{"lab": {"display_title": "4DN DCIC, HMS", "title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"center_title": "DCIC - DCIC", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "@type": ["Award", "Item"], "project": "4DN", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "name": "1U01CA200059-01", "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.", "@id": "/awards/1U01CA200059-01/", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "600510522d83cc8790ff6a7ae4fdef9f", "status": "released", "accession": "4DNFIVOMQVTQ", "file_size": 18011758575, "file_type": "alignments", "description": "This is an output file of the Hi-C processing pipeline", "file_format": {"status": "released", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "display_title": "bam", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-10-17T14:15:02.199953+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-03-28T16:12:47.736687+00:00"}, "public_release": "2018-11-05", "quality_metric": {"@id": "/quality-metrics-bamqc/8b99abde-0615-4bd7-a528-67475691e085/", "status": "released", "uuid": "8b99abde-0615-4bd7-a528-67475691e085", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2019-12-20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "128162948", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "27.448", "tooltip": "Percent of total reads (=35.18m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "12.21", "tooltip": "Percent of total reads (=15.65m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "2.342", "tooltip": "Percent of total reads (=3.0m)", "numberType": "percent"}, {"title": "Walks", "value": "0.001", "tooltip": "Percent of total reads (=0.0m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.095", "tooltip": "Percent of total reads (=0.12m)", "numberType": "percent"}]}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2018-11-05", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "uuid": "3c577664-affb-41c4-bf27-9e21c2fc1554", "display_title": "Job Dekker, UMMS", "@id": "/labs/job-dekker-lab/", "correspondence": [{"contact_email": "am9iLmRla2tlckB1bWFzc21lZC5lZHU=", "@id": "/users/83b5073a-069b-4162-9b30-6f42d5551e34/", "display_title": "Job Dekker"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.3c577664-affb-41c4-bf27-9e21c2fc1554"]}, "pi": {"error": "no view permissions"}}], "source_experiments": ["2d3c95f3-c65e-4ee9-86e4-62518371d80a"], "file_classification": "processed file", "percent_clipped_sites_with_re_motif": 76.54, "@id": "/files-processed/4DNFIVOMQVTQ/", "@type": ["FileProcessed", "File", "Item"], "uuid": "038c372f-8d24-4130-a5d4-7f2fa3c5b5b8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIVOMQVTQ.bam", "external_references": [], "experiments": [{"@id": "/experiments-hi-c/4DNEXQ4ZCIFU/", "accession": "4DNEXQ4ZCIFU", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "Dilution Hi-C on astrocyte of the spinal cord with HindIII - 4DNEXQ4ZCIFU", "status": "released", "uuid": "2d3c95f3-c65e-4ee9-86e4-62518371d80a", "biosample": {"@type": ["Biosample", "Item"], "treatments_summary": "None", "status": "released", "uuid": "db95b2f5-5b4e-4c04-8205-5790c2ca7974", "display_title": "4DNBSN32YF4W", "biosource_summary": "astrocyte of the spinal cord", "@id": "/biosamples/4DNBSN32YF4W/", "accession": "4DNBSN32YF4W", "modifications_summary": "None", "biosource": [{"status": "released", "biosource_type": "primary cell", "uuid": "2ac5fbce-a34a-4f70-ae08-499d26299f1d", "display_title": "astrocyte of the spinal cord - 4DNSRAHGM4C5", "cell_line_tier": "Unclassified", "@id": "/biosources/4DNSRAHGM4C5/", "@type": ["Biosource", "Item"], "organism": {"name": "human", "scientific_name": "Homo sapiens", "display_title": "H. sapiens", "@type": ["Organism", "Item"], "@id": "/organisms/9606/", "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"status": "released", "@type": ["OntologyTerm", "Item"], "term_name": "astrocyte of the spinal cord", "uuid": "58dd90d2-64e3-48f8-99a5-36ebb1475975", "display_title": "astrocyte of the spinal cord", "@id": "/ontology-terms/CL:0002606/", "term_id": "CL:0002606", "preferred_name": "astrocyte of the spinal cord", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINC7DHKGV", "uuid": "83e2002a-7813-486c-9b54-75fca8928e97", "@type": ["IndividualHuman", "Individual", "Item"], "status": "released", "protected_data": false, "@id": "/individuals-human/4DNINC7DHKGV/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"status": "released", "preferred_name": "spinal