{"lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "display_title": "4DN DCIC, HMS", "status": "current", "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"]}}, "tags": ["JAWG_supplementary"], "award": {"center_title": "DCIC - DCIC", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "@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.", "project": "4DN", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@id": "/awards/1U01CA200059-01/", "name": "1U01CA200059-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "691c488d0a98ce5704f6334720de3333", "status": "released", "accession": "4DNFI71OH4WW", "file_size": 25344596957, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFI71OH4WW/@@download/4DNFI71OH4WW.pairs.gz.px2", "uuid": "0819ec32-b2f4-4715-b3de-7cc18629aad9", "md5sum": "47c5bba83f5a31a9d34cfb351c959197", "status": "released", "filename": "4DNFI71OH4WW", "accession": "4DNFI71OH4WW", "file_size": 30203480, "upload_key": "0819ec32-b2f4-4715-b3de-7cc18629aad9/4DNFI71OH4WW.pairs.gz.px2", "file_format": {"status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2020-07-10T00:03:51.768177+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:13:35.916761+00:00"}, "public_release": "2021-01-04", "quality_metric": {"status": "released", "Short cis reads (<20kb)": 572833081, "Trans reads": 103242601, "display_title": "QualityMetricPairsqc from 2020-07-23", "@id": "/quality-metrics-pairsqc/cd984bbc-ab84-43d7-87e9-c5abda88b329/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI71OH4WW/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Cis reads (>20kb)": 648006648, "uuid": "cd984bbc-ab84-43d7-87e9-c5abda88b329", "Total reads": 1324082330, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "1324082330", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "48.94", "tooltip": "Percent of filtered reads (=648.01m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "43.263", "tooltip": "Percent of filtered reads (=572.83m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "7.797", "tooltip": "Percent of filtered reads (=103.24m)", "numberType": "percent"}]}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2020-08-11", "contributing_labs": [{"status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@type": ["Lab", "Item"], "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}, "pi": {"error": "no view permissions"}}], "source_experiments": ["fbd0e03b-3711-45c9-9ce8-f8f52c0c121c"], "file_classification": "processed file", "@id": "/files-processed/4DNFI71OH4WW/", "@type": ["FileProcessed", "File", "Item"], "uuid": "0819ec32-b2f4-4715-b3de-7cc18629aad9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI71OH4WW.pairs.gz", "external_references": [], "experiments": [{"display_title": "in situ Hi-C on HFFc6 (Tier 1) with DdeI - 4DNEX2SUQP87", "uuid": "fbd0e03b-3711-45c9-9ce8-f8f52c0c121c", "@id": "/experiments-hi-c/4DNEX2SUQP87/", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "accession": "4DNEX2SUQP87", "biosample": {"biosource_summary": "HFFc6 (Tier 1)", "accession": "4DNBS31QX9F6", "uuid": "6bfb05c7-382f-4ff9-8c1a-73a2b4015d73", "modifications_summary": "None", "@id": "/biosamples/4DNBS31QX9F6/", "status": "released", "display_title": "4DNBS31QX9F6", "treatments_summary": "None", "@type": ["Biosample", "Item"], "biosource": [{"status": "released", "biosource_type": "immortalized cell line", "@type": ["Biosource", "Item"], "cell_line_tier": "Tier 1", "uuid": "10aa2d32-9fd4-46ce-a585-827d8c7810c3", "display_title": "HFFc6 (Tier 1) - 4DNSRC6ZVYVP", "@id": "/biosources/4DNSRC6ZVYVP/", "modifications": [], "individual": {"protected_data": false, "display_title": "4DNINE5V67ON", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINE5V67ON/", "uuid": "0cce9739-e53b-4155-912e-74ddbaedd695", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"preferred_name": "skin fibroblast", "term_id": "CL:0002620", "uuid": "1a658f38-8dee-4ed2-92ca-c694b5cef902", "term_name": "skin fibroblast", "status": "released", "@id": "/ontology-terms/CL:0002620/", "display_title": "skin fibroblast", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"@id": "/organisms/9606/", "name": "human", "scientific_name": "Homo sapiens", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"@type": ["OntologyTerm", "Item"], "preferred_name": "HFFc6", "term_name": "HFFc6", "@id": "/ontology-terms/EFO:0009318/", "status": "released", "term_id": "EFO:0009318", "display_title": "HFFc6", "uuid": "426ef4ff-c1f7-486e-bfcf-612ebb52c8b0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_culture_details": [{"display_title": "BiosampleCellCulture from 