{"lab": {"title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"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", "@id": "/awards/1U01CA200059-01/", "@type": ["Award", "Item"], "name": "1U01CA200059-01", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "status": "current", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "center_title": "DCIC - DCIC", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "e19d19c2eeeff1ff9c2e1f939b9569ec", "status": "released", "aliases": [], "accession": "4DNFIMLQR82B", "file_size": 271741586, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIMLQR82B/@@download/4DNFIMLQR82B.pairs.gz.px2", "uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "md5sum": "639f0af217a0459dbe374697f5923ba1", "status": "released", "filename": "4DNFIMLQR82B", "accession": "4DNFIMLQR82B", "file_size": 14732708, "upload_key": "36af4e97-0888-431a-ace5-c9b9575d47e4/4DNFIMLQR82B.pairs.gz.px2", "file_format": {"display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content_md5sum": "639f0af217a0459dbe374697f5923ba1"}], "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-01-24T12:54:54.704607+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-11T15:59:11.066779+00:00"}, "content_md5sum": "6f173732c548b6d3c3a5fbfd056a7d65", "public_release": "2018-02-23", "quality_metric": {"status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "43699285-316e-4a34-9963-0c9bbf99f8cc", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMLQR82B/pairsqc_report.html", "Short cis reads (<20kb)": 3578876, "@id": "/quality-metrics-pairsqc/43699285-316e-4a34-9963-0c9bbf99f8cc/", "Trans reads": 2725794, "Cis reads (>20kb)": 6822234, "display_title": "QualityMetricPairsqc from 2018-01-26", "Total reads": 13126904, "quality_metric_summary": [{"title": "Filtered Reads", "value": "13126904", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "51.971", "tooltip": "Percent of filtered reads (=6.82m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "27.264", "tooltip": "Percent of filtered reads (=3.58m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "20.765", "tooltip": "Percent of filtered reads (=2.73m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2018-02-23", "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"}], "@type": ["Lab", "Item"], "@id": "/labs/erez-liebermanaiden-lab/", "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": ["cd128193-32a0-43be-a990-266a16574d1e"], "file_classification": "processed file", "@id": "/files-processed/4DNFIMLQR82B/", "@type": ["FileProcessed", "File", "Item"], "uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIMLQR82B.pairs.gz", "external_references": [], "experiments": [{"@id": "/experiments-hi-c/4DNEXAK4YH22/", "display_title": "in situ Hi-C on CC-2551 with MboI - 4DNEXAK4YH22", "@type": ["ExperimentHiC", "Experiment", "Item"], "status": "released", "uuid": "cd128193-32a0-43be-a990-266a16574d1e", "accession": "4DNEXAK4YH22", "biosample": {"display_title": "4DNBS28W97QT", "treatments_summary": "None", "@type": ["Biosample", "Item"], "uuid": "f5d1d3e2-f123-46a6-86f1-7a77ba51c28b", "@id": "/biosamples/4DNBS28W97QT/", "modifications_summary": "None", "biosource_summary": "CC-2551", "accession": "4DNBS28W97QT", "status": "released", "biosource": [{"status": "released", "uuid": "6d259b58-67fb-450b-9e0e-94a8335418b1", "biosource_type": "primary cell", "display_title": "CC-2551 - 4DNSRZZBX5T8", "cell_line_tier": "Unclassified", "@id": "/biosources/4DNSRZZBX5T8/", "@type": ["Biosource", "Item"], "organism": {"scientific_name": "Homo sapiens", "name": "human", "status": "released", "display_title": "H. sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"uuid": "b0b22248-9f2c-4f37-b167-b125a7a6594b", "preferred_name": "epithelium of mammary gland", "display_title": "epithelium of mammary gland", "@id": "/ontology-terms/UBERON:0003244/", "status": "released", "term_name": "epithelium of mammary gland", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0003244", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "cell_line": {"status": "released", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/4DN:0000006/", "uuid": "111205bc-8535-4448-903e-854af460a233", "preferred_name": "CC-2551", "display_title": "CC-2551", "term_id": "4DN:0000006", "term_name": "CC-2551", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@type": ["IndividualHuman", "Individual", "Item"], "protected_data": false, "@id": "/individuals-human/4DNINXXBWLRB/", "display_title": "4DNINXXBWLRB", "uuid": "e0715bde-6af0-47c9-a0fb-43606b537c4e", "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": {"title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "status": "released", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "name": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "display_title": "MboI", "@id": "/enzymes/MboI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "82bb67b5-b1c9-4f9e-aced-17121750deb8", "accession": "4DNESPSJPW7R", "@id": "/experiment-sets/4DNESPSJPW7R/", "display_title": "4DNESPSJPW7R", "status": "released", "@type": ["ExperimentSet", "Item"], "experimentset_type": "custom", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "7b535bf7-cd95-4a76-8134-3b43a1651b11", "accession": "4DNESIE5R9HS", "@id": "/experiment-set-replicates/4DNESIE5R9HS/", "display_title": "4DNESIE5R9HS", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2024-07-08T14:26:07.037382+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 