{"lab": {"uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "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.", "name": "1U01CA200059-01", "status": "current", "@type": ["Award", "Item"], "project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "@id": "/awards/1U01CA200059-01/", "center_title": "DCIC - DCIC", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "28e29b9b03fc0f0870e5b56be1250bfd", "status": "released", "accession": "4DNFIKNPZDGB", "file_size": 10986001659, "file_type": "alignments", "description": "This is an output file of the Hi-C processing pipeline", "file_format": {"display_title": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "file_format": "bam", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-12-05T01:09:05.460804+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-03-28T15:43:38.545076+00:00"}, "public_release": "2019-10-11", "quality_metric": {"@id": "/quality-metrics-bamqc/8bb1754b-2ff7-484b-b396-c4860bd6ba2f/", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2020-01-16", "status": "released", "uuid": "8bb1754b-2ff7-484b-b396-c4860bd6ba2f", "quality_metric_summary": [{"title": "Total Reads", "value": "105432662", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "20.02", "tooltip": "Percent of total reads (=21.11m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "9.472", "tooltip": "Percent of total reads (=9.99m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "23.445", "tooltip": "Percent of total reads (=24.72m)", "numberType": "percent"}, {"title": "Walks", "value": "0.004", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.267", "tooltip": "Percent of total reads (=0.28m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "galGal5", "project_release": "2019-10-11", "contributing_labs": [{"correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "display_title": "Job Dekker, UMMS", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "@id": "/labs/job-dekker-lab/", "status": "current", "@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": ["ef1866a8-5dcd-4a7a-a8b7-ac3240bd5a07"], "file_classification": "processed file", "percent_clipped_sites_with_re_motif": 60.67, "@id": "/files-processed/4DNFIKNPZDGB/", "@type": ["FileProcessed", "File", "Item"], "uuid": "07048f4b-1bd7-4e76-a1fd-9799fc25aa59", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIKNPZDGB.bam", "external_references": [], "experiments": [{"uuid": "ef1866a8-5dcd-4a7a-a8b7-ac3240bd5a07", "@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEX4G1FPER/", "accession": "4DNEX4G1FPER", "display_title": "Dilution Hi-C on DT40 with random integration of X. laevis Cdk1, CDK1 disruption with HindIII - 4DNEX4G1FPER", "status": "released", "biosample": {"biosource_summary": "DT40 with random integration of X. laevis Cdk1, CDK1 disruption", "@id": "/biosamples/4DNBSEF9OYA5/", "treatments_summary": "1NM-PP1 treatment (2.0 \u03bcM, 10.0h)", "status": "released", "display_title": "4DNBSEF9OYA5", "@type": ["Biosample", "Item"], "accession": "4DNBSEF9OYA5", "uuid": "2cfcb5e3-1122-41ed-896c-766a2e586f28", "modifications_summary": "None", "biosource": [{"display_title": "DT40 with random integration of X. laevis Cdk1, CDK1 disruption - 4DNSRFB455CY", "@id": "/biosources/4DNSRFB455CY/", "@type": ["Biosource", "Item"], "status": "released", "uuid": "bdb9d92e-1f52-4e84-a484-78e595791e5e", "cell_line_tier": "Unclassified", "biosource_type": "immortalized cell line", "organism": {"uuid": "fed8c206-762f-497f-821b-1c8ff7900bd2", "name": "chicken", "scientific_name": "Gallus gallus", "display_title": "G. gallus", "status": "released", "@id": "/organisms/9031/", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"@type": ["OntologyTerm", "Item"], "display_title": "bursa of Fabricius", "term_name": "bursa of Fabricius", "status": "released", "term_id": "UBERON:0003903", "uuid": "1bfd1088-3311-4711-8c41-83dbed3db972", "preferred_name": "bursa of Fabricius", "@id": "/ontology-terms/UBERON:0003903/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "modifications": [{"display_title": "random integration of X. laevis Cdk1", "override_modification_name": "random integration of X. laevis Cdk1", "status": "released", "@type": ["Modification", "Item"], "genomic_change": "insertion", "uuid": "4dca1ddb-ab74-44f5-ac84-738b0198886d", "@id": "/modifications/4dca1ddb-ab74-44f5-ac84-738b0198886d/", "modification_type": "Stable Transfection", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "Crispr disruption for CDK1 chicken