2020-06-24", "uuid": "c3b35d52-d800-4f1b-92f5-be5bacadf1d4", "status": "released", "in_vitro_differentiated": "No", "@id": "/biosample-cell-cultures/c3b35d52-d800-4f1b-92f5-be5bacadf1d4/", "@type": ["BiosampleCellCulture", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "experiment_sets": [{"experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESH5YI3CM", "uuid": "4ebb6f36-0fed-4676-b48c-cea3b3ff5806", "@id": "/experiment-set-replicates/4DNESH5YI3CM/", "display_title": "4DNESH5YI3CM", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"display_title": "in situ Hi-C", "title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "digestion_enzyme": {"uuid": "3802b968-d148-471d-b11e-b1011d61c6fa", "@type": ["Enzyme", "Item"], "status": "released", "display_title": "DdeI", "@id": "/enzymes/DdeI/", "name": "DdeI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2022-06-29T15:17:08.346990+00:00"}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "DdeI", "dataset": "Hi-C on HFF cells - protocol variations", "condition": "Formaldehyde+DSG, DdeI, HFFc6, (Tier 1)", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "HFFc6 (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFI71OH4WW", "href": "/files-processed/4DNFI71OH4WW/@@download/4DNFI71OH4WW.pairs.gz", "upload_key": "0819ec32-b2f4-4715-b3de-7cc18629aad9/4DNFI71OH4WW.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/0819ec32-b2f4-4715-b3de-7cc18629aad9/4DNFI71OH4WW.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"uuid": "834a9d71-79b1-4f4c-82c3-2aa7027d3dec", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/834a9d71-79b1-4f4c-82c3-2aa7027d3dec/", "display_title": "hi-c-processing-pairs 0.2.7 run 2020-07-13 00:01:18.677943", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"@id": "/files-processed/4DNFI8YIHWY9/", "@type": ["FileProcessed", "File", "Item"], "uuid": "6205a49b-2913-4462-aa9f-09f0fa0897d1", "status": "released", "display_title": "4DNFI8YIHWY9.pairs.gz", "accession": "4DNFI8YIHWY9", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@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": {"@id": "/files-processed/4DNFII84FBKM/", "@type": ["FileProcessed", "File", "Item"], "uuid": "2f5f0d6b-0b22-4936-93c9-0944d49c037b", "status": "released", "display_title": "4DNFII84FBKM.hic", "accession": "4DNFII84FBKM", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "hic", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "display_title": "hic", "@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": {"@id": "/files-processed/4DNFIGBKMVCD/", "@type": ["FileProcessed", "File", "Item"], "uuid": "74dbcb9e-0273-481f-acae-43c6861dcd46", "status": "released", "display_title": "4DNFIGBKMVCD.mcool", "accession": "4DNFIGBKMVCD", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "mcool", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "display_title": "mcool", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "status": "released", "accession": "4DNFI823LSII", "@id": "/files-reference/4DNFI823LSII/", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@id": "/file-formats/chromsizes/", "status": "released", "display_title": "chromsizes", "file_format": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "3562097e-6079-443b-8815-aa065423c429", "status": "released", "accession": "4DNFIEPZKDJE", "@id": "/files-processed/4DNFIEPZKDJE/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIEPZKDJE.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "display_title": "pairs", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0819ec32-b2f4-4715-b3de-7cc18629aad9", "status": "released", "accession": "4DNFI71OH4WW", "@id": "/files-processed/4DNFI71OH4WW/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI71OH4WW.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "display_title": "pairs", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"uuid": "4284a943-ed9f-4f55-9a25-5a010c1a9750", "status": "released", "accession": "4DNFI4YGL4RE", "@id": "/files-reference/4DNFI4YGL4RE/", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI4YGL4RE.txt", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@id": "/file-formats/juicer_format_restriction_site_file/", "status": "released", "display_title": "juicer_format_restriction_site_file", "file_format": "juicer_format_restriction_site_file", "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", "status": "released", "@id": "/workflows/4DNWF2YBHXQM/", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "a47350f0-e7b9-4376-ab95-ee894a950ffe", "status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/a47350f0-e7b9-4376-ab95-ee894a950ffe/", "display_title": "pairsqc-single 0.2.6 run 2020-07-23 14:36:15.039121", "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI71OH4WW/pairsqc_report.html", "uuid": "cd984bbc-ab84-43d7-87e9-c5abda88b329", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "display_title": "QualityMetricPairsqc from 2020-07-23", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/cd984bbc-ab84-43d7-87e9-c5abda88b329/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "status": "released", "accession": "4DNFI823LSII", "@id": "/files-reference/4DNFI823LSII/", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@id": "/file-formats/chromsizes/", "status": "released", "display_title": "chromsizes", "file_format": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0819ec32-b2f4-4715-b3de-7cc18629aad9", "status": "released", "accession": "4DNFI71OH4WW", "@id": "/files-processed/4DNFI71OH4WW/", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI71OH4WW.