{"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"]}}, "tags": ["JAWG_supplementary"], "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": "f53fc888697d58ab577630d52248a154", "status": "released", "accession": "4DNFI89L17XY", "file_size": 8418742384, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFI89L17XY/@@download/4DNFI89L17XY.pairs.gz.px2", "uuid": "da075dc9-ae2a-4045-8032-3affa0e064a6", "md5sum": "489afeff37fa369a237d47f4da6dbb45", "status": "released", "filename": "4DNFI89L17XY", "accession": "4DNFI89L17XY", "file_size": 27005882, "upload_key": "da075dc9-ae2a-4045-8032-3affa0e064a6/4DNFI89L17XY.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": "2019-02-21T04:22:37.884909+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-17T21:42:17.394202+00:00"}, "public_release": "2019-05-17", "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI89L17XY/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/ded82cdd-4ae8-4429-9cdf-71edf09e2010/", "uuid": "ded82cdd-4ae8-4429-9cdf-71edf09e2010", "status": "released", "Cis reads (>20kb)": 137444293, "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2019-02-28", "Trans reads": 51058768, "Total reads": 448601072, "Short cis reads (<20kb)": 260098011, "quality_metric_summary": [{"title": "Filtered Reads", "value": "448601072", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "30.638", "tooltip": "Percent of filtered reads (=137.44m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "57.98", "tooltip": "Percent of filtered reads (=260.1m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "11.382", "tooltip": "Percent of filtered reads (=51.06m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2019-03-12", "contributing_labs": [{"status": "current", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "@id": "/labs/job-dekker-lab/", "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}}], "source_experiments": ["8141525b-2460-4bdd-b090-6eeb345cc8b2"], "file_classification": "processed file", "@id": "/files-processed/4DNFI89L17XY/", "@type": ["FileProcessed", "File", "Item"], "uuid": "da075dc9-ae2a-4045-8032-3affa0e064a6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI89L17XY.pairs.gz", "external_references": [], "experiments": [{"accession": "4DNEXCL5AQ32", "@id": "/experiments-hi-c/4DNEXCL5AQ32/", "uuid": "8141525b-2460-4bdd-b090-6eeb345cc8b2", "status": "released", "display_title": "Micro-C on H1-hESC (Tier 1) with MNase - 4DNEXCL5AQ32", "@type": ["ExperimentHiC", "Experiment", "Item"], "biosample": {"biosource_summary": "H1-hESC (Tier 1)", "uuid": "21e8e324-be3a-4d08-a0ad-485725083bbd", "treatments_summary": "None", "@id": "/biosamples/4DNBSTNNFD79/", "modifications_summary": "None", "status": "released", "@type": ["Biosample", "Item"], "accession": "4DNBSTNNFD79", "display_title": "4DNBSTNNFD79", "biosource": [{"biosource_type": "stem cell derived cell line", "display_title": "H1-hESC (Tier 1) - 4DNSRV3SKQ8M", "uuid": "68172441-97c4-40cc-b73f-d0f5dbc5cc05", "cell_line_tier": "Tier 1", "@type": ["Biosource", "Item"], "status": "released", "@id": "/biosources/4DNSRV3SKQ8M/", "cell_line": {"preferred_name": "H1-hESC", "uuid": "c3f6e06f-900e-45f9-9c23-983c5673f58d", "display_title": "H1-hESC", "@id": "/ontology-terms/EFO:0003042/", "status": "released", "term_id": "EFO:0003042", "@type": ["OntologyTerm", "Item"], "term_name": "H1-hESC", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "tissue": {"@type": ["OntologyTerm", "Item"], "term_id": "CL:0000034", "display_title": "stem cell", "preferred_name": "stem cell", "uuid": "082f5be3-3617-4d3e-9ee9-78df53a71802", "@id": "/ontology-terms/CL:0000034/", "term_name": "stem cell", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@id": "/organisms/9606/", "display_title": "H. sapiens", "name": "human", "@type": ["Organism", "Item"], "scientific_name": "Homo sapiens", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "protected_data": false, "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNIN3RG3ZKE/", "display_title": "4DNIN3RG3ZKE", "uuid": "c97775b7-3d00-4132-9598-863797b8ef14", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"in_vitro_differentiated": "No", "uuid": "211bc7b3-a304-4046-8ef3-ef3eec0af1fc", "status": "released", "@type": ["BiosampleCellCulture", "Item"], "display_title": "BiosampleCellCulture