gene", "status": "released", "@type": ["Modification", "Item"], "genomic_change": "disruption", "uuid": "fb27fdf6-4199-4179-8bb0-6101b1404aee", "@id": "/modifications/fb27fdf6-4199-4179-8bb0-6101b1404aee/", "modification_type": "Crispr", "target_of_mod": [{"@type": ["BioFeature", "Item"], "display_title": "CDK1 chicken gene", "status": "released", "@id": "/bio-features/03ca1ef3-0276-46ce-b277-13c123c9e520/", "uuid": "03ca1ef3-0276-46ce-b277-13c123c9e520", "organism_name": "chicken", "feature_type": {"display_title": "gene", "uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/SO:0000704/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "relevant_genes": [{"display_title": "CDK1", "uuid": "ecf839a7-e4fb-4703-a47b-b36d8562ea2c", "@id": "/genes/396252/", "status": "released", "@type": ["Gene", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_line": {"@id": "/ontology-terms/EFO:0006274/", "@type": ["OntologyTerm", "Item"], "preferred_name": "DT40", "status": "released", "term_name": "DT40", "display_title": "DT40", "term_id": "EFO:0006274", "uuid": "fd057734-0765-4007-b7eb-d71ac7cbef65", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINYWTTO3D", "status": "released", "uuid": "836856fd-a0f7-4daf-afb2-4a098df8e8fc", "@type": ["IndividualChicken", "Individual", "Item"], "@id": "/individuals-chicken/4DNINYWTTO3D/", "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": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "accession": "4DNESS8PTK6F", "display_title": "4DNESS8PTK6F", "@id": "/experiment-set-replicates/4DNESS8PTK6F/", "experimentset_type": "replicate", "uuid": "af0182ff-f87a-4cca-bf5d-2b07808d2787", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"display_title": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/HindIII/", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "name": "HindIII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"display_title": "Dilution Hi-C", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "status": "released", "@type": ["ExperimentType", "Item"], "title": "Dilution Hi-C", "@id": "/experiment-types/dilution-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2019-10-11T20:54:41.875645+00:00"}}], "file_type_detailed": "alignments (bam)", "track_and_facet_info": {"experimental_lab": "Job Dekker, UMMS", "experiment_type": "Dilution Hi-C", "experiment_bucket": "processed file", "assay_info": "HindIII", "dataset": "HiC on sync. chicken cells", "condition": "prometaphase (30m)", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "DT40 with random integration of X. laevis Cdk1, CDK1 disruption", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIKNPZDGB", "href": "/files-processed/4DNFIKNPZDGB/@@download/4DNFIKNPZDGB.bam", "upload_key": "07048f4b-1bd7-4e76-a1fd-9799fc25aa59/4DNFIKNPZDGB.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/07048f4b-1bd7-4e76-a1fd-9799fc25aa59/4DNFIKNPZDGB.bam", "tsv_notes": "", "workflow_run_inputs": [{"status": "released", "display_title": "re_checker_workflow v1.1 run 2020-04-23 05:50:07.549052", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "5851a758-756c-4c71-abbd-6839acb26eba", "@id": "/workflow-runs-awsem/5851a758-756c-4c71-abbd-6839acb26eba/", "output_files": [{"workflow_argument_name": "motif_percent"}], "input_files": [{"workflow_argument_name": "bamfile", "value": {"display_title": "4DNFIKNPZDGB.bam", "status": "released", "accession": "4DNFIKNPZDGB", "uuid": "07048f4b-1bd7-4e76-a1fd-9799fc25aa59", "@id": "/files-processed/4DNFIKNPZDGB/", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "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": {"@type": ["Workflow", "Item"], "status": "released", "display_title": "Restriction Enzyme Check, 1.1 - 4DNWFA4YPAGI", "title": "Restriction Enzyme Check, 1.1", "@id": "/workflows/4DNWFA4YPAGI/", "uuid": "e9eefa69-39b1-4e61-8889-5cb1cea401c0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "display_title": "bamqc v3 run 2020-01-16 21:03:33.995886", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "ad63ad64-7a11-4668-a9d1-08ea0ebb06c6", "@id": "/workflow-runs-awsem/ad63ad64-7a11-4668-a9d1-08ea0ebb06c6/", "output_files": [{"workflow_argument_name": "bam_qc", "value_qc": {"overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/8bb1754b-2ff7-484b-b396-c4860bd6ba2f/", "status": "released", "uuid": "8bb1754b-2ff7-484b-b396-c4860bd6ba2f", "display_title": "QualityMetricBamqc from 