{"lab": {"@id": "/labs/4dn-dcic-lab/", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "display_title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "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": {"@id": "/awards/1U01CA200059-01/", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "center_title": "DCIC - DCIC", "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", "name": "1U01CA200059-01", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "9d7af1c2d78dfb62114c45fdb2f73e48", "status": "released", "aliases": [], "accession": "4DNFIJMOWTE1", "file_size": 48705838, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIJMOWTE1/@@download/4DNFIJMOWTE1.pairs.gz.px2", "uuid": "4b3a51d1-6360-4804-8595-d11593be6260", "md5sum": "af06ffab9eeeaabfc6c7527c3f1d9feb", "status": "released", "filename": "4DNFIJMOWTE1", "accession": "4DNFIJMOWTE1", "file_size": 4395163, "upload_key": "4b3a51d1-6360-4804-8595-d11593be6260/4DNFIJMOWTE1.pairs.gz.px2", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs_px2/", "display_title": "pairs_px2", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content_md5sum": "af06ffab9eeeaabfc6c7527c3f1d9feb"}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-02-23T22:02:03.165562+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-10T08:36:29.873741+00:00"}, "content_md5sum": "a48dc1dbf5451f9102036ac08ec8572d", "public_release": "2019-05-15", "quality_metric": {"Short cis reads (<20kb)": 508756, "@id": "/quality-metrics-pairsqc/7a7fb33e-6aa9-4d50-b065-5e5bc46c0f30/", "uuid": "7a7fb33e-6aa9-4d50-b065-5e5bc46c0f30", "Cis reads (>20kb)": 1433077, "Trans reads": 378483, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJMOWTE1/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2018-03-05", "Total reads": 2320316, "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "2320316", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "61.762", "tooltip": "Percent of filtered reads (=1.43m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.926", "tooltip": "Percent of filtered reads (=0.51m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.312", "tooltip": "Percent of filtered reads (=0.38m)", "numberType": "percent"}]}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2019-05-15", "contributing_labs": [{"@type": ["Lab", "Item"], "display_title": "Erez Lieberman Aiden, BCM", "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "@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": ["797095f5-1599-4844-8aad-3d4d18758073"], "file_classification": "processed file", "@id": "/files-processed/4DNFIJMOWTE1/", "@type": ["FileProcessed", "File", "Item"], "uuid": "4b3a51d1-6360-4804-8595-d11593be6260", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIJMOWTE1.pairs.gz", "external_references": [], "experiments": [{"accession": "4DNEXRIDF1WQ", "@type": ["ExperimentCaptureC", "Experiment", "Item"], "display_title": "Capture Hi-C on HAP-1 with MboI - 4DNEXRIDF1WQ", "@id": "/experiments-capture-c/4DNEXRIDF1WQ/", "uuid": "797095f5-1599-4844-8aad-3d4d18758073", "status": "released", "biosample": {"biosource_summary": "HAP-1", "@id": "/biosamples/4DNBSB5WE9MA/", "display_title": "4DNBSB5WE9MA", "treatments_summary": "None", "accession": "4DNBSB5WE9MA", "modifications_summary": "None", "status": "released", "@type": ["Biosample", "Item"], "uuid": "a0740ba1-c0e0-45b7-bfac-b939ba2f8a95", "biosource": [{"@type": ["Biosource", "Item"], "biosource_type": "immortalized cell line", "display_title": "HAP-1 - 4DNSRNIAESOK", "status": "released", "@id": "/biosources/4DNSRNIAESOK/", "uuid": "18fc203e-0b65-43b7-8373-0c8fdf5eff57", "cell_line_tier": "Unclassified", "tissue": {"preferred_name": "blood cell", "term_name": "blood cell", "@type": ["OntologyTerm", "Item"], "term_id": "CL:0000081", "@id": "/ontology-terms/CL:0000081/", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "display_title": "blood cell", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"preferred_name": "HAP-1", "status": "released", "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "term_id": "EFO:0007598", "term_name": "HAP-1", "display_title": "HAP-1", "@id": "/ontology-terms/EFO:0007598/", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [], "individual": {"protected_data": false, "display_title": "4DNINGLJ7A6Z", "@type": ["IndividualHuman", "Individual", "Item"], "@id": "/individuals-human/4DNINGLJ7A6Z/", "uuid": "6e37c213-33dd-4aff-aedb-b466a4b2aa45", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "scientific_name": "Homo