'), ('srna-align', '1'), ('srna-index-star', '1'), ('srna-mad-qc', '1'), ('srna-signals', '1'), ('trim-adapters-illumina', '2'), ('vcf2diploid', '1'), ('wigToBigWig', '2'), ('windowTrimmer', '1')]\u001b[0m\n",
      "\n",
      "--------------------------------- Publication ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Publication\u001b[0m\n",
      "AVAILABLE SUPPLEMENTAL DATA\n",
      "     \u001b[33mprod: [('HMM regions', '4'), ('HOT regions', '2'), ('RNA annotations', '1'), ('connectivity', '8'), ('enhancer annotations', '3'), ('genomic annotations', '2'), ('motifs', '2'), ('peak calls', '3'), ('promoter regions', '2'), ('website', '1')]\u001b[0m\n",
      "CATEGORY\n",
      "     \u001b[33mprod: [('basic biology', '833'), ('data standard', '6'), ('database', '4'), ('genomic annotations', '3'), ('human disease', '722'), ('model organism biology', '172'), ('pilot phase publication', '141'), ('production', '560'), ('software tool', '303'), ('technology development', '167')]\u001b[0m\n",
      "HAS DATASET\n",
      "     \u001b[33mprod: [('no', '3198'), ('yes', '6')]\u001b[0m\n",
      "JOURNAL\n",
      "     \u001b[33mprod: [('Aging Cell', '2'), ('Aging cell', '2'), ('Algorithms for molecular biology : AMB', '2'), ('American Journal of Human Genetics', '7'), ('American Journal of Pathology', '2'), ('American Journal of Respiratory and Critical Care Medicine', '2'), ('American journal of hematology', '2'), ('American journal of human genetics', '28'), ('American journal of respiratory and critical care medicine', '2'), ('Annals of the rheumatic diseases', '2'), ('Annual review of biochemistry', '2'), ('Antimicrobial Agents and Chemotherapy', '2'), ('Arthritis & rheumatology (Hoboken, N.J.)', '3'), ('Arthritis research & therapy', '3'), ('Atherosclerosis', '3'), ('BMC Bioinformatics', '9'), ('BMC Genetics', '2'), ('BMC Genomics', '10'), ('BMC bioinformatics', '40'), ('BMC biology', '4'), ('BMC cancer', '3'), ('BMC developmental biology', '2'), ('BMC evolutionary biology', '6'), ('BMC genetics', '6'), ('BMC genomics', '94'), ('BMC medical genetics', '8'), ('BMC medical genomics', '8'), ('BMC systems biology', '6'), ('BioEssays : news and reviews in molecular, cellular and developmental biology', '2'), ('BioMed research international', '6'), ('BioTechniques', '2'), ('Biochimica et biophysica acta', '2'), ('Bioinformatics', '9'), ('Bioinformatics (Oxford, England)', '91'), ('Biology direct', '2'), ('Biology of reproduction', '2'), ('Biostatistics (Oxford, England)', '2'), ('Blood', '21'), ('Brain : a journal of neurology', '2'), ('Breast cancer research : BCR', '3'), ('Briefings in bioinformatics', '6'), ('Cancer', '4'), ('Cancer Genetics and Cytogenetics', '3'), ('Cancer Research', '19'), ('Cancer cell', '2'), ('Cancer discovery', '2'), ('Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology', '5'), ('Cancer informatics', '3'), ('Cancers', '3'), ('Carcinogenesis', '9'), ('Cell', '76'), ('Cell Death and Differentiation', '2'), ('Cell Reports', '5'), ('Cell Stem Cell', '4'), ('Cell cycle (Georgetown, Tex.)', '5'), ('Cell death and differentiation', '2'), ('Cell metabolism', '3'), ('Cell reports', '19'), ('Cell research', '4'), ('Cell stem cell', '10'), ('Circulation', '4'), ('Circulation research', '3'), ('Circulation. 