cord", "@id": "/ontology-terms/UBERON:0002240/", "uuid": "111152bc-8535-4448-903e-854af460a233", "@type": ["OntologyTerm", "Item"], "term_id": "UBERON:0002240", "display_title": "spinal cord", "term_name": "spinal cord", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "cell_culture_details": [{"uuid": "5840cb8a-190d-4af7-9b3e-0254e1fa8db8", "@type": ["BiosampleCellCulture", "Item"], "@id": "/biosample-cell-cultures/5840cb8a-190d-4af7-9b3e-0254e1fa8db8/", "display_title": "BiosampleCellCulture from 2018-10-04", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"status": "released", "@id": "/experiment-types/dilution-hi-c/", "@type": ["ExperimentType", "Item"], "title": "Dilution Hi-C", "display_title": "Dilution Hi-C", "uuid": "832b7989-69ab-4bb6-97b9-195d5dd965ea", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"name": "HindIII", "@type": ["Enzyme", "Item"], "status": "released", "display_title": "HindIII", "uuid": "2ace2f00-c913-4bac-a6ef-0b316bc2108e", "@id": "/enzymes/HindIII/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2019-04-24T16:09:34.772692+00:00"}, "experiment_sets": [{"@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNES4ABKY9M", "display_title": "4DNES4ABKY9M", "@id": "/experiment-set-replicates/4DNES4ABKY9M/", "uuid": "b3a05c87-bc15-4972-b014-acdc8b19e975", "experimentset_type": "replicate", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "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": "Hi-C on ENCODE3 cell lines", "condition": "astrocyte of the spinal cord", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "astrocyte of the spinal cord", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIVOMQVTQ", "href": "/files-processed/4DNFIVOMQVTQ/@@download/4DNFIVOMQVTQ.bam", "upload_key": "038c372f-8d24-4130-a5d4-7f2fa3c5b5b8/4DNFIVOMQVTQ.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/038c372f-8d24-4130-a5d4-7f2fa3c5b5b8/4DNFIVOMQVTQ.bam", "tsv_notes": "", "workflow_run_inputs": [{"@id": "/workflow-runs-awsem/c482fb2a-7277-4674-afd3-ffc9e9e81d9d/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "c482fb2a-7277-4674-afd3-ffc9e9e81d9d", "display_title": "bamqc v2 run 2019-12-20 20:04:30.908637", "status": "released", "workflow": {"uuid": "dcfff5c8-2ec0-498b-bc89-074f7b681303", "status": "released", "@id": "/workflows/4DNWFBAMQCV1/", "title": "Quality metrics for annotated bam files", "display_title": "Quality metrics for annotated bam files - 4DNWFBAMQCV1", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "bamfile", "value": {"@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIVOMQVTQ.bam", "status": "released", "@id": "/files-processed/4DNFIVOMQVTQ/", "uuid": "038c372f-8d24-4130-a5d4-7f2fa3c5b5b8", "accession": "4DNFIVOMQVTQ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chromsizes", "value": {"@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSII.chrom.sizes", "filename": "hg38.mainonly.chrom.sizes", "status": "released", "@id": "/files-reference/4DNFI823LSII/", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "chromsizes", "@id": "/file-formats/chromsizes/", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "bam_qc", "value_qc": {"status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2019-12-20", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "@id": "/quality-metrics-bamqc/8b99abde-0615-4bd7-a528-67475691e085/", "uuid": "8b99abde-0615-4bd7-a528-67475691e085", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/workflow-runs-awsem/3841cf85-6810-4242-b361-2df64432a5e7/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "3841cf85-6810-4242-b361-2df64432a5e7", "display_title": "re_checker_workflow v1.1 run 2020-04-23 06:22:24.313815", "status": "released", "workflow": {"uuid": "e9eefa69-39b1-4e61-8889-5cb1cea401c0", "status": "released", "@id": "/workflows/4DNWFA4YPAGI/", "title": "Restriction Enzyme Check, 1.1", "display_title": "Restriction Enzyme Check, 1.1 - 