{"lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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.", "project": "4DN", "name": "1U01CA200059-01", "center_title": "DCIC - DCIC", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "be5f22cd3be15dd7506ba631c2659558", "status": "released", "accession": "4DNFIE856TH8", "file_size": 7218735933, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIE856TH8/@@download/4DNFIE856TH8.pairs.gz.px2", "uuid": "8ed6101d-5a01-4b0a-8505-676e98814c67", "md5sum": "eb53522f76fb49fa49f9c3b444295b7d", "status": "released", "filename": "4DNFIE856TH8", "accession": "4DNFIE856TH8", "file_size": 28024173, "upload_key": "8ed6101d-5a01-4b0a-8505-676e98814c67/4DNFIE856TH8.pairs.gz.px2", "file_format": {"@id": "/file-formats/pairs_px2/", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2019-05-20T12:44:38.212726+00:00", "notes_to_tsv": ["WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing."], "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:33:31.999085+00:00"}, "public_release": "2019-11-26", "quality_metric": {"@id": "/quality-metrics-pairsqc/1ef8cb77-3f33-4ce3-9832-bae88fa1a87a/", "Trans reads": 133014832, "uuid": "1ef8cb77-3f33-4ce3-9832-bae88fa1a87a", "Total reads": 495927118, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIE856TH8/pairsqc_report.html", "status": "released", "display_title": "QualityMetricPairsqc from 2019-05-23", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Short cis reads (<20kb)": 112487537, "Cis reads (>20kb)": 250424749, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "495927118", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "50.496", "tooltip": "Percent of filtered reads (=250.42m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "22.682", "tooltip": "Percent of filtered reads (=112.49m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "26.821", "tooltip": "Percent of filtered reads (=133.01m)", "numberType": "percent"}]}, "schema_version": "3", "static_headers": [], "genome_assembly": "GRCh38", "project_release": "2019-11-26", "contributing_labs": [{"uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "display_title": "Erez Lieberman Aiden, BCM", "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "@id": "/labs/erez-liebermanaiden-lab/", "@type": ["Lab", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}}], "source_experiments": ["168a4a09-112a-4930-95c2-368d52d43fa0"], "file_classification": "processed file", "@id": "/files-processed/4DNFIE856TH8/", "@type": ["FileProcessed", "File", "Item"], "uuid": "8ed6101d-5a01-4b0a-8505-676e98814c67", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIE856TH8.pairs.gz", "external_references": [], "experiments": [{"status": "released", "display_title": "in situ Hi-C on HCT116 with Crispr generated mClover and AID-tagged RAD21 with MboI - 4DNEXRRPUVSY", "@id": "/experiments-hi-c/4DNEXRRPUVSY/", "uuid": "168a4a09-112a-4930-95c2-368d52d43fa0", "accession": "4DNEXRRPUVSY", "@type": ["ExperimentHiC", "Experiment", "Item"], "experiment_sets": [{"display_title": "4DNES3QAGOZZ", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "a60be947-aedf-47bf-9b46-5274e695003b", "accession": "4DNES3QAGOZZ", "@id": "/experiment-set-replicates/4DNES3QAGOZZ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "biosample": {"@id": "/biosamples/4DNBSWF7O4HN/", "display_title": "4DNBSWF7O4HN", "@type": ["Biosample", "Item"], "status": "released", "treatments_summary": "None", "modifications_summary": "None", "uuid": "010a8a05-892e-423e-ac53-f32de9954617", "biosource_summary": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "accession": "4DNBSWF7O4HN", "biosource": [{"@id": "/biosources/4DNSRG1Q4WCR/", "biosource_type": "immortalized cell line", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "status": "released", "uuid": "2b46c4e3-780f-40bc-929f-f1c1a2e181f1", "display_title": "HCT116 with Crispr generated mClover and AID-tagged RAD21 - 4DNSRG1Q4WCR", "individual": {"protected_data": false, "@id": "/individuals-human/4DNINJ6WV6L1/", "display_title": "4DNINJ6WV6L1", "@type": ["IndividualHuman", "Individual", "Item"], "uuid": "1f0f0999-c5b4-430e-8650-8ebb3491d699", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"term_name": "colon", "term_id": "UBERON:0001155", "display_title": "colon", "preferred_name": "colon", "@id": "/ontology-terms/UBERON:0001155/", "status": "released", "uuid": "3e39f551-bc0b-4bee-b932-29d71956fb94", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"override_modification_name": "Crispr generated