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Pacific Symposium on Biocomputing', '3'), ('PloS one', '196'), ('Proceedings of the National Academy of Sciences of the United States of America', '91'), ('Proteomics', '3'), ('RNA (New York, N.Y.)', '16'), ('RNA biology', '3'), ('Retrovirology', '5'), ('Schizophrenia bulletin', '3'), ('Science', '5'), ('Science (New York, N.Y.)', '51'), ('Scientific Reports', '12'), ('Scientific reports', '35'), ('Stem cell reports', '3'), ('Stem cells and development', '3'), ('The EMBO journal', '14'), ('The Journal of allergy and clinical immunology', '4'), ('The Journal of biological chemistry', '14'), ('The Journal of clinical investigation', '8'), ('The Journal of experimental medicine', '4'), ('The Journal of neuroscience : the official journal of the Society for Neuroscience', '3'), ('Trends in genetics : TIG', '3'), ('eLIFE', '6'), ('eLife', '15')]\u001b[0m\n",
      "PUBLICATION STATUS\n",
      "     \u001b[33mprod: [('released', '3204')]\u001b[0m\n",
      "PUBLICATION YEAR\n",
      "     \u001b[33mprod: [('1967', '1'), ('1972', '1'), ('1973', '3'), ('1974', '2'), ('1975', '1'), ('1976', '3'), ('1977', '4'), ('1978', '3'), ('1979', '4'), ('1981', '4'), ('1982', '2'), ('1983', '1'), ('1985', '2'), ('1986', '1'), ('1987', '2'), ('1988', '1'), ('1989', '3'), ('1990', '3'), ('1991', '3'), ('1992', '4'), ('1993', '4'), ('1995', '2'), ('1996', '1'), ('1997', '4'), ('1998', '3'), ('1999', '4'), ('2000', '6'), ('2001', '4'), ('2002', '13'), ('2003', '5'), ('2004', '23'), ('2005', '28'), ('2006', '53'), ('2007', '79'), ('2008', '72'), ('2009', '91'), ('2010', '137'), ('2011', '241'), ('2012', '308'), ('2013', '488'), ('2014', '568'), ('2015', '562'), ('2016', '89'), ('2017', '2')]\u001b[0m\n",
      "PUBLISHED BY\n",
      "     \u001b[33mprod: [('ENCODE', '971'), ('community', '1949'), ('historical reference', '101'), ('modENCODE', '176'), ('mouseENCODE', '42')]\u001b[0m\n",
      "\n",
      "----------------------------------- Software -----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/search/?type=Software\u001b[0m\n",
      "CREATED BY\n",
      "     \u001b[33mprod: [('ENCODE', '39'), ('community', '21'), ('historical reference', '4'), ('modENCODE', '3'), ('mouseENCODE', '1')]\u001b[0m\n",
      "PURPOSE IN PROJECT\n",
      "     \u001b[33mprod: [('ChIP-seq', '14'), ('DNase-seq', '23'), ('HiC', '1'), ('RNA-seq', '37'), ('community resource', '16'), ('data QC', '8'), ('integrative analysis', '7'), ('variant analysis', '8')]\u001b[0m\n",
      "SOFTWARE TYPE\n",
      "     \u001b[33mprod: [('aligner', '14'), ('database', '7'), ('file format conversion', '14'), ('filtering', '9'), ('genome segmentation', '4'), ('other', '19'), ('peak caller', '13'), ('quality metric', '17'), ('transcript identification', '5'), ('transcriptome assembly', '1'), ('variant annotation', '8')]\u001b[0m\n",
      "\n",
      "---------------------------------- Experiment ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/matrix/?type=Experiment\u001b[0m\n",
      "ASSAY\n",
