{"lab": {"status": "current", "title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"center_title": "DCIC - DCIC", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "project": "4DN", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "name": "1U01CA200059-01", "status": "current", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators with a strong track record in analysis of chromatin interaction data, image processing and three-dimensional data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and flexible cloud technologies. In Aim 1, we will develop efficient submission pipelines for data and metadata from 4DN data production groups. We will define data/metadata requirements and quality metrics in conjunction with the production groups and ensure that high-quality, well- annotated data become available to the wider scientific community in a timely manner. In Aim 2, we will develop a user-friendly data portal for the broad scientific community. This portal will provide an easy-to-navigate interface for accessing raw and intermediate data files, allow for programmatic access via APIs, and will incorporate novel analysis and visualization tools developed by DCIC as well as other Network members. For computing and storage scalability and cost-effectiveness, significant efforts will be devoted to development and deployment of cloud-based technology. We will conduct tutorials and workshops to facilitate the use of 4DN data and tools by external investigators. In Aim 3, we will coordinate and assist in conducting integrative analysis of the multiple data types. These efforts will examine key questions in higher-order chromatin organization using both sequence and image data, and the tools and algorithms developed here will be incorporated into the data portal for use by other investigators. These three aims will ensure that the data generated in 4DN will have maximal impact for the scientific community.", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "cba5108810244771a023286982957324", "status": "released", "accession": "4DNFIZLIE6PG", "file_size": 713806917, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIZLIE6PG/@@download/4DNFIZLIE6PG.pairs.gz.px2", "uuid": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749", "md5sum": "40a3ea6f17f3f14736581d9033116113", "status": "released", "filename": "4DNFIZLIE6PG", "accession": "4DNFIZLIE6PG", "file_size": 13740187, "upload_key": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749/4DNFIZLIE6PG.pairs.gz.px2", "file_format": {"@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-11-27T15:23:13.201997+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-17T21:52:57.694177+00:00"}, "public_release": "2018-12-01", "quality_metric": {"@id": "/quality-metrics-pairsqc/740e9ac0-d236-439f-ac59-55ee6fd30029/", "Trans reads": 4334017, "uuid": "740e9ac0-d236-439f-ac59-55ee6fd30029", "Cis reads (>20kb)": 10310907, "Total reads": 51077861, "display_title": "QualityMetricPairsqc from 2018-11-28", "Short cis reads (<20kb)": 36432937, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZLIE6PG/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Filtered Reads", "value": "51077861", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "20.187", "tooltip": "Percent of filtered reads (=10.31m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "71.328", "tooltip": "Percent of filtered reads (=36.43m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "8.485", "tooltip": "Percent of filtered reads (=4.33m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2018-12-01", "contributing_labs": [{"uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "correspondence": [{"contact_email": "bGVvbmlkQG1pdC5lZHU=", "@id": "/users/f520d12a-e4c4-4774-a230-08d6dc4f5ef1/", "display_title": "Leonid Mirny"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}, {"uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/francois-spitz-lab/", "display_title": "Francois Spitz, PASTEUR", "correspondence": [{"contact_email": "ZnNwaXR6QHVjaGljYWdvLmVkdQ==", "@id": "/users/fbcf7895-3eba-4844-950f-855c02be74a2/", "display_title": "Francois Spitz"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}], "source_experiments": ["cbabaf13-d076-4ed0-83ed-b8b58e829b17"], "file_classification": "processed file", "@id": "/files-processed/4DNFIZLIE6PG/", "@type": ["FileProcessed", "File", "Item"], "uuid": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIZLIE6PG.pairs.gz", "external_references": [], "experiments": [{"uuid": "cbabaf13-d076-4ed0-83ed-b8b58e829b17", "@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEXGWOOI8I/", "status": "released", "display_title": "TCC on hepatocyte with HindIII - 4DNEXGWOOI8I", "accession": "4DNEXGWOOI8I", "biosample": {"display_title": "4DNBSA9YD494", "status": "released", "@id": "/biosamples/4DNBSA9YD494/", "biosource_summary": "hepatocyte", "@type": ["Biosample", "Item"], "uuid": "4083ce1d-3f80-4ed9-81a2-2ae05e047559", "accession": "4DNBSA9YD494", "treatments_summary": "Tamoxifen