mClover and AID-tagged RAD21", "modification_type": "Crispr", "@id": "/modifications/1cc89862-1db3-48d0-8d1e-2f954f133e2e/", "@type": ["Modification", "Item"], "display_title": "Crispr generated mClover and AID-tagged RAD21", "status": "released", "uuid": "1cc89862-1db3-48d0-8d1e-2f954f133e2e", "genomic_change": "insertion", "target_of_mod": [{"organism_name": "human", "status": "released", "uuid": "c3ce0816-5481-4342-b95b-6c8b93199744", "display_title": "RAD21 gene", "@type": ["BioFeature", "Item"], "@id": "/bio-features/c3ce0816-5481-4342-b95b-6c8b93199744/", "relevant_genes": [{"uuid": "a093769c-d596-4a26-8916-06ae491575ba", "status": "released", "@type": ["Gene", "Item"], "display_title": "RAD21", "@id": "/genes/5885/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "feature_type": {"uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@id": "/ontology-terms/SO:0000704/", "display_title": "gene", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "organism": {"display_title": "H. sapiens", "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "name": "human", "status": "released", "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "49d090b2-5326-40ce-9c19-7a214c682272", "@id": "/ontology-terms/EFO:0002824/", "status": "released", "term_name": "HCT116", "preferred_name": "HCT116", "term_id": "EFO:0002824", "display_title": "HCT116", "@type": ["OntologyTerm", "Item"], "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_type": {"@id": "/experiment-types/in-situ-hi-c/", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "title": "in situ Hi-C", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "MboI", "display_title": "MboI", "@type": ["Enzyme", "Item"], "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-07-08T14:25:20.871206+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 RAD21-AID tagged HCT-116", "condition": "no auxin treatment", "replicate_info": "Biorep 1, Techrep 3", "biosource_name": "HCT116 with Crispr generated mClover and AID-tagged RAD21", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIE856TH8", "href": "/files-processed/4DNFIE856TH8/@@download/4DNFIE856TH8.pairs.gz", "upload_key": "8ed6101d-5a01-4b0a-8505-676e98814c67/4DNFIE856TH8.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8ed6101d-5a01-4b0a-8505-676e98814c67/4DNFIE856TH8.pairs.gz", "tsv_notes": "WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing.", "workflow_run_inputs": [{"uuid": "f1e84335-9c5e-48c0-8e5b-40d4656472ee", "display_title": "pairsqc-single 0.2.6 run 2019-05-23 02:02:26.681930", "@id": "/workflow-runs-awsem/f1e84335-9c5e-48c0-8e5b-40d4656472ee/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIE856TH8/pairsqc_report.html", "overall_quality_status": "PASS", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2019-05-23", "uuid": "1ef8cb77-3f33-4ce3-9832-bae88fa1a87a", "status": "released", "@id": "/quality-metrics-pairsqc/1ef8cb77-3f33-4ce3-9832-bae88fa1a87a/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSII.chrom.sizes", "accession": "4DNFI823LSII", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "8ed6101d-5a01-4b0a-8505-676e98814c67", "@id": "/files-processed/4DNFIE856TH8/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIE856TH8.pairs.gz", "accession": "4DNFIE856TH8", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "PairsQC 0.2.6", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "@id": "/workflows/4DNWFHB26CID/", "@type": ["Workflow", "Item"], "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "d579bc24-693b-4ed4-a313-5fd9507cd177", "display_title": "hi-c-processing-pairs 0.2.7 run 2019-05-23 14:27:52.307564", "@id": "/workflow-runs-awsem/d579bc24-693b-4ed4-a313-5fd9507cd177/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"@id": "/files-processed/4DNFITH9KJF1/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFITH9KJF1.pairs.gz", "uuid": "4107d360-7f4c-4bd5-94b8-f2b95d042bb6", "accession": "4DNFITH9KJF1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "pairs", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "hic", "value": {"@id": "/files-processed/4DNFIP71EWXC/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIP71EWXC.hic", "uuid": "1cff8afa-5a13-4ad4-bcad-91fc3ced759c", "accession": "4DNFIP71EWXC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "hic", "@type": ["FileFormat", "Item"], "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@id": "/file-formats/hic/", "status": "released", "display_title": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "mcool", "value": {"@id": "/files