      "     \u001b[33mprod: [(\"5' RLM RACE\", '2'), ('5C', '13'), ('ATAC-seq', '180'), ('CAGE', '121'), ('CRISPR RNA-seq', '50'), ('CRISPRi RNA-seq', '77'), ('ChIA-PET', '62'), ('ChIP-seq', '8911'), ('Circulome-seq', '1'), ('DNA-PET', '6'), ('DNAme array', '259'), ('DNase-seq', '873'), ('FAIRE-seq', '37'), ('Hi-C', '36'), ('MNase-seq', '2'), ('MRE-seq', '68'), ('MS-MS', '14'), ('MeDIP-seq', '55'), ('PAS-seq', '47'), ('RAMPAGE', '168'), ('RIP-chip', '32'), ('RIP-seq', '73'), ('RNA Bind-n-Seq', '161'), ('RNA microarray', '291'), ('RNA-PET', '31'), ('RRBS', '218'), ('Repli-chip', '63'), ('Repli-seq', '119'), ('Switchgear', '2'), ('TAB-seq', '8'), ('WGBS', '258'), ('eCLIP', '359'), ('genetic modification DNase-seq', '40'), ('genotyping HTS', '16'), ('genotyping array', '142'), ('iCLIP', '7'), ('microRNA counts', '115'), ('microRNA-seq', '185'), ('polyA RNA-seq', '817'), ('polyA depleted RNA-seq', '32'), ('shRNA RNA-seq', '533'), ('siRNA RNA-seq', '113'), ('single cell RNA-seq', '120'), ('small RNA-seq', '216'), ('total RNA-seq', '413'), ('whole genome sequencing assay', '21')]\u001b[0m\n",
      "ASSAY CATEGORY\n",
      "     \u001b[33mprod: [('3D chromatin structure', '111'), ('DNA accessibility', '1132'), ('DNA binding', '8911'), ('DNA methylation', '866'), ('DNA sequencing', '22'), ('Genotyping', '164'), ('Proteomics', '14'), ('RNA binding', '634'), ('Replication timing', '182'), ('Transcription', '3331')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('control extremely low read depth', '24'), ('extremely low coverage', '7'), ('extremely low read depth', '221'), ('extremely low read length', '10'), ('extremely low spot score', '49'), ('inconsistent control', '3'), ('inconsistent library biosample', '1'), ('inconsistent read count', '2'), ('missing antibody', '75'), ('missing control alignments', '418'), ('missing donor', '1'), ('missing nih_institutional_certification', '33'), ('missing possible_controls', '2')]\u001b[0m\n",
      "AUDIT CATEGORY2\n",
      "     \u001b[33mprod: [('antibody not characterized to standard', '25'), ('control insufficient read depth', '952'), ('insufficient coverage', '4'), ('insufficient read depth', '1757'), ('insufficient read length', '511'), ('insufficient replicate concordance', '48'), ('missing RNA fragment size', '2'), ('missing controlled_by', '596'), ('missing documents', '30'), ('missing input control', '2'), ('missing possible_controls', '27'), ('missing spikeins', '173'), ('partially characterized antibody', '139'), ('poor library complexity', '283'), ('severe bottlenecking', '271'), ('uncharacterized antibody', '11'), ('unreplicated experiment', '341')]\u001b[0m\n",
      "AUDIT CATEGORY3\n",
      "     \u001b[33mprod: [('antibody characterized with exemption', '676'), ('borderline replicate concordance', '455'), ('control low read depth', '659'), ('file validation error', '40'), ('high lambda C methylation ratio', '3'), ('inconsistent assembly', '18'), ('inconsistent control read length', '907'), ('inconsistent control run_type', '158'), ('inconsistent platforms', '1032'), ('inconsistent target of control experiment', '217'), ('low coverage', '4'), ('low read depth', '2545'), ('low read length', '3292'), ('low replicate concordance', '89'), ('low spot score', '321'), ('mild to moderate bottlenecking', '2873'), ('missing external identifiers', '330'), ('missing genetic modification characterization', '2307'), ('missing genotype', '116'), ('missing spikeins', '28'), ('mixed read lengths', '482'), ('mixed run types', '101'), ('moderate library complexity', '1280')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('CEL', '4'), ('bam', '12757'), ('bed