treatment (10.0 mg/mL, 5.0d)", "modifications_summary": "None", "biosource": [{"status": "released", "@id": "/biosources/4DNSRSRV279T/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "display_title": "hepatocyte - 4DNSRSRV279T", "biosource_type": "primary cell", "uuid": "54f6a5b4-3d38-44bd-96e5-e597c5ab1794", "cell_line": {"term_id": "CL:0000182", "status": "released", "uuid": "a1b0f241-64ca-47a4-b9b8-19c28b5bdedb", "@type": ["OntologyTerm", "Item"], "preferred_name": "hepatocyte", "display_title": "hepatocyte", "@id": "/ontology-terms/CL:0000182/", "term_name": "hepatocyte", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "@id": "/organisms/10090/", "name": "mouse", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"uuid": "111182bc-8535-4448-903e-854af460a233", "preferred_name": "liver", "term_name": "liver", "display_title": "liver", "@id": "/ontology-terms/UBERON:0002107/", "term_id": "UBERON:0002107", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "ca962708-d4c3-41e0-a042-e18a60a89467", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNIN864968B/", "display_title": "4DNIN864968B", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "digestion_enzyme": {"uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@id": "/enzymes/HindIII/", "display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "name": "HindIII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"title": "TCC", "status": "released", "uuid": "e95e3626-aadc-464b-9ef0-0cdbea689744", "@type": ["ExperimentType", "Item"], "display_title": "TCC", "@id": "/experiment-types/tcc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNESLUJ3INP/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESLUJ3INP", "display_title": "4DNESLUJ3INP", "status": "released", "uuid": "1357d675-11f6-4810-88e2-dbdaec41d800", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2019-04-24T16:48:55.428106+00:00"}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Francois Spitz, PASTEUR", "experiment_type": "TCC", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "TCC on hepatocytes +/- NIPBL", "condition": "TAM-treated control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIZLIE6PG", "href": "/files-processed/4DNFIZLIE6PG/@@download/4DNFIZLIE6PG.pairs.gz", "upload_key": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749/4DNFIZLIE6PG.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b1e36bb3-5c18-4745-8d1b-71e5e7d8c749/4DNFIZLIE6PG.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "115318c8-c185-4c97-becc-cc80a7f03f12", "display_title": "pairsqc-single 0.2.6 run 2018-11-28 20:02:30.550111", "status": "released", "@id": "/workflow-runs-awsem/115318c8-c185-4c97-becc-cc80a7f03f12/", "output_files": [{"workflow_argument_name": "report", "value_qc": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/740e9ac0-d236-439f-ac59-55ee6fd30029/", "display_title": "QualityMetricPairsqc from 2018-11-28", "uuid": "740e9ac0-d236-439f-ac59-55ee6fd30029", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZLIE6PG/pairsqc_report.html", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "PairsQC 0.2.6", "@id": "/workflows/4DNWFHB26CID/", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"accession": "4DNFI3UBJ3HZ", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIZLIE6PG", "uuid": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749", "@id": "/files-processed/4DNFIZLIE6PG/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIZLIE6PG.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "374f0522-7f62-4e18-9db7-489725d0b5a6", "display_title": "hi-c-processing-pairs 0.2.6 run 2018-11-28 20:56:14.271066", "status": "released", "@id": "/workflow-runs-awsem/374f0522-7f62-4e18-9db7-489725d0b5a6/", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"accession": "4DNFI6ZBEODU", "display_title": "4DNFI6ZBEODU.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI6ZBEODU/", "uuid": "f4b3b9e4-54c2-41e5-b229-311cdf12596a", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"accession": "4DNFIQY5K7ES", "display_title": "4DNFIQY5K7ES.hic", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIQY5K7ES/", "uuid": "e938527f-abf3-499c-aa54-0c7455f7db55", "file_format": {"display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "hic", "status": "released", "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"accession": "4DNFIAOYIWTK", "display_title": "4DNFIAOYIWTK.mcool", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIAOYIWTK/", "uuid": "672bb8af-ed44-4f94-9241-824d7557fbd8", "file_format": {"display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "mcool", "status": "released", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "cooler_normvector", "value": {"accession": "4DNFI3IYQXYT", "display_title": "4DNFI3IYQXYT.normvector.juicerformat.