from 2019-02-19", "@id": "/biosample-cell-cultures/211bc7b3-a304-4046-8ef3-ef3eec0af1fc/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "MNase", "@id": "/enzymes/MNase/", "uuid": "e781b59c-ef3d-4ae4-9a94-4a34190bc6d2", "status": "released", "@type": ["Enzyme", "Item"], "display_title": "MNase", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2022-06-29T15:17:03.708604+00:00"}, "experiment_type": {"display_title": "Micro-C", "@type": ["ExperimentType", "Item"], "status": "released", "title": "Micro-C", "uuid": "bc7899cf-8352-4360-b9be-efc3c7e3a574", "@id": "/experiment-types/micro-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"accession": "4DNES21D8SP8", "uuid": "a9007b58-6a8c-4d22-8f6f-f9f347e58165", "@id": "/experiment-set-replicates/4DNES21D8SP8/", "experimentset_type": "replicate", "status": "released", "display_title": "4DNES21D8SP8", "@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": "Job Dekker, UMMS", "experiment_type": "Micro-C", "experiment_bucket": "processed file", "assay_info": "MNase", "dataset": "Micro-C on H1 and HFF cells", "condition": "H1", "replicate_info": "Biorep 2, Techrep 4", "biosource_name": "H1-hESC (Tier 1)", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFI89L17XY", "href": "/files-processed/4DNFI89L17XY/@@download/4DNFI89L17XY.pairs.gz", "upload_key": "da075dc9-ae2a-4045-8032-3affa0e064a6/4DNFI89L17XY.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/da075dc9-ae2a-4045-8032-3affa0e064a6/4DNFI89L17XY.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "hi-c-processing-pairs-nore 0.2.6 run 2019-02-25 20:17:51.176191", "uuid": "cb7b5b72-4021-451f-92b5-ea67940dbb7e", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/cb7b5b72-4021-451f-92b5-ea67940dbb7e/", "status": "released", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"status": "released", "accession": "4DNFI1O6IL1Q", "@id": "/files-processed/4DNFI1O6IL1Q/", "uuid": "8875caed-2919-4c1c-930d-c45168c4378a", "display_title": "4DNFI1O6IL1Q.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": "4DNFI2TK7L2F", "@id": "/files-processed/4DNFI2TK7L2F/", "uuid": "0abd0cb2-6e62-492f-97a8-6cd19f814e99", "display_title": "4DNFI2TK7L2F.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": "4DNFI9GMP2J8", "@id": "/files-processed/4DNFI9GMP2J8/", "uuid": "d13aa1ea-053c-4113-94fe-a1e7ab1dbbab", "display_title": "4DNFI9GMP2J8.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": "4DNFI8B6A6A2", "@id": "/files-processed/4DNFI8B6A6A2/", "uuid": "2e6a2d0e-407b-4bfd-b4fb-d4b4ba410d40", "display_title": "4DNFI8B6A6A2.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, no restriction enzyme 0.2.6", "uuid": "c19ee11e-9d5a-454f-af50-600a0cf990b6", "@id": "/workflows/4DNWFQVDVA37/", "status": "released", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists, no restriction enzyme 0.2.6 - 4DNWFQVDVA37", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"@id": "/files-reference/4DNFI823LSII/", "status": "released", "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "@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/4DNFI8GM4EL9/", "status": "released", "display_title": "4DNFI8GM4EL9.pairs.gz", "uuid": "513ae1b6-bfd1-4d63-b3c0-fbab5612cb71", "accession": "4DNFI8GM4EL9", "@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/4DNFIMT4PHZ1/", "status": "released", "display_title": "4DNFIMT4PHZ1.pairs.gz", "uuid": "700e4c70-576c-4383-a897-2c4c8907636c", "accession": "4DNFIMT4PHZ1", "@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/4DNFIULY29IQ/", "status": "released", "display_title": "4DNFIULY29IQ.pairs.gz", "uuid": "d435a562-0128-4ee0-ad43-dea17c90e80b", "accession": "4DNFIULY29IQ", "@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/4DNFI2YHYAJO/", "status": "released", "display_title": "4DNFI2YHYAJO.pairs.gz", "uuid": "74278d7e-2111-427d-8b80-598228c208eb", "accession": "4DNFI2YHYAJO", "@