bed12', '43'), ('bed bed3', '7'), ('bed bed3+', '869'), ('bed bed6+', '115'), ('bed bed9', '18'), ('bed bedExonScore', '27'), ('bed bedGraph', '30'), ('bed bedLogR', '64'), ('bed bedMethyl', '278'), ('bed bedRnaElements', '288'), ('bed broadPeak', '2451'), ('bed idr_peak', '134'), ('bed modPepMap', '6'), ('bed narrowPeak', '7324'), ('bed pepMap', '6'), ('bed peptideMapping', '8'), ('bed tss_peak', '235'), ('bedpe', '5'), ('bigBed bed12', '43'), ('bigBed bed3', '7'), ('bigBed bed3+', '13'), ('bigBed bed6+', '115'), ('bigBed bed9', '18'), ('bigBed bedExonScore', '27'), ('bigBed bedLogR', '63'), ('bigBed bedMethyl', '278'), ('bigBed bedRnaElements', '288'), ('bigBed broadPeak', '1992'), ('bigBed idr_peak', '134'), ('bigBed modPepMap', '6'), ('bigBed narrowPeak', '7313'), ('bigBed pepMap', '6'), ('bigBed peptideMapping', '8'), ('bigBed tss_peak', '235'), ('bigWig', '11714'), ('csfasta', '25'), ('csqual', '13'), ('fasta', '3'), ('fastq', '13745'), ('gff gff3', '235'), ('gtf', '269'), ('hdf5', '20'), ('hic', '5'), ('idat', '277'), ('rcc', '115'), ('sam', '59'), ('sra', '672'), ('tagAlign', '1368'), ('tar', '110'), ('tsv', '2470'), ('vcf', '13'), ('wig', '59')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '5779'), ('cell-free sample', '161'), ('in vitro differentiated cells', '679'), ('induced pluripotent stem cell line', '137'), ('primary cell', '1678'), ('stem cell', '506'), ('tissue', '4375'), ('whole organisms', '2052')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2011', '149'), ('April, 2012', '77'), ('April, 2013', '6'), ('April, 2014', '2'), ('April, 2015', '28'), ('April, 2016', '170'), ('April, 2017', '52'), ('April, 2018', '48'), ('August, 2011', '88'), ('August, 2012', '257'), ('August, 2015', '180'), ('August, 2016', '265'), ('August, 2017', '71'), ('December, 2010', '68'), ('December, 2011', '87'), ('December, 2014', '247'), ('December, 2015', '40'), ('December, 2016', '174'), ('December, 2017', '139'), ('February, 2011', '255'), ('February, 2012', '264'), ('February, 2013', '1'), ('February, 2014', '7'), ('February, 2015', '3'), ('February, 2016', '183'), ('February, 2017', '138'), ('February, 2018', '177'), ('January, 2011', '6'), ('January, 2012', '59'), ('January, 2015', '8'), ('January, 2016', '110'), ('January, 2017', '399'), ('January, 2018', '156'), ('July, 2009', '22'), ('July, 2011', '263'), ('July, 2012', '128'), ('July, 2013', '2761'), ('July, 2014', '300'), ('July, 2015', '103'), ('July, 2016', '614'), ('July, 2017', '39'), ('June, 2011', '83'), ('June, 2012', '75'), ('June, 2014', '432'), ('June, 2015', '106'), ('June, 2016', '221'), ('June, 2017', '272'), ('March, 2011', '160'), ('March, 2012', '170'), ('March, 2013', '1'), ('March, 2014', '887'), ('March, 2015', '2'), ('March, 2016', '291'), ('March, 2017', '96'), ('March, 2018', '134'), ('May, 2011', '35'), ('May, 2012', '138'), ('May, 2013', '2'), ('May, 2014', '8'), ('May, 2015', '12'), ('May, 2016', '569'), ('May, 2017', '66'), ('May, 2018', '15'), ('November, 2010', '9'), ('November, 2011', '76'), ('November, 2012', '7'), ('November, 2014', '98'), ('November, 2015', '225'), ('November, 2016', '400'), ('November, 2017', '428'), ('October, 2009', '4'), ('October, 2010', '1'), ('October, 2011', '456'), ('October, 2014', '86'), ('October, 2015', '106'), ('October, 2016', '485'), ('October, 2017', '200'), ('September, 2011', '134'), ('September, 2012', '190'), ('September, 2014', '41'), ('September, 2015', '17'), ('September, 2016', '209'), ('September, 2017', '115')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('GRCh38', '7315'), ('ce10', '838'), ('ce11', '897'), ('dm3', '835'), ('dm6', '811'), ('hg19', '7492'), ('mm10', '1508'), ('mm9', '338')]\u001b[0m\n",
