{"lab": {"@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"project": "4DN", "@type": ["Award", "Item"], "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.", "status": "current", "center_title": "DCIC - DCIC", "name": "1U01CA200059-01", "@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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": "927e4a23fbf569df68c4c94c35df7c6c", "status": "released", "aliases": [], "accession": "4DNFIKFV5Y88", "file_size": 1167154731, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIKFV5Y88/@@download/4DNFIKFV5Y88.pairs.gz.px2", "uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "md5sum": "a8cfd47a6ed340a9e86257dec4609298", "status": "released", "filename": "4DNFIKFV5Y88", "accession": "4DNFIKFV5Y88", "file_size": 23465509, "upload_key": "1d5b9ec9-3829-49a2-9576-f4299166c938/4DNFIKFV5Y88.pairs.gz.px2", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "display_title": "pairs_px2", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content_md5sum": "a8cfd47a6ed340a9e86257dec4609298"}], "file_format": {"file_format": "pairs", "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-02-23T21:55:34.626330+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-11T15:57:06.005042+00:00"}, "content_md5sum": "fd5dc1892f1a405f4166f37675700988", "public_release": "2018-03-23", "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "ebedfb6a-9352-4ddd-824b-02ccf8c22952", "Short cis reads (<20kb)": 6200586, "Cis reads (>20kb)": 30335282, "display_title": "QualityMetricPairsqc from 2018-03-05", "@id": "/quality-metrics-pairsqc/ebedfb6a-9352-4ddd-824b-02ccf8c22952/", "status": "released", "Trans reads": 18895416, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKFV5Y88/pairsqc_report.html", "Total reads": 55431284, "quality_metric_summary": [{"title": "Filtered Reads", "value": "55431284", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "54.726", "tooltip": "Percent of filtered reads (=30.34m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "11.186", "tooltip": "Percent of filtered reads (=6.2m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "34.088", "tooltip": "Percent of filtered reads (=18.9m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2018-03-23", "contributing_labs": [{"status": "current", "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "@id": "/labs/erez-liebermanaiden-lab/", "display_title": "Erez Lieberman Aiden, BCM", "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}, "pi": {"error": "no view permissions"}}], "source_experiments": ["80811dbf-3bbd-4c0a-aa45-8781c11ac68b"], "file_classification": "processed file", "@id": "/files-processed/4DNFIKFV5Y88/", "@type": ["FileProcessed", "File", "Item"], "uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIKFV5Y88.pairs.gz", "external_references": [], "experiments": [{"uuid": "80811dbf-3bbd-4c0a-aa45-8781c11ac68b", "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXC7SDGS9", "status": "released", "@id": "/experiments-hi-c/4DNEXC7SDGS9/", "display_title": "in situ Hi-C on K562 with MboI - 4DNEXC7SDGS9", "biosample": {"status": "released", "@id": "/biosamples/4DNBS5UORKBT/", "@type": ["Biosample", "Item"], "uuid": "921327ac-cc80-46b9-a05f-3c2c41a17f81", "treatments_summary": "None", "display_title": "4DNBS5UORKBT", "accession": "4DNBS5UORKBT", "modifications_summary": "None", "biosource_summary": "K562", "biosource": [{"status": "released", "@type": ["Biosource", "Item"], "display_title": "K562 - 4DNSRP5XBV7W", "uuid": "304b1fca-909f-4da1-9fb9-eab9d2bd69db", "cell_line_tier": "Unclassified", "biosource_type": "immortalized cell line", "@id": "/biosources/4DNSRP5XBV7W/", "cell_line": {"display_title": "K562", "uuid": "0f1257b4-30e2-4c34-b8a3-e564c65ec55a", "preferred_name": "K562", "@id": "/ontology-terms/EFO:0002067/", "term_id": "EFO:0002067", "@type": ["OntologyTerm", "Item"], "status": "released", "term_name": "K562", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "organism": {"@id": "/organisms/9606/", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "@type": ["Organism", "Item"], "name": "human", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "display_title": "blood cell", "term_name": "blood cell", "preferred_name": "blood