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI3IYQXYT/", "uuid": "a1e0fe4d-18fd-4e33-844d-2cab057bc836", "file_format": {"display_title": "normvector_juicerformat", "uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "@type": ["FileFormat", "Item"], "file_format": "normvector_juicerformat", "status": "released", "@id": "/file-formats/normvector_juicerformat/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6", "@id": "/workflows/4DNWFTKI1QLK/", "uuid": "c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6 - 4DNWFTKI1QLK", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"accession": "4DNFI3UBJ3HZ", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIZLIE6PG", "uuid": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749", "@id": "/files-processed/4DNFIZLIE6PG/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIZLIE6PG.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIU7JQQZ1", "uuid": "da2a34db-f480-4069-b1f0-b115ecb19e82", "@id": "/files-processed/4DNFIU7JQQZ1/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIU7JQQZ1.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"accession": "4DNFI6V32T9J", "uuid": "8e29e9ae-f13c-4a7b-9236-dba35a69bbff", "@id": "/files-reference/4DNFI6V32T9J/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "MM10_HindIII.txt", "display_title": "4DNFI6V32T9J.txt", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/juicer_format_restriction_site_file/", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"@id": "/workflow-runs-awsem/805f4fd8-6c5c-45a8-b5b3-2fe035456afc/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "hi-c-processing-bam 0.2.6 run 2018-11-27 15:23:13.388577", "uuid": "805f4fd8-6c5c-45a8-b5b3-2fe035456afc", "status": "released", "workflow": {"@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "@id": "/workflows/4DNWFT69RBY4/", "title": "Hi-C Post-alignment Processing 0.2.6", "status": "released", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsize", "value": {"filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "status": "released", "@id": "/files-reference/4DNFI3UBJ3HZ/", "accession": "4DNFI3UBJ3HZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "@id": "/file-formats/chromsizes/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "6b86665b-fec6-44f3-8a41-4e52d2c10636", "display_title": "4DNFIQB88C7X.bam", "status": "released", "@id": "/files-processed/4DNFIQB88C7X/", "accession": "4DNFIQB88C7X", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "692baace-a75e-40ae-88a1-ad86cc9944f8", "display_title": "4DNFI1NU7N8E.bam", "status": "released", "@id": "/files-processed/4DNFI1NU7N8E/", "accession": "4DNFI1NU7N8E", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "bab1f227-7ec3-4c55-81cb-f9523a88d27d", "display_title": "4DNFI3W5WENE.bam", "status": "released", "@id": "/files-processed/4DNFI3W5WENE/", "accession": "4DNFI3W5WENE", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "3e0d39b2-4f0f-42cd-a4a4-94e1df183622", "display_title": "4DNFIK71ZQQG.bam", "status": "released", "@id": "/files-processed/4DNFIK71ZQQG/", "accession": "4DNFIK71ZQQG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "11beff30-690d-4eea-840e-2f80d3970baf", "display_title": "4DNFIPHUSN6Y.bam", "status": "released", "@id": "/files-processed/4DNFIPHUSN6Y/", "accession": "4DNFIPHUSN6Y", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "5c4777a3-28b1-4add-bdd8-bd838efc125e", "display_title": "4DNFIYMWQHTH.bam", "status": "released", "@id": "/files-processed/4DNFIYMWQHTH/", "accession": "4DNFIYMWQHTH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "6c6255ac-5159-463c-b19c-5d4e950a4ed2", "display_title": "4DNFITV5JWSJ.bam", "status": "released", "@id": "/files-processed/4DNFITV5JWSJ/", "accession": "4DNFITV5JWSJ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "a039e1b2-63bd-441b-a2f6-a1b3cfb4c3e2", "display_title": "4DNFIX21V21R.bam", "status": "released", "@id": "/files-processed/4DNFIX21V21R/", "accession": "4DNFIX21V21R", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIB6YAL6D/", "accession": "4DNFIB6YAL6D", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIB6YAL6D.bam", "uuid": "1b26f967-752d-4f26-964c-2a68b05bdb20", "status": "released", "file_format": {"file_format": "bam", "status": "released", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "filtered_pairs", "value": {"@id": "/files-processed/4DNFIZLIE6PG/", "accession": "4DNFIZLIE6PG", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIZLIE6PG.pairs.gz", "uuid": "b1e36bb3-5c18-4745-8d1b-71e5e7d8c749", "status": "released", "file_format": {"file_format": "pairs", "status": "released", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "pairsqc_table": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIZLIE6PG/4DNFIZLIE6PG.plot_table.out", "source_experiment_sets": [{"uuid": "1357d675-11f6-4810-88e2-dbdaec41d800", "display_title": "4DNESLUJ3INP", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESLUJ3INP/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXGWOOI8I/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2019-04-24T16:48:55.428106+00:00"}}, {"parent": "/files-processed/4DNFIZLIE6PG/", "embedded_path": "last_modified", "item": {"date_modified": "2021-05-17T21:52:57.694177+00:00"}}]}, "validation-errors": []}