CC-2551", "condition": "Preferred protocol - in situ Hi-C on CC2551 with MboI and bio-dATP", "replicate_info": "Biorep 2, Techrep 5", "biosource_name": "CC-2551", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIMLQR82B", "href": "/files-processed/4DNFIMLQR82B/@@download/4DNFIMLQR82B.pairs.gz", "upload_key": "36af4e97-0888-431a-ace5-c9b9575d47e4/4DNFIMLQR82B.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/36af4e97-0888-431a-ace5-c9b9575d47e4/4DNFIMLQR82B.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "pairsqc-single 0.2.5 run 2018-01-26 14:59:01.287310", "@id": "/workflow-runs-awsem/9c1bb630-1d9c-4180-87c4-0607c7dabe14/", "uuid": "9c1bb630-1d9c-4180-87c4-0607c7dabe14", "input_files": [{"workflow_argument_name": "input_pairs", "value": {"@id": "/files-processed/4DNFIMLQR82B/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIMLQR82B.pairs.gz", "accession": "4DNFIMLQR82B", "uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsizes", "value": {"@id": "/files-reference/4DNFI823LSII/", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "accession": "4DNFI823LSII", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "file_format": {"file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report", "value_qc": {"status": "released", "@id": "/quality-metrics-pairsqc/43699285-316e-4a34-9963-0c9bbf99f8cc/", "uuid": "43699285-316e-4a34-9963-0c9bbf99f8cc", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2018-01-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMLQR82B/pairsqc_report.html", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "workflow": {"status": "released", "title": "PairsQC 0.2.5", "@id": "/workflows/4DNWF36CF3A1/", "uuid": "ae3a87cb-3fa2-469e-97c7-540fc2d0a117", "@type": ["Workflow", "Item"], "display_title": "PairsQC 0.2.5 - 4DNWF36CF3A1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "hi-c-processing-pairs 0.2.6 run 2018-02-14 07:34:52.451076", "@id": "/workflow-runs-awsem/819a378d-77aa-4cb1-8fc7-577cf49ce7e6/", "uuid": "819a378d-77aa-4cb1-8fc7-577cf49ce7e6", "input_files": [{"workflow_argument_name": "chromsizes", "value": {"@id": "/files-reference/4DNFI823LSII/", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "display_title": "4DNFI823LSII.chrom.sizes", "accession": "4DNFI823LSII", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "file_format": {"file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFI97O9SAZ/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI97O9SAZ.pairs.gz", "accession": "4DNFI97O9SAZ", "uuid": "85802239-0bf9-44a4-90dc-99dc2a74d6fd", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFIKZP38N6/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIKZP38N6.pairs.gz", "accession": "4DNFIKZP38N6", "uuid": "d8c7f71d-5a12-4335-a3af-c365092268d0", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFIMCSMWKT/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIMCSMWKT.pairs.gz", "accession": "4DNFIMCSMWKT", "uuid": "3a2ac827-8e85-436f-b325-64663073bd33", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFI7QWGXGQ/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI7QWGXGQ.pairs.gz", "accession": "4DNFI7QWGXGQ", "uuid": "b37fa850-12dc-4068-9790-74b39572f1a5", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFIWSXKIRR/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIWSXKIRR.pairs.gz", "accession": "4DNFIWSXKIRR", "uuid": "ef9015ad-fe89-454b-88fd-e9d6a1d782dd", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFIMLQR82B/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIMLQR82B.pairs.gz", "accession": "4DNFIMLQR82B", "uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "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/4DNFI823L812/", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38_MboI.txt", "display_title": "4DNFI823L812.txt", "accession": "4DNFI823L812", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d582084", "file_format": {"file_format": "juicer_format_restriction_site_file", "@id": "/file-formats/juicer_format_restriction_site_file/", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "juicer_format_restriction_site_file", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"display_title": "4DNFIIFAUT24.pairs.gz", "accession": "4DNFIIFAUT24", "uuid": "d35fb922-8f81-4603-957b-fe2ebd2d1599", "@id": "/files-processed/4DNFIIFAUT24/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "@type": ["FileFormat", "Item"], "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