cell", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "status": "released", "term_id": "CL:0000081", "@id": "/ontology-terms/CL:0000081/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@id": "/individuals-human/4DNIN4YSFWCS/", "@type": ["IndividualHuman", "Individual", "Item"], "display_title": "4DNIN4YSFWCS", "protected_data": false, "uuid": "2a0c64b1-25f1-44c1-88c3-7da6291f5b69", "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": [{"experimentset_type": "custom", "uuid": "7ab09aed-207d-4bb9-aa36-b7bed43d8dc6", "@type": ["ExperimentSet", "Item"], "@id": "/experiment-sets/4DNESNWX979D/", "display_title": "4DNESNWX979D", "accession": "4DNESNWX979D", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"experimentset_type": "replicate", "uuid": "369f6940-8510-4e1f-a07c-8c3b00f85dff", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESI7DEJTM/", "display_title": "4DNESI7DEJTM", "accession": "4DNESI7DEJTM", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "display_title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "@id": "/enzymes/MboI/", "display_title": "MboI", "name": "MboI", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-16T14:55:44.302260+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Erez Lieberman Aiden, BCM", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on K562", "condition": "in situ Hi-C on K562 with MboI and bio-dATP (higher crosslinker concentration)", "replicate_info": "Biorep 2, Techrep 3", "biosource_name": "K562", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIKFV5Y88", "href": "/files-processed/4DNFIKFV5Y88/@@download/4DNFIKFV5Y88.pairs.gz", "upload_key": "1d5b9ec9-3829-49a2-9576-f4299166c938/4DNFIKFV5Y88.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1d5b9ec9-3829-49a2-9576-f4299166c938/4DNFIKFV5Y88.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"status": "released", "uuid": "966161a0-754b-4844-9930-7e966242c393", "display_title": "hi-c-processing-pairs 0.2.6 run 2018-03-01 20:15:45.746236", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/966161a0-754b-4844-9930-7e966242c393/", "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI823LSII", "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "file_format": "chromsizes", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "dfddedef-bb56-4179-8303-277300c7e8d5", "display_title": "4DNFI9G9FRJJ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI9G9FRJJ", "@id": "/files-processed/4DNFI9G9FRJJ/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "c0d31291-e263-4d38-8542-a4e8998ca47d", "display_title": "4DNFI4DGNY7J.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI4DGNY7J", "@id": "/files-processed/4DNFI4DGNY7J/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "62c1e496-3194-455e-80cf-9dd0a5802f3d", "display_title": "4DNFIRHH2E7D.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIRHH2E7D", "@id": "/files-processed/4DNFIRHH2E7D/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "7cf40e22-0211-4805-b364-ccfcc5f2c85e", "display_title": "4DNFID8N3SCC.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFID8N3SCC", "@id": "/files-processed/4DNFID8N3SCC/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "display_title": "4DNFIKFV5Y88.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIKFV5Y88", "@id": "/files-processed/4DNFIKFV5Y88/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "b0d8efde-3d34-4c04-8fe5-71bcea2dfce2", "display_title": "4DNFI7CIF2JL.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI7CIF2JL", "@id": "/files-processed/4DNFI7CIF2JL/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d582084", "display_title": "4DNFI823L812.txt", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI823L812", "filename": "hg38_MboI.txt", "@id": "/files-reference/4DNFI823L812/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/juicer_format_restriction_site_file/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"display_title": "4DNFI2R1W3YW.pairs.gz", "@id": "/files-processed/4DNFI2R1W3YW/", "accession": "4DNFI2R1W3YW", "uuid": "0b823a67-45b6-46f9-86aa-2f609fbcb02c", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"display_title": "4DNFITUOMFUQ.hic", "@id": "/files-processed/4DNFITUOMFUQ/", "accession": "4DNFITUOMFUQ", "uuid": "dcfcb009-f006-4ab8-a4c7-af72be58c12c", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "display_title": "hic", "status": "released", "@id": "/file-formats/hic/", "file_format": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"display_title": "4DNFI18UHVRO.mcool", "@id": "/files-processed/4DNFI18UHVRO/", "accession": "4DNFI18UHVRO", "uuid": "230ad652-0232-47f2-97ef-296c7a040bd9", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "display_title": "mcool", "status": "released", "@id": "/file-formats/mcool/", "file_format": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "cooler_normvector", "value": {"display_title": "4DNFIF3ONCWH.normvector.juicerformat.gz", "@id": "/files-processed/4DNFIF3ONCWH/", "accession": "4DNFIF3ONCWH", "uuid": "fc823b55-551b-4631-a0b5-a6866ce4b7b5", "status": "released", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "display_title": "normvector_juicerformat", "status": "released", "@id": "/file-formats/normvector_juicerformat/", "file_format": "normvector_juicerformat", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"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", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWFTKI1QLK/", "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "8edc6b96-549a-4397-9636-24e98c87291f", "display_title": "pairsqc-single 0.2.5 run 2018-03-05 21:26:23.620836", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/8edc6b96-549a-4397-9636-24e98c87291f/", "input_files": [{"workflow_argument_name": "input_pairs", "value": {"uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "display_title": "4DNFIKFV5Y88.