{"lab": {"status": "current", "title": "4DN DCIC, HMS", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "@type": ["Lab", "Item"], "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "award": {"center_title": "DCIC - DCIC", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "project": "4DN", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "name": "1U01CA200059-01", "status": "current", "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.", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "53d4b7134c65d25a8a35befdddfd6d12", "status": "released", "accession": "4DNFIHMAQJ22", "file_size": 2182777172, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline", "extra_files": [{"href": "/files-processed/4DNFIHMAQJ22/@@download/4DNFIHMAQJ22.pairs.gz.px2", "uuid": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4", "md5sum": "a6c5b6476a0fca66a4f57bfc4cca8c22", "status": "released", "filename": "4DNFIHMAQJ22", "accession": "4DNFIHMAQJ22", "file_size": 18014496, "upload_key": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4/4DNFIHMAQJ22.pairs.gz.px2", "file_format": {"@id": "/file-formats/pairs_px2/", "status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-11-30T14:50:21.610514+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-05-17T21:49:30.560080+00:00"}, "public_release": "2019-11-25", "quality_metric": {"@id": "/quality-metrics-pairsqc/c9cdeb46-bb7d-4568-bfcf-ce52e5779799/", "Trans reads": 26652936, "uuid": "c9cdeb46-bb7d-4568-bfcf-ce52e5779799", "Cis reads (>20kb)": 53303724, "Total reads": 104898803, "display_title": "QualityMetricPairsqc from 2018-12-05", "Short cis reads (<20kb)": 24942143, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHMAQJ22/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "quality_metric_summary": [{"title": "Filtered Reads", "value": "104898803", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "50.814", "tooltip": "Percent of filtered reads (=53.3m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "23.777", "tooltip": "Percent of filtered reads (=24.94m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "25.408", "tooltip": "Percent of filtered reads (=26.65m)", "numberType": "percent"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "schema_version": "3", "genome_assembly": "GRCm38", "project_release": "2019-11-25", "contributing_labs": [{"uuid": "ce54a7f7-af8a-4505-8327-e430634f494b", "status": "current", "@type": ["Lab", "Item"], "@id": "/labs/rafael-casellas-lab/", "display_title": "Rafael Casellas, NIH", "correspondence": [{"contact_email": "Y2FzZWxsYXJAbWFpbC5uaWguZ292", "@id": "/users/68b09572-0c3e-48c7-90a9-7bad21d6bac1/", "display_title": "Rafael Casellas"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.ce54a7f7-af8a-4505-8327-e430634f494b"]}}], "source_experiments": ["1311a9c5-80fb-4e45-8ae0-e43e656d245e"], "file_classification": "processed file", "@id": "/files-processed/4DNFIHMAQJ22/", "@type": ["FileProcessed", "File", "Item"], "uuid": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIHMAQJ22.pairs.gz", "external_references": [], "experiments": [{"uuid": "1311a9c5-80fb-4e45-8ae0-e43e656d245e", "@type": ["ExperimentHiC", "Experiment", "Item"], "@id": "/experiments-hi-c/4DNEX8H5J2FE/", "status": "released", "display_title": "in situ Hi-C on CH12 with MboI - 4DNEX8H5J2FE", "accession": "4DNEX8H5J2FE", "biosample": {"display_title": "4DNBSC4UV2KG", "status": "released", "@id": "/biosamples/4DNBSC4UV2KG/", "biosource_summary": "CH12", "@type": ["Biosample", "Item"], "uuid": "6037cda8-7c02-4a56-bfa3-d86037582527", "accession": "4DNBSC4UV2KG", "treatments_summary": "None", "modifications_summary": "None", "biosource": [{"status": "released", "@id": "/biosources/4DNSRPNYPN22/", "@type": ["Biosource", "Item"], "cell_line_tier": "Unclassified", "display_title": "CH12 - 4DNSRPNYPN22", "biosource_type": "immortalized cell