-processed/4DNFIFLDVASC/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIFLDVASC.mcool", "uuid": "5641a676-44f2-4e24-95bd-c93e6e57b0cf", "accession": "4DNFIFLDVASC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "mcool", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@id": "/file-formats/mcool/", "status": "released", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSII.chrom.sizes", "accession": "4DNFI823LSII", "status": "released", "file_format": {"@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "cd034bed-9d73-41bc-91ee-79722709f362", "@id": "/files-processed/4DNFIDQDCBHF/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIDQDCBHF.pairs.gz", "accession": "4DNFIDQDCBHF", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "22e9084c-f61a-4958-be76-62a8061cf418", "@id": "/files-processed/4DNFIT2UJSJE/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIT2UJSJE.pairs.gz", "accession": "4DNFIT2UJSJE", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "8ed6101d-5a01-4b0a-8505-676e98814c67", "@id": "/files-processed/4DNFIE856TH8/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIE856TH8.pairs.gz", "accession": "4DNFIE856TH8", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "8bec995f-fdc7-40b2-94df-36797180e281", "@id": "/files-processed/4DNFII4WQS3O/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFII4WQS3O.pairs.gz", "accession": "4DNFII4WQS3O", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "2f5c1cae-cecb-4c01-b727-7428794ba993", "@id": "/files-processed/4DNFIKV1KZL9/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIKV1KZL9.pairs.gz", "accession": "4DNFIKV1KZL9", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "dca883b5-f2f7-4a39-bdf1-c9461f058201", "@id": "/files-processed/4DNFILTJ56D4/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFILTJ56D4.pairs.gz", "accession": "4DNFILTJ56D4", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "1b230ecd-9b2b-42a0-815c-dac2657701b7", "@id": "/files-processed/4DNFI2EM4MI3/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI2EM4MI3.pairs.gz", "accession": "4DNFI2EM4MI3", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "6effdcff-6cd4-4db1-a15e-8ff4a259eca8", "@id": "/files-processed/4DNFIF8R6E7E/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIF8R6E7E.pairs.gz", "accession": "4DNFIF8R6E7E", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "ba53783a-88df-4f94-a8cf-2ec38cef9f81", "@id": "/files-processed/4DNFIV6NZH4O/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIV6NZH4O.pairs.gz", "accession": "4DNFIV6NZH4O", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "67ea1b71-8a2a-4ed1-aed4-047df53cb9cc", "@id": "/files-processed/4DNFIQLZQN9H/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIQLZQN9H.pairs.gz", "accession": "4DNFIQLZQN9H", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "13620872-fe29-4db1-8cd6-5e413436ccac", "@id": "/files-processed/4DNFID2STU5W/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFID2STU5W.pairs.gz", "accession": "4DNFID2STU5W", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "ac4d340c-2bac-4693-950b-f6b62a0fa324", "@id": "/files-processed/4DNFI7SFMDP1/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI7SFMDP1.pairs.gz", "accession": "4DNFI7SFMDP1", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0c847786-5e9d-45f8-8356-2ee823e1d2aa", "@id": "/files-processed/4DNFILD1LBBV/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFILD1LBBV.pairs.gz", "accession": "4DNFILD1LBBV", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "3e8f5f95-f49a-491e-b97f-3dec983ce501", "@id": "/files-processed/4DNFILGAQFM2/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFILGAQFM2.pairs.gz", "accession": "4DNFILGAQFM2", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "79a7e68e-849e-4c8b-acc1-3d293462fce7", "@id": "/files-processed/4DNFIM4G8GPZ/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIM4G8GPZ.pairs.gz", "accession": "4DNFIM4G8GPZ", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "6696a408-da55-4833-84da-eeb236857f6f", "@id": "/files-processed/4DNFIF9K4ZP3/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIF9K4ZP3.pairs.gz", "accession": "4DNFIF9K4ZP3", "status": "released", "file_format": {"@id": "/file-formats/pairs/", "status": "released", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "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", "@id": "/files-reference/4DNFI823L812/", "filename": "hg38_MboI.txt", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823L812.txt", "accession": "4DNFI823L812", "status": "released", "file_format": {"@id": "/file-formats/juicer_format_restriction_site_file/", "status": "released", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7", "uuid": "23bd6d73-4190-496d-837c-21bcdb3802ed", "@id": "/workflows/4DNWF2YBHXQM/", "@type": ["Workflow", "Item"], "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "status": "released", "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 