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/4DNFI89L17XY/", "status": "released", "display_title": "4DNFI89L17XY.pairs.gz", "uuid": "da075dc9-ae2a-4045-8032-3affa0e064a6", "accession": "4DNFI89L17XY", "@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/4DNFIIYUGYBU/", "status": "released", "display_title": "4DNFIIYUGYBU.pairs.gz", "uuid": "698f025e-f870-4b15-aed7-ab56d032253c", "accession": "4DNFIIYUGYBU", "@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/4DNFING6ZFDF/", "status": "released", "display_title": "4DNFING6ZFDF.pairs.gz", "uuid": "8db74241-ffd5-4c2d-aa6b-81d64c80c5a3", "accession": "4DNFING6ZFDF", "@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/4DNFIBMG8YA3/", "status": "released", "display_title": "4DNFIBMG8YA3.pairs.gz", "uuid": "9f197b31-ee6e-481c-94b7-880d811392e5", "accession": "4DNFIBMG8YA3", "@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/4DNFIXP9MVBU/", "status": "released", "display_title": "4DNFIXP9MVBU.pairs.gz", "uuid": "5f7934e4-2f67-42c3-8a2c-2efd9f50bee8", "accession": "4DNFIXP9MVBU", "@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": "pairsqc-single 0.2.6 run 2019-02-28 18:09:14.967488", "uuid": "256294ca-fc5f-4d43-a2e6-a513efdf9b3a", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/256294ca-fc5f-4d43-a2e6-a513efdf9b3a/", "status": "released", "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI89L17XY/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/ded82cdd-4ae8-4429-9cdf-71edf09e2010/", "status": "released", "uuid": "ded82cdd-4ae8-4429-9cdf-71edf09e2010", "display_title": "QualityMetricPairsqc from 2019-02-28", "@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/4DNFI823LSII/", "status": "released", "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "@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/4DNFI89L17XY/", "status": "released", "display_title": "4DNFI89L17XY.pairs.gz", "uuid": "da075dc9-ae2a-4045-8032-3affa0e064a6", "accession": "4DNFI89L17XY", "@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"]}}], "workflow_run_outputs": [{"display_title": "hi-c-processing-bam 0.2.6 run 2019-02-21 04:22:38.111726", "@id": "/workflow-runs-awsem/112720e8-e39b-4998-a120-ef222e3062fe/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "uuid": "112720e8-e39b-4998-a120-ef222e3062fe", "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": "4DNFI5PXT1KG.bam", "uuid": "bec29091-7013-4fa7-9ccf-e41416b51798", "status": "released", "accession": "4DNFI5PXT1KG", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI5PXT1KG/", "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": "4DNFI89L17XY.pairs.gz", "uuid": "da075dc9-ae2a-4045-8032-3affa0e064a6", "status": "released", "accession": "4DNFI89L17XY", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI89L17XY/", "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": "hg38.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823LSII/", "status": "released", "display_title": "4DNFI823LSII.chrom.sizes", "accession": "4DNFI823LSII", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "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/4DNFIZB7TKTR/", "status": "released", "display_title": "4DNFIZB7TKTR.bam", "accession": "4DNFIZB7TKTR", "uuid": "6dc6dfa0-e698-4050-bebc-26ba280977f8", "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/4DNFISLSJ4JC/", "status": "released", "display_title": "4DNFISLSJ4JC.bam", "accession": "4DNFISLSJ4JC", "uuid": "7f8a6109-e9b7-44c0-9cc0-4fcd8c1bcb08", "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/4DNFI89L17XY/4DNFI89L17XY.plot_table.out", "source_experiment_sets": [{"status": "released", "display_title": "4DNES21D8SP8", "@id": "/experiment-set-replicates/4DNES21D8SP8/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "a9007b58-6a8c-4d22-8f6f-f9f347e58165", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXCL5AQ32/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2022-06-29T15:17:03.708604+00:00"}}, {"parent": "/files-processed/4DNFI89L17XY/", "embedded_path": "last_modified", "item": {"date_modified": "2021-05-17T21:42:17.394202+00:00"}}]}, "validation-errors": []}