2020-01-16", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "bamfile", "value": {"display_title": "4DNFIKNPZDGB.bam", "status": "released", "accession": "4DNFIKNPZDGB", "uuid": "07048f4b-1bd7-4e76-a1fd-9799fc25aa59", "@id": "/files-processed/4DNFIKNPZDGB/", "@type": ["FileProcessed", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "file_format": "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": "chromsizes", "value": {"display_title": "4DNFIQFZW4DX.chrom.sizes", "filename": "galGal5.chrom.sizes", "status": "released", "accession": "4DNFIQFZW4DX", "uuid": "a863a0f9-327d-4db5-857a-110997ffc307", "@id": "/files-reference/4DNFIQFZW4DX/", "@type": ["FileReference", "File", "Item"], "file_format": {"@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "status": "released", "file_format": "chromsizes", "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": {"@type": ["Workflow", "Item"], "status": "released", "display_title": "Quality metrics for annotated bam files - 4DNWFBAMQCV3", "title": "Quality metrics for annotated bam files", "@id": "/workflows/4DNWFBAMQCV3/", "uuid": "42683ab1-59bf-4ec5-a973-030053a134f1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"@id": "/workflow-runs-awsem/efc73044-77a7-4133-a452-35314a5577f0/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "efc73044-77a7-4133-a452-35314a5577f0", "display_title": "hi-c-processing-bam 0.2.6 run 2018-12-05 01:09:06.131019", "status": "released", "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIKNPZDGB/", "accession": "4DNFIKNPZDGB", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "07048f4b-1bd7-4e76-a1fd-9799fc25aa59", "display_title": "4DNFIKNPZDGB.bam", "file_format": {"display_title": "bam", "file_format": "bam", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "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/4DNFIYH5QV8N/", "accession": "4DNFIYH5QV8N", "@type": ["FileProcessed", "File", "Item"], "status": "released", "uuid": "24e46e43-f7d8-447d-b6a5-737c4e29b841", "display_title": "4DNFIYH5QV8N.pairs.gz", "file_format": {"display_title": "pairs", "file_format": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsize", "value": {"filename": "galGal5.chrom.sizes", "display_title": "4DNFIQFZW4DX.chrom.sizes", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFIQFZW4DX/", "status": "released", "uuid": "a863a0f9-327d-4db5-857a-110997ffc307", "accession": "4DNFIQFZW4DX", "file_format": {"file_format": "chromsizes", "display_title": "chromsizes", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@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": {"display_title": "4DNFIDZGFGYE.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIDZGFGYE/", "status": "released", "uuid": "42c78653-a689-40d2-8da4-f28b2fe0749a", "accession": "4DNFIDZGFGYE", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIVYWMNFE.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIVYWMNFE/", "status": "released", "uuid": "85f5c45e-aaa3-442d-aabd-e6a81ab9b23f", "accession": "4DNFIVYWMNFE", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFISOIFQ1F.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISOIFQ1F/", "status": "released", "uuid": "ffb6a833-6e0c-472b-b415-6a0a66a8a529", "accession": "4DNFISOIFQ1F", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI7S5BMT3.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI7S5BMT3/", "status": "released", "uuid": "6414271c-8936-45cb-8912-d1d1627b7cf6", "accession": "4DNFI7S5BMT3", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIGXM5358.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIGXM5358/", "status": "released", "uuid": "7ef6df31-e7ca-44ab-a028-ff1d0668c2f1", "accession": "4DNFIGXM5358", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI2HCYW4U.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI2HCYW4U/", "status": "released", "uuid": "3a6ffa6a-0bf0-404c-9212-0711db5fec2b", "accession": "4DNFI2HCYW4U", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI1Y2SPJO.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1Y2SPJO/", "status": "released", "uuid": "ff796803-e260-4d82-9387-7c4c0e8680ab", "accession": "4DNFI1Y2SPJO", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIC18ED52.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIC18ED52/", "status": "released", "uuid": "36de0468-7d36-4869-9c88-e02d41b5b595", "accession": "4DNFIC18ED52", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI2Z3JLCW.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI2Z3JLCW/", "status": "released", "uuid": "afaad532-0e22-45a5-953e-ae67d723775f", "accession": "4DNFI2Z3JLCW", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIYRPGFNI.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIYRPGFNI/", "status": "released", "uuid": "696d2f49-426a-4de5-9120-a15ed88e93ea", "accession": "4DNFIYRPGFNI", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIPDGNR8W.