      "LAB\n",
      "     \u001b[33mprod: [('Alexander Urban, Stanford', '3'), ('Ali Mortazavi, UCI', '231'), ('Andrew Z. Fire, Stanford', '4'), ('Barbara Wold, Caltech', '287'), ('Bing Ren, UCSD', '1379'), ('Bradley Bernstein, Broad', '1957'), ('Brenton Graveley, UConn', '789'), ('Brian Oliver, NIH', '27'), ('Chris Burge, MIT', '161'), ('Christina Leslie, MSKCC', '32'), ('David Gilbert, FSU', '77'), ('David MacAlpine, Duke', '39'), ('Eric Lécuyer, IRCM', '30'), ('Gene Yeo, UCSD', '366'), ('Gregory Crawford, Duke', '162'), ('Jason Lieb, UNC', '37'), ('Job Dekker, UMass', '26'), ('Joe Ecker, Salk', '193'), ('John Rinn, Broad', '35'), ('John Stamatoyannopoulos, UW', '1594'), ('Joseph Costello, UCSF', '595'), ('Kevin Struhl, HMS', '43'), ('Kevin White, UChicago', '1064'), ('Manuel Garber, UMass', '68'), ('Michael Snyder, Stanford', '2401'), ('Morgan Giddings, UNC', '14'), ('Paul Khavari, Stanford', '13'), ('Peggy Farnham, USC', '125'), ('Piero Carninci, RIKEN', '78'), ('Richard Myers, HAIB', '1423'), ('Ross Hardison, PennState', '128'), ('Scott Tenenbaum, SUNY-Albany', '42'), ('Sherman Weissman, Yale', '65'), ('Susan Celniker, LBNL', '239'), ('Terry Orr-Weaver, MIT', '2'), ('Thomas Gingeras, CSHL', '736'), ('Tim Reddy, Duke', '298'), ('Valerie Reinke, Yale', '361'), ('Vishwanath Iyer, UTA', '85'), ('Will Greenleaf, Stanford', '13'), ('Xiang-Dong Fu, UCSD', '97'), ('Yijun Ruan, JAX', '48')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '137'), ('adrenal gland', '105'), ('artery', '42'), ('blood', '2614'), ('blood vessel', '208'), ('bodily fluid', '2614'), ('bone element', '117'), ('bone marrow', '38'), ('brain', '937'), ('breast', '49'), ('bronchus', '20'), ('connective tissue', '571'), ('embryo', '984'), ('epithelium', '723'), ('esophagus', '117'), ('extraembryonic component', '203'), ('eye', '36'), ('gonad', '130'), ('heart', '340'), ('intestine', '559'), ('kidney', '571'), ('large intestine', '359'), ('limb', '356'), ('liver', '1184'), ('lung', '927'), ('lymph node', '169'), ('lymphatic vessel', '6'), ('lymphoid tissue', '41'), ('mammary gland', '427'), ('mouth', '25'), ('musculature of body', '553'), ('nerve', '39'), ('nose', '2'), ('ovary', '55'), ('pancreas', '146'), ('penis', '212'), ('pericardium', '4'), ('placenta', '65'), ('prostate gland', '118'), ('skeleton', '5'), ('skin of body', '565'), ('small intestine', '107'), ('spinal cord', '28'), ('spleen', '195'), ('stomach', '250'), ('testis', '69'), ('thymus', '53'), ('thyroid gland', '60'), ('tongue', '5'), ('trachea', '3'), ('ureter', '31'), ('urinary bladder', '21'), ('uterus', '230'), ('vagina', '29'), ('vasculature', '231'), ('vein', '69')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Caenorhabditis elegans', '975'), ('Drosophila ananassae', '1'), ('Drosophila melanogaster', '1435'), ('Drosophila mojavensis', '4'), ('Drosophila pseudoobscura', '12'), ('Drosophila simulans', '8'), ('Drosophila virilis', '1'), ('Drosophila yakuba', '1'), ('Homo sapiens', '10891'), ('Mus musculus', '1864')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '9701'), ('GGR', '461'), ('Roadmap', '2761'), ('community', '7'), ('modENCODE', '1330'), ('modERN', '1107')]\u001b[0m\n",
