{"lab": {"@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "title": "4DN DCIC, HMS", "display_title": "4DN DCIC, HMS", "status": "current", "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": {"display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "name": "1U01CA200059-01", "status": "current", "project": "4DN", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@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.", "center_title": "DCIC - DCIC", "@id": "/awards/1U01CA200059-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "552b850effcc5c8c7cb57a83fa2b2be9", "status": "released", "accession": "4DNFIT3MMU1S", "file_size": 1126693324, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIT3MMU1S/@@download/4DNFIT3MMU1S.pairs.gz.px2", "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "md5sum": "cb11941eca13847256fc52fec1d2f45e", "status": "released", "filename": "4DNFIT3MMU1S", "accession": "4DNFIT3MMU1S", "file_size": 16976466, "upload_key": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8/4DNFIT3MMU1S.pairs.gz.px2", "file_format": {"@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-11-27T15:24:17.981036+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-17T21:52:51.582043+00:00"}, "public_release": "2018-12-01", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT3MMU1S/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/baaf39b3-33e9-4b00-80f1-0b913476200f/", "uuid": "baaf39b3-33e9-4b00-80f1-0b913476200f", "status": "released", "Cis reads (>20kb)": 36915408, "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2018-11-28", "Trans reads": 14399404, "Total reads": 73308190, "Short cis reads (<20kb)": 21993378, "quality_metric_summary": [{"title": "Filtered Reads", "value": "73308190", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "50.356", "tooltip": "Percent of filtered reads (=36.92m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "30.001", "tooltip": "Percent of filtered reads (=21.99m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "19.642", "tooltip": "Percent of filtered reads (=14.4m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2018-12-01", "contributing_labs": [{"status": "current", "correspondence": [{"contact_email": "bGVvbmlkQG1pdC5lZHU=", "@id": "/users/f520d12a-e4c4-4774-a230-08d6dc4f5ef1/", "display_title": "Leonid Mirny"}], "@id": "/labs/leonid-mirny-lab/", "display_title": "Leonid Mirny, MIT", "uuid": "82ebab19-8a20-47c5-baeb-9a08a9524b10", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.82ebab19-8a20-47c5-baeb-9a08a9524b10"]}}, {"status": "current", "correspondence": [{"contact_email": "ZnNwaXR6QHVjaGljYWdvLmVkdQ==", "@id": "/users/fbcf7895-3eba-4844-950f-855c02be74a2/", "display_title": "Francois Spitz"}], "@id": "/labs/francois-spitz-lab/", "display_title": "Francois Spitz, PASTEUR", "uuid": "06d4f485-ccf2-4332-b226-d8a05e5497db", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.06d4f485-ccf2-4332-b226-d8a05e5497db"]}}], "source_experiments": ["dfc5e2b1-ccc7-4337-a292-fce5b519099f"], "file_classification": "processed file", "@id": "/files-processed/4DNFIT3MMU1S/", "@type": ["FileProcessed", "File", "Item"], "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIT3MMU1S.pairs.gz", "external_references": [], "experiments": [{"accession": "4DNEXN25ESPT", "@id": "/experiments-hi-c/4DNEXN25ESPT/", "uuid": "dfc5e2b1-ccc7-4337-a292-fce5b519099f", "status": "released", "display_title": "TCC on hepatocyte with HindIII - 4DNEXN25ESPT", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"biosource_summary": "hepatocyte", "uuid": "92f95a5e-e8dd-43a8-a7d1-11617cfb7258", "treatments_summary": "mock treatment (5.0d)", "@id": "/biosamples/4DNBSU328LQ3/", "modifications_summary": "None", "status": "released", "@type": ["Biosample", "Item"], "accession": "4DNBSU328LQ3", "display_title": "4DNBSU328LQ3", "biosource": [{"biosource_type": "primary cell", "display_title": "hepatocyte - 4DNSRMDUDYLW", "uuid": "13e689ba-3ae3-4302-817b-3818bda0862f", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRMDUDYLW/", "cell_line": {"preferred_name": "hepatocyte", "uuid": "a1b0f241-64ca-47a4-b9b8-19c28b5bdedb", "display_title": "hepatocyte", "@id": "/ontology-terms/CL:0000182/", "status": "released", "term_id": "CL:0000182", "@type": ["OntologyTerm", "Item"], "term_name": "hepatocyte", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0002107", "display_title": "liver", "preferred_name": "liver", "uuid": "111182bc-8535-4448-903e-854af460a233", "@id": "/ontology-terms/UBERON:0002107/", "term_name": "liver", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "@id": "/organisms/10090/", "display_title": "M. musculus", "name": "mouse", "@type": ["Organism", "Item"], "scientific_name": "Mus musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNIN2BSSV7N/", "display_title": "4DNIN2BSSV7N", "uuid": "5483ddbf-d764-43a8-9c83-049f6237c64d", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "HindIII", "@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "status": "released", "@type": ["Enzyme", "Item"], "display_title": "HindIII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-04-24T16:48:57.337259+00:00"}, "experiment_type": {"display_title": "TCC", "@type": ["ExperimentType", "Item"], "status": "released", "title": "TCC", "uuid": "e95e3626-aadc-464b-9ef0-0cdbea689744", "@id": "/experiment-types/tcc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"accession": "4DNESAOU4AAQ", "uuid": "37adea6e-6a27-41af-bf03-1f2edc8cbf91", "@id": "/experiment-set-replicates/4DNESAOU4AAQ/", "experimentset_type": "replicate", "status": "released", "display_title": "4DNESAOU4AAQ", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Francois Spitz, PASTEUR", "experiment_type": "TCC", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "TCC on hepatocytes +/- NIPBL", "condition": "uninduced control", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "hepatocyte", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIT3MMU1S", "href": "/files-processed/4DNFIT3MMU1S/@@download/4DNFIT3MMU1S.pairs.gz", "upload_key": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8/4DNFIT3MMU1S.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a7148ecc-b808-4e2b-9a61-32a5af8cb6d8/4DNFIT3MMU1S.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "pairsqc-single 0.2.6 run 2018-11-28 20:02:13.302433", "uuid": "0fb58a8c-97cd-4b01-b8c7-bc2f1992c89d", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/0fb58a8c-97cd-4b01-b8c7-bc2f1992c89d/", "status": "released", "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT3MMU1S/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/baaf39b3-33e9-4b00-80f1-0b913476200f/", "status": "released", "uuid": "baaf39b3-33e9-4b00-80f1-0b913476200f", "display_title": "QualityMetricPairsqc from 2018-11-28", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "PairsQC 0.2.6", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "@id": "/workflows/4DNWFHB26CID/", "status": "released", "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"@id": "/files-reference/4DNFI3UBJ3HZ/", "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "accession": "4DNFI3UBJ3HZ", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "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": {"@id": "/files-processed/4DNFIT3MMU1S/", "status": "released", "display_title": "4DNFIT3MMU1S.pairs.gz", "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "accession": "4DNFIT3MMU1S", "@type": ["FileProcessed", "File", "Item"], "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"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "hi-c-processing-pairs 0.2.6 run 2018-11-30 15:53:11.410428", "uuid": "1b9df11b-139c-4900-b8cf-99fd9439853c", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/1b9df11b-139c-4900-b8cf-99fd9439853c/", "status": "released", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"status": "released", "accession": "4DNFIQH7KU2L", "@id": "/files-processed/4DNFIQH7KU2L/", "uuid": "af3764a3-0e6a-4ba5-9bd7-4f7ae13cd229", "display_title": "4DNFIQH7KU2L.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "display_title": "pairs", "status": "released", "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": "hic", "value": {"status": "released", "accession": "4DNFIFULDMGN", "@id": "/files-processed/4DNFIFULDMGN/", "uuid": "57ecaa79-5c9c-49c7-b841-0a4bf3117555", "display_title": "4DNFIFULDMGN.hic", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "hic", "@id": "/file-formats/hic/", "display_title": "hic", "status": "released", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"status": "released", "accession": "4DNFIIW2JEZ8", "@id": "/files-processed/4DNFIIW2JEZ8/", "uuid": "69b3238e-d118-424f-8244-786fdc82f5a6", "display_title": "4DNFIIW2JEZ8.mcool", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "mcool", "@id": "/file-formats/mcool/", "display_title": "mcool", "status": "released", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "cooler_normvector", "value": {"status": "released", "accession": "4DNFILIANP51", "@id": "/files-processed/4DNFILIANP51/", "uuid": "14d7bd85-fb79-4f5a-98e0-4d8a15464414", "display_title": "4DNFILIANP51.normvector.juicerformat.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "normvector_juicerformat", "@id": "/file-formats/normvector_juicerformat/", "display_title": "normvector_juicerformat", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6", "uuid": "c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0", "@id": "/workflows/4DNWFTKI1QLK/", "status": "released", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6 - 