sapiens", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "status": "released", "@id": "/organisms/9606/", "name": "human", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "MboI", "display_title": "MboI", "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "c5295325-d69e-4d4d-953a-322e52017272", "experimentset_type": "replicate", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNESEYZC9D9", "status": "released", "display_title": "4DNESEYZC9D9", "@id": "/experiment-set-replicates/4DNESEYZC9D9/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"@type": ["ExperimentType", "Item"], "@id": "/experiment-types/capture-hi-c/", "status": "released", "display_title": "Capture Hi-C", "uuid": "62ddb15e-4907-4b8a-bfca-cdd4371cb179", "title": "Capture Hi-C", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2020-11-04T16:36:11.142981+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": "Capture Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "replicate_info": "Biorep 4, Techrep 3", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIJMOWTE1", "href": "/files-processed/4DNFIJMOWTE1/@@download/4DNFIJMOWTE1.pairs.gz", "upload_key": "4b3a51d1-6360-4804-8595-d11593be6260/4DNFIJMOWTE1.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/4b3a51d1-6360-4804-8595-d11593be6260/4DNFIJMOWTE1.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"display_title": "pairsqc-single 0.2.5 run 2018-03-05 23:17:27.472211", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "@id": "/workflow-runs-awsem/405784df-7d96-4b46-93ca-728ec7e10b99/", "uuid": "405784df-7d96-4b46-93ca-728ec7e10b99", "input_files": [{"workflow_argument_name": "input_pairs", "value": {"uuid": "4b3a51d1-6360-4804-8595-d11593be6260", "display_title": "4DNFIJMOWTE1.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIJMOWTE1/", "accession": "4DNFIJMOWTE1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "accession": "4DNFI823LSII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "@id": "/file-formats/chromsizes/", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "report", "value_qc": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJMOWTE1/pairsqc_report.html", "overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/7a7fb33e-6aa9-4d50-b065-5e5bc46c0f30/", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2018-03-05", "uuid": "7a7fb33e-6aa9-4d50-b065-5e5bc46c0f30", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "display_title": "PairsQC 0.2.5 - 4DNWF36CF3A1", "uuid": "ae3a87cb-3fa2-469e-97c7-540fc2d0a117", "@id": "/workflows/4DNWF36CF3A1/", "status": "released", "title": "PairsQC 0.2.5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "hi-c-processing-pairs-nonorm 0.2.6 run 2018-06-01 13:20:37.560715", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "@id": "/workflow-runs-awsem/d979b13f-71ba-4450-a602-526370f6cd4d/", "uuid": "d979b13f-71ba-4450-a602-526370f6cd4d", "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38.mainonly.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "accession": "4DNFI823LSII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "@id": "/file-formats/chromsizes/", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "d2df9612-1a43-4d62-8a84-3bdea94c3f29", "display_title": "4DNFIEXMANLK.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIEXMANLK/", "accession": "4DNFIEXMANLK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "d14e2179-e383-4464-9327-5b529183648b", "display_title": "4DNFI2HTCYH7.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI2HTCYH7/", "accession": "4DNFI2HTCYH7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "4b3a51d1-6360-4804-8595-d11593be6260", "display_title": "4DNFIJMOWTE1.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIJMOWTE1/", "accession": "4DNFIJMOWTE1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "c604d8ca-3aa6-4317-8b87-0668e294762b", "display_title": "4DNFIH2DFKQM.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIH2DFKQM/", "accession": "4DNFIH2DFKQM", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "738f4f6d-d788-45ee-adf1-d4231a3c0407", "display_title": "4DNFISVDXLEZ.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISVDXLEZ/", "accession": "4DNFISVDXLEZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "f5895c78-f472-43f7-9cef-465c97c33284", "display_title": "4DNFIFH9S9J5.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIFH9S9J5/", "accession": "4DNFIFH9S9J5", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "28ef54d9-ef43-4134-aa2f-de76a03a3fef", "display_title": "4DNFIPMCVMBU.