      "TARGET OF ASSAY\n",
      "     \u001b[33mprod: [('RNA binding protein', '1466'), ('broad histone mark', '1727'), ('chromatin remodeller', '254'), ('control', '2568'), ('histone', '3102'), ('narrow histone mark', '1265'), ('nucleotide modification', '70'), ('other context', '58'), ('other post-translational modification', '76'), ('recombinant protein', '1271'), ('tag', '1'), ('transcription factor', '3971')]\u001b[0m\n",
      "\n",
      "---------------------------------- Annotation ----------------------------------\n",
      "Comparing data between URLs.\n",
      "As user: Public\n",
      "Browser: Chrome\n",
      "First URL: https://www.encodeproject.org\n",
      "Second URL: https://v71rc1-master.demo.encodedcc.org/\n",
      "Item type: \u001b[1;32m/matrix/?type=Annotation\u001b[0m\n",
      "ANNOTATION TYPE\n",
      "     \u001b[33mprod: [('binding sites', '2'), ('blacklist', '3'), ('candidate regulatory elements', '2178'), ('chromatin state', '330'), ('enhancer predictions', '111'), ('gene expression', '14'), ('other', '3048'), ('overlap', '17'), ('representative DNase hypersensitivity sites', '6'), ('transcript expression', '14'), ('validated enhancers', '6')]\u001b[0m\n",
      "AUDIT CATEGORY\n",
      "     \u001b[33mprod: [('inconsistent assembly', '28')]\u001b[0m\n",
      "AVAILABLE DATA\n",
      "     \u001b[33mprod: [('bam', '3'), ('bed bed3', '4'), ('bed bed3+', '2164'), ('bed bed6', '2'), ('bed bed9', '91'), ('bed candidate enhancer predictions', '46'), ('bed enhancer predictions', '50'), ('bed enhancerAssay', '2'), ('bed narrowPeak', '2'), ('bed openChromCombinedPeaks', '17'), ('bigBed bed3+', '2154'), ('bigBed bed6', '2'), ('bigBed bed9', '218'), ('bigBed broadPeak', '1'), ('bigBed enhancerAssay', '2'), ('bigBed openChromCombinedPeaks', '17'), ('bigBed unknown', '9'), ('bigWig', '3049'), ('fasta', '1'), ('fastq', '20'), ('tsv', '39')]\u001b[0m\n",
      "BIOSAMPLE TYPE\n",
      "     \u001b[33mprod: [('cell line', '393'), ('in vitro differentiated cells', '124'), ('induced pluripotent stem cell line', '44'), ('primary cell', '603'), ('stem cell', '101'), ('tissue', '1362'), ('whole organisms', '6')]\u001b[0m\n",
      "DATE RELEASED\n",
      "     \u001b[33mprod: [('April, 2014', '3'), ('April, 2017', '3'), ('April, 2018', '3048'), ('August, 2015', '92'), ('August, 2016', '452'), ('August, 2017', '779'), ('December, 2011', '1'), ('February, 2012', '10'), ('February, 2015', '2'), ('July, 2013', '225'), ('July, 2016', '3'), ('June, 2011', '16'), ('June, 2015', '2'), ('June, 2016', '276'), ('March, 2014', '9'), ('March, 2016', '1'), ('November, 2016', '17'), ('October, 2011', '2'), ('October, 2015', '10'), ('September, 2012', '2'), ('September, 2014', '22'), ('September, 2015', '2'), ('September, 2017', '758')]\u001b[0m\n",
      "ENCYCLOPEDIA VERSION\n",
      "     \u001b[33mprod: [('1', '3'), ('2', '141'), ('3', '847'), ('4', '4587'), ('Blacklists', '2'), ('ENCODE2', '27'), ('ROADMAP', '127')]\u001b[0m\n",
      "GENOME ASSEMBLY (VISUALIZATION)\n",