4DNWFTKI1QLK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"@id": "/files-reference/4DNFI3UBJ3HZ/", "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "accession": "4DNFI3UBJ3HZ", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "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": {"@id": "/files-processed/4DNFIT3MMU1S/", "status": "released", "display_title": "4DNFIT3MMU1S.pairs.gz", "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "accession": "4DNFIT3MMU1S", "@type": ["FileProcessed", "File", "Item"], "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_argument_name": "input_pairs", "value": {"@id": "/files-processed/4DNFIGZZ9LOB/", "status": "released", "display_title": "4DNFIGZZ9LOB.pairs.gz", "uuid": "33d5d238-eb55-4a05-8b56-4fe8a330c793", "accession": "4DNFIGZZ9LOB", "@type": ["FileProcessed", "File", "Item"], "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_argument_name": "restriction_file", "value": {"@id": "/files-reference/4DNFI6V32T9J/", "status": "released", "filename": "MM10_HindIII.txt", "display_title": "4DNFI6V32T9J.txt", "uuid": "8e29e9ae-f13c-4a7b-9236-dba35a69bbff", "accession": "4DNFI6V32T9J", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "file_format": "juicer_format_restriction_site_file", "@id": "/file-formats/juicer_format_restriction_site_file/", "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "display_title": "juicer_format_restriction_site_file", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"display_title": "hi-c-processing-bam 0.2.6 run 2018-11-27 15:24:18.288489", "@id": "/workflow-runs-awsem/265def9d-9f50-4fc6-b72f-0c080bbdc13d/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "uuid": "265def9d-9f50-4fc6-b72f-0c080bbdc13d", "workflow": {"@type": ["Workflow", "Item"], "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@id": "/workflows/4DNWFT69RBY4/", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "title": "Hi-C Post-alignment Processing 0.2.6", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"display_title": "4DNFIN92AY28.bam", "uuid": "05073cdb-2612-4e34-a756-a8cc2f4cbe9d", "status": "released", "accession": "4DNFIN92AY28", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIN92AY28/", "file_format": {"status": "released", "file_format": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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": {"display_title": "4DNFIT3MMU1S.pairs.gz", "uuid": "a7148ecc-b808-4e2b-9a61-32a5af8cb6d8", "status": "released", "accession": "4DNFIT3MMU1S", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIT3MMU1S/", "file_format": {"status": "released", "file_format": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "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"]}}}], "input_files": [{"workflow_argument_name": "chromsize", "value": {"filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI3UBJ3HZ/", "status": "released", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "accession": "4DNFI3UBJ3HZ", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "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"], "@id": "/files-processed/4DNFIP43M9B3/", "status": "released", "display_title": "4DNFIP43M9B3.bam", "accession": "4DNFIP43M9B3", "uuid": "d91d8890-d639-4237-958f-a552fbdf3928", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFI5XIZAHP/", "status": "released", "display_title": "4DNFI5XIZAHP.bam", "accession": "4DNFI5XIZAHP", "uuid": "c6e902de-bdd5-4778-9ac5-bbfe8f7b38c6", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFIJYT23LN/", "status": "released", "display_title": "4DNFIJYT23LN.bam", "accession": "4DNFIJYT23LN", "uuid": "fc5a6eef-c26f-4e91-bbb6-149c5981fb24", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFIWKET6HW/", "status": "released", "display_title": "4DNFIWKET6HW.bam", "accession": "4DNFIWKET6HW", "uuid": "aba42274-9bb9-4d36-8081-a2cfacc8a3ad", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFI6G6S9OK/", "status": "released", "display_title": "4DNFI6G6S9OK.bam", "accession": "4DNFI6G6S9OK", "uuid": "31f8e268-a88e-4aaa-b818-587dd810b09b", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFITCC5NN6/", "status": "released", "display_title": "4DNFITCC5NN6.bam", "accession": "4DNFITCC5NN6", "uuid": "da7bccb8-a86c-498a-8457-9abbfb2d932c", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFIZL97VBE/", "status": "released", "display_title": "4DNFIZL97VBE.bam", "accession": "4DNFIZL97VBE", "uuid": "7d0cb142-bb1b-40f9-8f03-3eb07d0daf41", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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"], "@id": "/files-processed/4DNFI1841KWD/", "status": "released", "display_title": "4DNFI1841KWD.bam", "accession": "4DNFI1841KWD", "uuid": "19026347-1af7-46ae-bd3f-21e8b7a26b01", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "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/4DNFIT3MMU1S/4DNFIT3MMU1S.plot_table.out", "source_experiment_sets": [{"status": "released", "display_title": "4DNESAOU4AAQ", "@id": "/experiment-set-replicates/4DNESAOU4AAQ/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "37adea6e-6a27-41af-bf03-1f2edc8cbf91", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXN25ESPT/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2019-04-24T16:48:57.337259+00:00"}}, {"parent": "/files-processed/4DNFIT3MMU1S/", "embedded_path": "last_modified", "item": {"date_modified": "2021-05-17T21:52:51.582043+00:00"}}]}, "validation-errors": []}