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "status": "released", "display_title": "pairs", "file_format": "pairs", "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", "status": "released", "@id": "/workflows/4DNWFHB26CID/", "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/28e39d36-1c02-4b55-bbb6-44143c2e59f4/", "uuid": "28e39d36-1c02-4b55-bbb6-44143c2e59f4", "display_title": "hi-c-processing-bam 0.2.6 run 2020-07-10 00:03:53.133427", "input_files": [{"workflow_argument_name": "chromsize", "value": {"@type": ["FileReference", "File", "Item"], "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "status": "released", "@id": "/files-reference/4DNFI823LSII/", "accession": "4DNFI823LSII", "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "@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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "8d901481-c617-464f-a20e-d062bee67853", "status": "released", "@id": "/files-processed/4DNFI52NFRJ8/", "accession": "4DNFI52NFRJ8", "display_title": "4DNFI52NFRJ8.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "e716ea27-0c8e-4ab7-b48e-ab27c7a5e189", "status": "released", "@id": "/files-processed/4DNFIMIFM4TO/", "accession": "4DNFIMIFM4TO", "display_title": "4DNFIMIFM4TO.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "6921873b-8452-41c6-84c2-1c8033da71f0", "status": "released", "@id": "/files-processed/4DNFIBFLV7FH/", "accession": "4DNFIBFLV7FH", "display_title": "4DNFIBFLV7FH.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "3cc5db69-0055-41db-bf29-a512a000d395", "status": "released", "@id": "/files-processed/4DNFI132IVMW/", "accession": "4DNFI132IVMW", "display_title": "4DNFI132IVMW.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "906fc6b6-3cae-44ec-870d-f6c92c5f76c5", "status": "released", "@id": "/files-processed/4DNFIEH762MM/", "accession": "4DNFIEH762MM", "display_title": "4DNFIEH762MM.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "568edde3-85b4-4cc8-883b-3bb71c55b5aa", "status": "released", "@id": "/files-processed/4DNFIH6MO57T/", "accession": "4DNFIH6MO57T", "display_title": "4DNFIH6MO57T.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "ed249949-1d26-4745-a804-b3dbd6c030db", "status": "released", "@id": "/files-processed/4DNFIFDAFOEE/", "accession": "4DNFIFDAFOEE", "display_title": "4DNFIFDAFOEE.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "86be1a26-8223-4bd9-a515-79d29c359c80", "status": "released", "@id": "/files-processed/4DNFIRPIJ51V/", "accession": "4DNFIRPIJ51V", "display_title": "4DNFIRPIJ51V.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["FileProcessed", "File", "Item"], "uuid": "d3a26f6d-8831-41f8-abcf-df244739d33a", "status": "released", "@id": "/files-processed/4DNFIIVITKR5/", "accession": "4DNFIIVITKR5", "display_title": "4DNFIIVITKR5.bam", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"status": "released", "@id": "/files-processed/4DNFI7AE8IGU/", "uuid": "e8d24088-acca-4470-bd7c-4ae35bff02b7", "accession": "4DNFI7AE8IGU", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI7AE8IGU.bam", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "bam", "@id": "/file-formats/bam/", "status": "released", "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": {"status": "released", "@id": "/files-processed/4DNFI71OH4WW/", "uuid": "0819ec32-b2f4-4715-b3de-7cc18629aad9", "accession": "4DNFI71OH4WW", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI71OH4WW.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "@id": "/file-formats/pairs/", "status": "released", "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": {"@id": "/workflows/4DNWFT69RBY4/", "@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "title": "Hi-C Post-alignment Processing 0.2.6", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "status": "released", "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/4DNFI71OH4WW/4DNFI71OH4WW.plot_table.out", "source_experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESH5YI3CM/", "display_title": "4DNESH5YI3CM", "uuid": "4ebb6f36-0fed-4676-b48c-cea3b3ff5806", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEX2SUQP87/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2022-06-29T15:17:08.346990+00:00"}}, {"parent": "/files-processed/4DNFI71OH4WW/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:13:35.916761+00:00"}}]}, "validation-errors": []}