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPMCVMBU/", "accession": "4DNFIPMCVMBU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "restriction_file", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d582084", "display_title": "4DNFI823L812.txt", "status": "released", "@type": ["FileReference", "File", "Item"], "filename": "hg38_MboI.txt", "@id": "/files-reference/4DNFI823L812/", "accession": "4DNFI823L812", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "juicer_format_restriction_site_file", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "status": "released", "@id": "/file-formats/juicer_format_restriction_site_file/", "display_title": "juicer_format_restriction_site_file", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"display_title": "4DNFIG5TY53R.pairs.gz", "uuid": "4ad7ccfc-eed6-49df-b481-41f8225193fd", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIG5TY53R", "status": "released", "@id": "/files-processed/4DNFIG5TY53R/", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"display_title": "4DNFILIQWMDB.hic", "uuid": "dded1778-d705-4e73-b466-2b4a230a277a", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFILIQWMDB", "status": "released", "@id": "/files-processed/4DNFILIQWMDB/", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "file_format": "hic", "display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"display_title": "4DNFICMDXA2S.mcool", "uuid": "9b8bda8b-d10d-4f67-89b3-de0f0e27470b", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFICMDXA2S", "status": "released", "@id": "/files-processed/4DNFICMDXA2S/", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "file_format": "mcool", "display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists, no normalization 0.2.6 - 4DNWF7WTHVSA", "uuid": "bd6e25ea-f368-4758-a821-d30e0b5a4100", "@id": "/workflows/4DNWF7WTHVSA/", "status": "released", "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists, no normalization 0.2.6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"error": "no view permissions"}, {"error": "no view permissions"}], "workflow_run_outputs": [{"@id": "/workflow-runs-awsem/d46bd5c9-4dd0-410f-8379-3379af5a965e/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "hi-c-processing-bam 0.2.6 run 2018-02-23 22:02:03.274046", "uuid": "d46bd5c9-4dd0-410f-8379-3379af5a965e", "input_files": [{"workflow_argument_name": "input_bams", "value": {"accession": "4DNFI6W3ZKLN", "display_title": "4DNFI6W3ZKLN.bam", "@id": "/files-processed/4DNFI6W3ZKLN/", "uuid": "bc0c3640-ddcc-4cad-a295-a7e4a1e1a1e5", "status": "released", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIP19EG6G", "display_title": "4DNFIP19EG6G.bam", "@id": "/files-processed/4DNFIP19EG6G/", "uuid": "58a0d860-16a2-4321-8e26-18c27fc1d909", "status": "released", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFIN16HNSV", "display_title": "4DNFIN16HNSV.bam", "@id": "/files-processed/4DNFIN16HNSV/", "uuid": "c63fc2cd-b724-4fa9-bbdd-1ed2f51ef450", "status": "released", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"accession": "4DNFI9J7WU2M", "display_title": "4DNFI9J7WU2M.bam", "@id": "/files-processed/4DNFI9J7WU2M/", "uuid": "c9779e44-41df-4827-8366-a33834fa97df", "status": "released", "@type": ["FileProcessed", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chromsize", "value": {"accession": "4DNFI823LSII", "display_title": "4DNFI823LSII.chrom.sizes", "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "status": "released", "@type": ["FileReference", "File", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIA8RUFMX/", "status": "released", "accession": "4DNFIA8RUFMX", "uuid": "9b2e1b08-48c4-4b42-a7bc-05ecc393c3fd", "display_title": "4DNFIA8RUFMX.bam", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "bam", "status": "released", "display_title": "bam", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@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": {"@id": "/files-processed/4DNFIJMOWTE1/", "status": "released", "accession": "4DNFIJMOWTE1", "uuid": "4b3a51d1-6360-4804-8595-d11593be6260", "display_title": "4DNFIJMOWTE1.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "file_format": {"file_format": "pairs", "status": "released", "display_title": "pairs", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Hi-C Post-alignment Processing 0.2.6", "@id": "/workflows/4DNWFT69RBY4/", "@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "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/4DNFIJMOWTE1/4DNFIJMOWTE1.plot_table.out", "source_experiment_sets": [{"@id": "/experiment-set-replicates/4DNESEYZC9D9/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESEYZC9D9", "uuid": "c5295325-d69e-4d4d-953a-322e52017272", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-capture-c/4DNEXRIDF1WQ/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2020-11-04T16:36:11.142981+00:00"}}, {"parent": "/files-processed/4DNFIJMOWTE1/", "embedded_path": "last_modified", "item": {"date_modified": "2022-01-10T08:36:29.873741+00:00"}}]}, "validation-errors": []}