line", "uuid": "5c4f486e-4f36-4d57-a38a-966e0ea29716", "cell_line": {"term_id": "4DN:0000263", "status": "released", "uuid": "8647e451-5e4c-41d1-98b6-b3c57226fbb3", "@type": ["OntologyTerm", "Item"], "preferred_name": "CH12", "display_title": "CH12", "@id": "/ontology-terms/4DN:0000263/", "term_name": "CH12", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "organism": {"uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "status": "released", "display_title": "M. musculus", "scientific_name": "Mus musculus", "@id": "/organisms/10090/", "name": "mouse", "@type": ["Organism", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "tissue": {"uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "preferred_name": "B-lymphocyte", "term_name": "lymphocyte of B lineage", "display_title": "B-lymphocyte", "@id": "/ontology-terms/CL:0000945/", "term_id": "CL:0000945", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "a247155e-e826-464e-ae9a-ac1f0017af64", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNINGX2D3T7/", "display_title": "4DNINGX2D3T7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "digestion_enzyme": {"uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "@id": "/enzymes/MboI/", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "name": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"title": "in situ Hi-C", "status": "released", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@type": ["ExperimentType", "Item"], "display_title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES7C6LBWI/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "accession": "4DNES7C6LBWI", "display_title": "4DNES7C6LBWI", "status": "released", "uuid": "227520f7-0c41-47e9-a82c-c5486ad3ca17", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "last_modified": {"date_modified": "2024-07-15T20:37:08.479351+00:00"}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Rafael Casellas, NIH", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on CH12 +/- CTCF ZF domain", "condition": "WT", "replicate_info": "Biorep 4, Techrep 1", "biosource_name": "CH12", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFIHMAQJ22", "href": "/files-processed/4DNFIHMAQJ22/@@download/4DNFIHMAQJ22.pairs.gz", "upload_key": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4/4DNFIHMAQJ22.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/8847edd5-0a29-4f52-ad7c-7aa40821c5b4/4DNFIHMAQJ22.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "1bb10acc-bcbf-40e7-8424-e2754300d11a", "display_title": "hi-c-processing-pairs 0.2.7 run 2019-04-22 19:58:31.400160", "status": "released", "@id": "/workflow-runs-awsem/1bb10acc-bcbf-40e7-8424-e2754300d11a/", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"accession": "4DNFI1519ZZL", "display_title": "4DNFI1519ZZL.pairs.gz", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1519ZZL/", "uuid": "f96a54ac-4f5c-4f36-8158-b74da27cb91a", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "pairs", "status": "released", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"accession": "4DNFIV8MLWJB", "display_title": "4DNFIV8MLWJB.hic", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIV8MLWJB/", "uuid": "3a6a943f-2cc0-4433-a27d-c89f3fdd3309", "file_format": {"display_title": "hic", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "hic", "status": "released", "@id": "/file-formats/hic/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"accession": "4DNFIASQYF5S", "display_title": "4DNFIASQYF5S.mcool", "status": "released", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIASQYF5S/", "uuid": "893b2807-9a4b-4c1b-8b83-f22d608df3a6", "file_format": {"display_title": "mcool", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "@type": ["FileFormat", "Item"], "file_format": "mcool", "status": "released", "@id": "/file-formats/mcool/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7", "@id": "/workflows/4DNWF2YBHXQM/", "uuid": "23bd6d73-4190-496d-837c-21bcdb3802ed", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.7 - 4DNWF2YBHXQM", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"accession": "4DNFI3UBJ3HZ", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFINBBSQLQ", "uuid": "b574c4fe-a1d0-4278-a6df-d316b38ed407", "@id": "/files-processed/4DNFINBBSQLQ/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFINBBSQLQ.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIDISBY6F", "uuid": "02dd5512-1dfe-4f1a-87a1-94ee0b399b5f", "@id": "/files-processed/4DNFIDISBY6F/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIDISBY6F.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFI4F9SJWN", "uuid": "819853c6-d79a-4105-8fea-1b0dee137c83", "@id": "/files-processed/4DNFI4F9SJWN/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFI4F9SJWN.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIHMAQJ22", "uuid": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4", "@id": "/files-processed/4DNFIHMAQJ22/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIHMAQJ22.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIPAU2ITC", "uuid": "3f54c7ef-28a2-427a-991c-f64e658cd97f", "@id": "/files-processed/4DNFIPAU2ITC/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIPAU2ITC.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIG57E6OZ", "uuid": "28678813-d31e-44d4-83b2-2a694424cdb5", "@id": "/files-processed/4DNFIG57E6OZ/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIG57E6OZ.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"accession": "4DNFIONK4G14", "uuid": "cb3c293b-b5fe-4f47-9373-a29399ea1edc", "@id": "/files-reference/4DNFIONK4G14/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "mm10_MboI.txt", "display_title": "4DNFIONK4G14.txt", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/juicer_format_restriction_site_file/", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "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"]}}, {"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "dc45394c-602c-4abb-997d-c886732d2b91", "display_title": "pairsqc-single 0.2.6 run 2018-12-05 22:13:57.169441", "status": "released", "@id": "/workflow-runs-awsem/dc45394c-602c-4abb-997d-c886732d2b91/", "output_files": [{"workflow_argument_name": "report", "value_qc": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "@id": "/quality-metrics-pairsqc/c9cdeb46-bb7d-4568-bfcf-ce52e5779799/", "display_title": "QualityMetricPairsqc from 2018-12-05", "uuid": "c9cdeb46-bb7d-4568-bfcf-ce52e5779799", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHMAQJ22/pairsqc_report.html", "status": "released", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "title": "PairsQC 0.2.6", "@id": "/workflows/4DNWFHB26CID/", "uuid": "b8c533e0-f8c0-4510-b4a1-ac35158e27c3", "display_title": "PairsQC 0.2.6 - 4DNWFHB26CID", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsizes", "value": {"accession": "4DNFI3UBJ3HZ", "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "@id": "/files-reference/4DNFI3UBJ3HZ/", "@type": ["FileReference", "File", "Item"], "status": "released", "filename": "mm10.mainonly.chrom.sizes", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"accession": "4DNFIHMAQJ22", "uuid": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4", "@id": "/files-processed/4DNFIHMAQJ22/", "@type": ["FileProcessed", "File", "Item"], "status": "released", "display_title": "4DNFIHMAQJ22.pairs.gz", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "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"]}}], "workflow_run_outputs": [{"@id": "/workflow-runs-awsem/44be2ebd-2eaf-4615-bf87-d19a4047c740/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "hi-c-processing-bam 0.2.6 run 2018-11-30 14:50:21.822920", "uuid": "44be2ebd-2eaf-4615-bf87-d19a4047c740", "status": "released", "workflow": {"@type": ["Workflow", "Item"], "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "@id": "/workflows/4DNWFT69RBY4/", "title": "Hi-C Post-alignment Processing 