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIKFV5Y88", "@id": "/files-processed/4DNFIKFV5Y88/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "accession": "4DNFI823LSII", "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "file_format": "chromsizes", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIKFV5Y88/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/ebedfb6a-9352-4ddd-824b-02ccf8c22952/", "uuid": "ebedfb6a-9352-4ddd-824b-02ccf8c22952", "overall_quality_status": "PASS", "status": "released", "display_title": "QualityMetricPairsqc from 2018-03-05", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"uuid": "ae3a87cb-3fa2-469e-97c7-540fc2d0a117", "display_title": "PairsQC 0.2.5 - 4DNWF36CF3A1", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWF36CF3A1/", "title": "PairsQC 0.2.5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "uuid": "b632bcb1-cd31-4e09-8f28-ed68660a3616", "display_title": "md5 0.2.6 run 2022-01-11 15:51:50.190162", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/b632bcb1-cd31-4e09-8f28-ed68660a3616/", "input_files": [{"workflow_argument_name": "input_file", "value": {"uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "display_title": "4DNFIKFV5Y88.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIKFV5Y88", "@id": "/files-processed/4DNFIKFV5Y88/", "status": "released", "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report"}], "workflow": {"uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWF2HFF82B/", "title": "md5 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"display_title": "hi-c-processing-bam 0.2.6 run 2018-02-23 21:55:34.714960", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "uuid": "f829d152-c331-496e-8580-4a82d2afadd5", "@id": "/workflow-runs-awsem/f829d152-c331-496e-8580-4a82d2afadd5/", "input_files": [{"workflow_argument_name": "input_bams", "value": {"display_title": "4DNFID96999X.bam", "@type": ["FileProcessed", "File", "Item"], "uuid": "0127184f-6532-471d-83fc-65372bda98cb", "accession": "4DNFID96999X", "@id": "/files-processed/4DNFID96999X/", "status": "released", "file_format": {"status": "released", "@id": "/file-formats/bam/", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"display_title": "4DNFIE84HTMF.bam", "@type": ["FileProcessed", "File", "Item"], "uuid": "92f62f45-5585-4f8e-8496-7caac93deab3", "accession": "4DNFIE84HTMF", "@id": "/files-processed/4DNFIE84HTMF/", "status": "released", "file_format": {"status": "released", "@id": "/file-formats/bam/", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsize", "value": {"filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "file_format": {"status": "released", "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "@type": ["Workflow", "Item"], "@id": "/workflows/4DNWFT69RBY4/", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "status": "released", "title": "Hi-C Post-alignment Processing 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIKSP1NXL", "status": "released", "uuid": "4300b504-aa09-4a87-86fb-b6b30b2fd656", "@id": "/files-processed/4DNFIKSP1NXL/", "display_title": "4DNFIKSP1NXL.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "filtered_pairs", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIKFV5Y88", "status": "released", "uuid": "1d5b9ec9-3829-49a2-9576-f4299166c938", "@id": "/files-processed/4DNFIKFV5Y88/", "display_title": "4DNFIKFV5Y88.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "display_title": "pairs", "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/4DNFIKFV5Y88/4DNFIKFV5Y88.plot_table.out", "source_experiment_sets": [{"status": "released", "@id": "/experiment-sets/4DNESNWX979D/", "uuid": "7ab09aed-207d-4bb9-aa36-b7bed43d8dc6", "@type": ["ExperimentSet", "Item"], "display_title": "4DNESNWX979D", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/experiment-set-replicates/4DNESI7DEJTM/", "uuid": "369f6940-8510-4e1f-a07c-8c3b00f85dff", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESI7DEJTM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXC7SDGS9/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-16T14:55:44.302260+00:00"}}, {"parent": "/files-processed/4DNFIKFV5Y88/", "embedded_path": "last_modified", "item": {"date_modified": "2022-01-11T15:57:06.005042+00:00"}}]}, "validation-errors": []}