"display_title": "4DNFIMEG1QIC.hic", "accession": "4DNFIMEG1QIC", "uuid": "fc01b381-3665-4225-88ee-2e5e9ecb7324", "@id": "/files-processed/4DNFIMEG1QIC/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "status": "released", "@id": "/file-formats/hic/", "display_title": "hic", "@type": ["FileFormat", "Item"], "file_format": "hic", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"display_title": "4DNFIGUIV5KO.mcool", "accession": "4DNFIGUIV5KO", "uuid": "e79fac75-3777-4f11-ab91-2afdb21f74a5", "@id": "/files-processed/4DNFIGUIV5KO/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "@id": "/file-formats/mcool/", "display_title": "mcool", "@type": ["FileFormat", "Item"], "file_format": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "cooler_normvector", "value": {"display_title": "4DNFIRHI7CGL.normvector.juicerformat.gz", "accession": "4DNFIRHI7CGL", "uuid": "6ac6f43b-ae76-45a5-b77d-6a288497c6f7", "@id": "/files-processed/4DNFIRHI7CGL/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "status": "released", "@id": "/file-formats/normvector_juicerformat/", "display_title": "normvector_juicerformat", "@type": ["FileFormat", "Item"], "file_format": "normvector_juicerformat", "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": {"status": "released", "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6", "@id": "/workflows/4DNWFTKI1QLK/", "uuid": "c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0", "@type": ["Workflow", "Item"], "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"]}}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "md5 0.2.6 run 2022-01-11 15:53:55.710917", "@id": "/workflow-runs-awsem/47bff2a6-8d19-480b-9406-98c3d6142a29/", "uuid": "47bff2a6-8d19-480b-9406-98c3d6142a29", "input_files": [{"workflow_argument_name": "input_file", "value": {"@id": "/files-processed/4DNFIMLQR82B/", "status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIMLQR82B.pairs.gz", "accession": "4DNFIMLQR82B", "uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "file_format": {"file_format": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "report"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "workflow": {"status": "released", "title": "md5 0.2.6", "@id": "/workflows/4DNWF2HFF82B/", "uuid": "c77a117b-9a58-477e-aaa5-291a109a99f6", "@type": ["Workflow", "Item"], "display_title": "md5 0.2.6 - 4DNWF2HFF82B", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow_run_outputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "hi-c-processing-bam 0.2.6 run 2018-01-24 12:54:54.848550", "uuid": "15f3496d-ef73-4081-b469-29d2ab145f25", "@id": "/workflow-runs-awsem/15f3496d-ef73-4081-b469-29d2ab145f25/", "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"uuid": "a4423c42-6000-4561-bb64-088b24dd496f", "display_title": "4DNFIT2Z8ULY.bam", "@id": "/files-processed/4DNFIT2Z8ULY/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIT2Z8ULY", "file_format": {"display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "status": "released", "@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": "filtered_pairs", "value": {"uuid": "36af4e97-0888-431a-ace5-c9b9575d47e4", "display_title": "4DNFIMLQR82B.pairs.gz", "@id": "/files-processed/4DNFIMLQR82B/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "accession": "4DNFIMLQR82B", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_bams", "value": {"display_title": "4DNFIH4I9N3P.bam", "@id": "/files-processed/4DNFIH4I9N3P/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIH4I9N3P", "uuid": "5430e9aa-66a2-4b10-ba45-3768418f4f9c", "status": "released", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "file_format": "bam", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsize", "value": {"display_title": "4DNFI823LSII.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "accession": "4DNFI823LSII", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "status": "released", "file_format": {"display_title": "chromsizes", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "title": "Hi-C Post-alignment Processing 0.2.6", "@type": ["Workflow", "Item"], "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@id": "/workflows/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/4DNFIMLQR82B/4DNFIMLQR82B.plot_table.out", "source_experiment_sets": [{"uuid": "82bb67b5-b1c9-4f9e-aced-17121750deb8", "display_title": "4DNESPSJPW7R", "status": "released", "@type": ["ExperimentSet", "Item"], "@id": "/experiment-sets/4DNESPSJPW7R/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "7b535bf7-cd95-4a76-8134-3b43a1651b11", "display_title": "4DNESIE5R9HS", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNESIE5R9HS/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXAK4YH22/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-08T14:26:07.037382+00:00"}}, {"parent": "/files-processed/4DNFIMLQR82B/", "embedded_path": "last_modified", "item": {"date_modified": "2022-01-11T15:59:11.066779+00:00"}}]}, "validation-errors": []}