0.2.6", "status": "released", "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "input_files": [{"workflow_argument_name": "chromsize", "value": {"filename": "mm10.mainonly.chrom.sizes", "@type": ["FileReference", "File", "Item"], "uuid": "bd0784a5-2a3d-42f0-ba9c-d9b3dc0539c6", "display_title": "4DNFI3UBJ3HZ.chrom.sizes", "status": "released", "@id": "/files-reference/4DNFI3UBJ3HZ/", "accession": "4DNFI3UBJ3HZ", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "display_title": "chromsizes", "@id": "/file-formats/chromsizes/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "319fe618-fb26-4349-9abd-73c3647f3828", "display_title": "4DNFI32RL2CI.bam", "status": "released", "@id": "/files-processed/4DNFI32RL2CI/", "accession": "4DNFI32RL2CI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "23af229d-a603-444e-aac3-4c5eb2ecf108", "display_title": "4DNFIE71GIYV.bam", "status": "released", "@id": "/files-processed/4DNFIE71GIYV/", "accession": "4DNFIE71GIYV", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "5aa7e5fa-5bf9-4ea5-8433-b9c50ef030a4", "display_title": "4DNFI7WMAI5D.bam", "status": "released", "@id": "/files-processed/4DNFI7WMAI5D/", "accession": "4DNFI7WMAI5D", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "e3803a95-c09f-48d6-b236-73b7c2281ac3", "display_title": "4DNFIVPMF75M.bam", "status": "released", "@id": "/files-processed/4DNFIVPMF75M/", "accession": "4DNFIVPMF75M", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "c87bd092-4b67-4628-8ac1-366a2caa558c", "display_title": "4DNFIRNBILTH.bam", "status": "released", "@id": "/files-processed/4DNFIRNBILTH/", "accession": "4DNFIRNBILTH", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "70556b2d-6ba9-42b4-a45b-789e06dbd6a8", "display_title": "4DNFIMQTBOKG.bam", "status": "released", "@id": "/files-processed/4DNFIMQTBOKG/", "accession": "4DNFIMQTBOKG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "93f6a24e-053d-4f31-b6b8-7db8de97058a", "display_title": "4DNFIKVXJ5H8.bam", "status": "released", "@id": "/files-processed/4DNFIKVXJ5H8/", "accession": "4DNFIKVXJ5H8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "c1931f65-12c0-4157-8910-bba86ca1a5dc", "display_title": "4DNFIMA2VLYS.bam", "status": "released", "@id": "/files-processed/4DNFIMA2VLYS/", "accession": "4DNFIMA2VLYS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "d3a2bb30-f541-4bd0-94b3-e53fc9dce804", "display_title": "4DNFIE3TQVK1.bam", "status": "released", "@id": "/files-processed/4DNFIE3TQVK1/", "accession": "4DNFIE3TQVK1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "af51e306-8df4-4dfc-9665-6576074e7515", "display_title": "4DNFISPNC4I6.bam", "status": "released", "@id": "/files-processed/4DNFISPNC4I6/", "accession": "4DNFISPNC4I6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "777c1f07-61ac-4e14-9e78-3b91965bf4c3", "display_title": "4DNFIJ1L5LXY.bam", "status": "released", "@id": "/files-processed/4DNFIJ1L5LXY/", "accession": "4DNFIJ1L5LXY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "uuid": "b787e8ec-bd5c-4545-bf18-776d50f5b324", "display_title": "4DNFI18BSPZ3.bam", "status": "released", "@id": "/files-processed/4DNFI18BSPZ3/", "accession": "4DNFI18BSPZ3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@id": "/file-formats/bam/", "status": "released", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIOD8OOFV/", "accession": "4DNFIOD8OOFV", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIOD8OOFV.bam", "uuid": "bd8db11e-6212-4f3e-994d-dd76b70d2a81", "status": "released", "file_format": {"file_format": "bam", "status": "released", "display_title": "bam", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "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/4DNFIHMAQJ22/", "accession": "4DNFIHMAQJ22", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIHMAQJ22.pairs.gz", "uuid": "8847edd5-0a29-4f52-ad7c-7aa40821c5b4", "status": "released", "file_format": {"file_format": "pairs", "status": "released", "display_title": "pairs", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [], "pairsqc_table": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIHMAQJ22/4DNFIHMAQJ22.plot_table.out", "source_experiment_sets": [{"uuid": "227520f7-0c41-47e9-a82c-c5486ad3ca17", "display_title": "4DNES7C6LBWI", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "@id": "/experiment-set-replicates/4DNES7C6LBWI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEX8H5J2FE/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2024-07-15T20:37:08.479351+00:00"}}, {"parent": "/files-processed/4DNFIHMAQJ22/", "embedded_path": "last_modified", "item": {"date_modified": "2021-05-17T21:49:30.560080+00:00"}}]}, "validation-errors": []}