      "     \u001b[33mprod: [('hg19', '4166'), ('mm10', '455'), ('mm9', '17')]\u001b[0m\n",
      "ORGAN\n",
      "     \u001b[33mprod: [('adipose tissue', '9'), ('adrenal gland', '21'), ('artery', '10'), ('blood', '228'), ('blood vessel', '52'), ('bodily fluid', '228'), ('bone element', '33'), ('bone marrow', '15'), ('brain', '331'), ('breast', '1'), ('bronchus', '8'), ('connective tissue', '200'), ('embryo', '217'), ('epithelium', '174'), ('esophagus', '17'), ('extraembryonic component', '52'), ('eye', '30'), ('gonad', '26'), ('heart', '109'), ('intestine', '156'), ('kidney', '123'), ('large intestine', '90'), ('limb', '108'), ('liver', '89'), ('lung', '162'), ('lymph node', '50'), ('lymphatic vessel', '2'), ('lymphoid tissue', '2'), ('mammary gland', '44'), ('mouth', '17'), ('musculature of body', '155'), ('ovary', '12'), ('pancreas', '33'), ('penis', '54'), ('placenta', '27'), ('prostate gland', '15'), ('skin of body', '129'), ('small intestine', '41'), ('spinal cord', '15'), ('spleen', '29'), ('stomach', '70'), ('testis', '13'), ('thymus', '34'), ('thyroid gland', '8'), ('tongue', '4'), ('ureter', '14'), ('urinary bladder', '2'), ('uterus', '22'), ('vagina', '3'), ('vasculature', '64'), ('vein', '15')]\u001b[0m\n",
      "ORGANISM\n",
      "     \u001b[33mprod: [('Homo sapiens', '4951'), ('Mus musculus', '784')]\u001b[0m\n",
      "PROJECT\n",
      "     \u001b[33mprod: [('ENCODE', '5510'), ('Roadmap', '225')]\u001b[0m\n",
      "TARGET(S) OF ASSAY\n",
      "     \u001b[33mprod: [('CTCF', '235'), ('H3K27ac', '684'), ('H3K4me1', '1'), ('H3K4me3', '860'), ('H3K9ac', '1')]\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "qa.compare_facets(users=['Public'], browsers=['Chrome'], browser_comparison=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#qa.compare_facets(users=['encoded.test4@gmail.com'], browsers=['Chrome'], item_types=['/search/?type=Experiment'], browser_comparison=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "#.find_differences(users=['encoded.test4@gmail.com'], browsers=['Safari'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.find_differences(users=['encoded.test4@gmail.com'], browsers=['Chrome'], item_types=['/experiments/ENCSR524OCB/'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.show_differences()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.check_downloads(browsers=['Safari'], users=['Public'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "#qa.check_trackhubs(browsers=['Safari'], users=['Public'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": true,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "#qa.check_permissions(browsers=['Chrome'], users=['Public'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": true,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "#qa.check_permissions(browsers=['Chrome'], users=['encoded.test@gmail.com'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.check_permissions(browsers=['Chrome'], users=['encoded.test2@gmail.com'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.check_permissions(browsers=['Chrome'], users=['encoded.test4@gmail.com'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.check_requests()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "#qa.check_tools()"
   ]
  }
 ],
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