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPDGNR8W/", "status": "released", "uuid": "e5aaff75-f910-4e3e-b830-ba1cefd009a5", "accession": "4DNFIPDGNR8W", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIIKN8YF9.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIIKN8YF9/", "status": "released", "uuid": "1c14678e-ac52-4f35-a6ae-17ec21517fb4", "accession": "4DNFIIKN8YF9", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIJ3PCTUI.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIJ3PCTUI/", "status": "released", "uuid": "98670a49-abc2-4790-a5d5-c2f6d9908479", "accession": "4DNFIJ3PCTUI", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIDLQSTSS.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIDLQSTSS/", "status": "released", "uuid": "85b272f8-dc61-475d-953f-da02d4ef6d47", "accession": "4DNFIDLQSTSS", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIGRN3U95.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIGRN3U95/", "status": "released", "uuid": "e6001b76-483c-49d0-b15d-093a2e5309b2", "accession": "4DNFIGRN3U95", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFITB9ODUA.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFITB9ODUA/", "status": "released", "uuid": "a13ecd32-1766-4b93-8a71-7d0ec73d247a", "accession": "4DNFITB9ODUA", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI85XTZWZ.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI85XTZWZ/", "status": "released", "uuid": "0d5f494a-d0ad-4ddb-9a49-c448e3fff44e", "accession": "4DNFI85XTZWZ", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI9G165FD.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI9G165FD/", "status": "released", "uuid": "35e38d93-0fec-4da4-9b56-49431a3003e3", "accession": "4DNFI9G165FD", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIPLFZB3T.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIPLFZB3T/", "status": "released", "uuid": "da5cada1-224b-4a32-b90c-52100341fe8c", "accession": "4DNFIPLFZB3T", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI7H33P1P.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI7H33P1P/", "status": "released", "uuid": "c55d2d67-f571-45c4-9a08-5f455fcd440b", "accession": "4DNFI7H33P1P", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIAQCB42J.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIAQCB42J/", "status": "released", "uuid": "b014f8c0-bf02-4d57-8919-db83ca1b6342", "accession": "4DNFIAQCB42J", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIBY13NJM.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIBY13NJM/", "status": "released", "uuid": "44415709-f970-4665-bec2-2e98479fc4a7", "accession": "4DNFIBY13NJM", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI6NI2PVT.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI6NI2PVT/", "status": "released", "uuid": "8d70918a-21a4-4209-9eb3-3691e53e90f1", "accession": "4DNFI6NI2PVT", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIWK9TVCE.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIWK9TVCE/", "status": "released", "uuid": "6c6b01a4-6b2f-4733-9bd3-ac550d79ec95", "accession": "4DNFIWK9TVCE", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFISSFUFVV.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFISSFUFVV/", "status": "released", "uuid": "b5edbb42-2c63-4b90-a603-0044df59c77d", "accession": "4DNFISSFUFVV", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFIHRXP55R.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIHRXP55R/", "status": "released", "uuid": "147eb940-06e8-404b-ab13-301425d29a0b", "accession": "4DNFIHRXP55R", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": "input_bams", "value": {"display_title": "4DNFI9P5CO2Z.bam", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI9P5CO2Z/", "status": "released", "uuid": "a1352ec6-dc34-4222-8c65-fa2626cae3ef", "accession": "4DNFI9P5CO2Z", "file_format": {"file_format": "bam", "display_title": "bam", "@type": ["FileFormat", "Item"], "status": "released", "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": {"title": "Hi-C Post-alignment Processing 0.2.6", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWFT69RBY4/", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "source_experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "uuid": "af0182ff-f87a-4cca-bf5d-2b07808d2787", "@id": "/experiment-set-replicates/4DNESS8PTK6F/", "display_title": "4DNESS8PTK6F", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEX4G1FPER/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2019-10-11T20:54:41.875645+00:00"}}, {"parent": "/files-processed/4DNFIKNPZDGB/", "embedded_path": "last_modified", "item": {"date_modified": "2021-03-28T15:43:38.545076+00:00"}}]}, "validation-errors": []}