2019-05-20 12:44:38.441181", "@id": "/workflow-runs-awsem/b210c3f3-cfbe-4210-ba43-4b1784d95693/", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "b210c3f3-cfbe-4210-ba43-4b1784d95693", "input_files": [{"workflow_argument_name": "chromsize", "value": {"@id": "/files-reference/4DNFI823LSII/", "accession": "4DNFI823LSII", "display_title": "4DNFI823LSII.chrom.sizes", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "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_bams", "value": {"@id": "/files-processed/4DNFI86PZY62/", "accession": "4DNFI86PZY62", "display_title": "4DNFI86PZY62.bam", "uuid": "f378729f-3dca-441e-b82f-cb58e2cd23c5", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFISUCTN8W/", "accession": "4DNFISUCTN8W", "display_title": "4DNFISUCTN8W.bam", "uuid": "d595e9c3-d01a-441c-9010-909ad6e3bfeb", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFI452E5MA/", "accession": "4DNFI452E5MA", "display_title": "4DNFI452E5MA.bam", "uuid": "9f8c8a70-56ed-45be-b298-9805bac2a407", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIXR8H97D/", "accession": "4DNFIXR8H97D", "display_title": "4DNFIXR8H97D.bam", "uuid": "f180cf13-d9df-4238-a720-2f25cc3f64ad", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFI6TGLOI2/", "accession": "4DNFI6TGLOI2", "display_title": "4DNFI6TGLOI2.bam", "uuid": "99cf8bad-91df-401b-ba5c-4e31f56cfded", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIUDE1W68/", "accession": "4DNFIUDE1W68", "display_title": "4DNFIUDE1W68.bam", "uuid": "d8322ad4-0aa5-4058-9da7-ac3015ae4809", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFI7X7PE2Y/", "accession": "4DNFI7X7PE2Y", "display_title": "4DNFI7X7PE2Y.bam", "uuid": "0b6c4214-2599-4cf1-8d40-06e4da70f306", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIHRTQZGO/", "accession": "4DNFIHRTQZGO", "display_title": "4DNFIHRTQZGO.bam", "uuid": "cb0abbba-5e50-4566-b50f-1e46f50e1cda", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIU92PGKT/", "accession": "4DNFIU92PGKT", "display_title": "4DNFIU92PGKT.bam", "uuid": "866e05bf-1079-44ba-84ae-62bfe533a613", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIH7EJTLA/", "accession": "4DNFIH7EJTLA", "display_title": "4DNFIH7EJTLA.bam", "uuid": "ba073b30-76a4-432f-b89b-f88d4ae44508", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFITH63CA7/", "accession": "4DNFITH63CA7", "display_title": "4DNFITH63CA7.bam", "uuid": "278d14d5-4202-4aaa-976a-999d2a1e0f09", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_bams", "value": {"@id": "/files-processed/4DNFIIBMMQ74/", "accession": "4DNFIIBMMQ74", "display_title": "4DNFIIBMMQ74.bam", "uuid": "7785fae2-d91a-4ff7-a652-392e5e79471d", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"accession": "4DNFIE8JESDT", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "dc0c52a5-7177-4aa7-9104-18cefbab6c5b", "display_title": "4DNFIE8JESDT.bam", "@id": "/files-processed/4DNFIE8JESDT/", "file_format": {"file_format": "bam", "status": "released", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "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": {"accession": "4DNFIE856TH8", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "8ed6101d-5a01-4b0a-8505-676e98814c67", "display_title": "4DNFIE856TH8.pairs.gz", "@id": "/files-processed/4DNFIE856TH8/", "file_format": {"file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"status": "released", "@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@id": "/workflows/4DNWFT69RBY4/", "title": "Hi-C Post-alignment Processing 0.2.6", "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/4DNFIE856TH8/4DNFIE856TH8.plot_table.out", "source_experiment_sets": [{"display_title": "4DNES3QAGOZZ", "status": "released", "uuid": "a60be947-aedf-47bf-9b46-5274e695003b", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES3QAGOZZ/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXRRPUVSY/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-08T14:25:20.871206+00:00"}}, {"parent": "/files-processed/4DNFIE856TH8/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:33:31.999085+00:00"}}]}, "validation-errors": []}