4DNWFA4YPAGI", "@type": ["Workflow", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "bamfile", "value": {"@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIVOMQVTQ.bam", "status": "released", "@id": "/files-processed/4DNFIVOMQVTQ/", "uuid": "038c372f-8d24-4130-a5d4-7f2fa3c5b5b8", "accession": "4DNFIVOMQVTQ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "motif_percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"@id": "/workflow-runs-awsem/2c872bc7-e99e-4274-aa63-43be81ad1a15/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "status": "released", "display_title": "hi-c-processing-bam 0.2.6 run 2018-10-17 14:15:02.810716", "uuid": "2c872bc7-e99e-4274-aa63-43be81ad1a15", "workflow": {"@type": ["Workflow", "Item"], "title": "Hi-C Post-alignment Processing 0.2.6", "@id": "/workflows/4DNWFT69RBY4/", "status": "released", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "input_bams", "value": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI2AZ4N7O.bam", "uuid": "d9b6d8dd-05d2-4977-95dd-8f08110375b6", "@id": "/files-processed/4DNFI2AZ4N7O/", "accession": "4DNFI2AZ4N7O", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI8SOQQY9.bam", "uuid": "f153baff-ef07-4bdf-b71e-1e0c3f54da00", "@id": "/files-processed/4DNFI8SOQQY9/", "accession": "4DNFI8SOQQY9", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFICYXU7O6.bam", "uuid": "efea50bc-3f06-49de-b617-948fcaecdccd", "@id": "/files-processed/4DNFICYXU7O6/", "accession": "4DNFICYXU7O6", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIHSWB25O.bam", "uuid": "b36d6962-91e7-4483-90f1-534e67c2e159", "@id": "/files-processed/4DNFIHSWB25O/", "accession": "4DNFIHSWB25O", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFITLKV63S.bam", "uuid": "0801781c-a07d-478e-bbc4-b75042e87e2d", "@id": "/files-processed/4DNFITLKV63S/", "accession": "4DNFITLKV63S", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIN1JWWRP.bam", "uuid": "5e9d4bb8-22fc-4df8-ac19-2b572e1d4fa2", "@id": "/files-processed/4DNFIN1JWWRP/", "accession": "4DNFIN1JWWRP", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIM3TFO4Q.bam", "uuid": "33bba708-b1a3-4ef4-a360-9c05c33eede3", "@id": "/files-processed/4DNFIM3TFO4Q/", "accession": "4DNFIM3TFO4Q", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI7YIUGT1.bam", "uuid": "591cf486-48a4-451c-8c7e-13ff1ced9815", "@id": "/files-processed/4DNFI7YIUGT1/", "accession": "4DNFI7YIUGT1", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIPNWUY6W.bam", "uuid": "717e6f2a-ccd6-4016-9323-b3b545905626", "@id": "/files-processed/4DNFIPNWUY6W/", "accession": "4DNFIPNWUY6W", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIGQNJPQ4.bam", "uuid": "6820ffb1-b9c4-47f8-ac6d-bdc502f54d65", "@id": "/files-processed/4DNFIGQNJPQ4/", "accession": "4DNFIGQNJPQ4", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIPNM8CIA.bam", "uuid": "1503954c-a5c2-43c6-b18d-34fdc128a0a6", "@id": "/files-processed/4DNFIPNM8CIA/", "accession": "4DNFIPNM8CIA", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIJJNQDDQ.bam", "uuid": "cdbf3e26-df5b-48c4-a853-025cd349e7c1", "@id": "/files-processed/4DNFIJJNQDDQ/", "accession": "4DNFIJJNQDDQ", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIS43SD2W.bam", "uuid": "e3edf6fb-37c7-4ad3-a3f9-56e5c1de28a2", "@id": "/files-processed/4DNFIS43SD2W/", "accession": "4DNFIS43SD2W", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI537Q9FS.bam", "uuid": "4f52eabb-d7b3-4d52-afb3-97c9412a7377", "@id": "/files-processed/4DNFI537Q9FS/", "accession": "4DNFI537Q9FS", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIBLVXID1.bam", "uuid": "1ad10e7a-8b33-460d-8930-3d6dc32c5ae4", "@id": "/files-processed/4DNFIBLVXID1/", "accession": "4DNFIBLVXID1", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIU5HR9TS.bam", "uuid": "83a7a12a-8605-4db5-b2d3-57332e67ca98", "@id": "/files-processed/4DNFIU5HR9TS/", "accession": "4DNFIU5HR9TS", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIL7A9W6H.bam", "uuid": "cb93bc73-d029-46c8-84d9-af462954942a", "@id": "/files-processed/4DNFIL7A9W6H/", "accession": "4DNFIL7A9W6H", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIOU8BW22.bam", "uuid": "d22e592c-c81a-4d0e-80b4-fcafe9d75ff6", "@id": "/files-processed/4DNFIOU8BW22/", "accession": "4DNFIOU8BW22", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIEEG44WY.bam", "uuid": "01118f22-853d-4d70-a0b1-28771da4466e", "@id": "/files-processed/4DNFIEEG44WY/", "accession": "4DNFIEEG44WY", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFITKWMCK5.bam", "uuid": "369bed51-89d8-4961-a5c7-042cf08c89db", "@id": "/files-processed/4DNFITKWMCK5/", "accession": "4DNFITKWMCK5", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI4JNQGVE.bam", "uuid": "c004771d-ef7c-4b63-94d7-ba07febae570", "@id": "/files-processed/4DNFI4JNQGVE/", "accession": "4DNFI4JNQGVE", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIIMMOK1Z.bam", "uuid": "e950a39e-54c0-46ca-a679-3d2942ac91cc", "@id": "/files-processed/4DNFIIMMOK1Z/", "accession": "4DNFIIMMOK1Z", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI3HWJZ66.bam", "uuid": "8d7c031d-8890-44fd-8673-697f375f969f", "@id": "/files-processed/4DNFI3HWJZ66/", "accession": "4DNFI3HWJZ66", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIH1U27NI.bam", "uuid": "42508527-e8a2-4d30-ac04-e1a0a44890d2", "@id": "/files-processed/4DNFIH1U27NI/", "accession": "4DNFIH1U27NI", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIIVWMSFW.bam", "uuid": "c6fe5f0a-4de3-43fb-a3f6-4af11b7d99b0", "@id": "/files-processed/4DNFIIVWMSFW/", "accession": "4DNFIIVWMSFW", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIH1LM6YI.bam", "uuid": "3b086404-5461-4989-bd78-942eac0b508e", "@id": "/files-processed/4DNFIH1LM6YI/", "accession": "4DNFIH1LM6YI", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI5GTLZM3.bam", "uuid": "7bbd2584-47b1-409c-b551-6cb1d1828270", "@id": "/files-processed/4DNFI5GTLZM3/", "accession": "4DNFI5GTLZM3", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFISPC8JEC.bam", "uuid": "e4708a25-1c9a-4652-8d2b-3acefcbdbce3", "@id": "/files-processed/4DNFISPC8JEC/", "accession": "4DNFISPC8JEC", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIF6GFBSU.bam", "uuid": "6d00b690-c052-445b-a2be-65ba4aff8670", "@id": "/files-processed/4DNFIF6GFBSU/", "accession": "4DNFIF6GFBSU", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI4AKPPD7.bam", "uuid": "810fa4a3-588e-43a0-9af6-13d876b965e3", "@id": "/files-processed/4DNFI4AKPPD7/", "accession": "4DNFI4AKPPD7", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI5TR63HS.bam", "uuid": "890afa9b-5db3-469d-9a5b-8b43a38fa369", "@id": "/files-processed/4DNFI5TR63HS/", "accession": "4DNFI5TR63HS", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIDBQB8WM.bam", "uuid": "21d0137b-9ad2-4ba8-b09e-7f30f2b9d04f", "@id": "/files-processed/4DNFIDBQB8WM/", "accession": "4DNFIDBQB8WM", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@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": {"status": "released", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIZVLX57W.bam", "uuid": "827f9129-61e3-40b0-8a02-f38a8342a8d7", "@id": "/files-processed/4DNFIZVLX57W/", "accession": "4DNFIZVLX57W", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "released", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsize", "value": {"status": "released", "@type": ["FileReference", "File", "Item"], "display_title": "4DNFI823LSII.chrom.sizes", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "accession": "4DNFI823LSII", "file_format": {"@type": ["FileFormat", "Item"], "display_title": "chromsizes", "file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "status": "released", "@id": "/file-formats/chromsizes/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIVOMQVTQ/", "uuid": "038c372f-8d24-4130-a5d4-7f2fa3c5b5b8", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIVOMQVTQ.bam", "accession": "4DNFIVOMQVTQ", "status": "released", "file_format": {"display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "file_format": "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/4DNFI5463BGB/", "uuid": "f82743c7-9931-4656-ac35-9b6de511e16a", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFI5463BGB.pairs.gz", "accession": "4DNFI5463BGB", "status": "released", "file_format": {"display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "file_format": "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"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "source_experiment_sets": [{"uuid": "b3a05c87-bc15-4972-b014-acdc8b19e975", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES4ABKY9M", "@id": "/experiment-set-replicates/4DNES4ABKY9M/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXQ4ZCIFU/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2019-04-24T16:09:34.772692+00:00"}}, {"parent": "/files-processed/4DNFIVOMQVTQ/", "embedded_path": "last_modified", "item": {"date_modified": "2021-03-28T16:12:47.736687+00:00"}}]}, "validation-errors": []}