{"lab": {"display_title": "4DN DCIC, HMS", "status": "current", "title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "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", "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.", "center_title": "DCIC - DCIC", "status": "current", "@type": ["Award", "Item"], "@id": "/awards/1U01CA200059-01/", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "project": "4DN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "d57aaa93b6581bf0dda0fb6bb447a75b", "status": "released", "aliases": [], "accession": "4DNFI563E6GS", "file_size": 2415571465, "file_type": "contact list-replicate", "description": "This is an output file of the Hi-C processing pipeline.", "extra_files": [{"href": "/files-processed/4DNFI563E6GS/@@download/4DNFI563E6GS.pairs.gz.px2", "uuid": "eb172b70-6864-41af-9b21-7ee6d03dd453", "md5sum": "6b1ab75ae18719515fc038b476cfb2a6", "status": "released", "filename": "4DNFI563E6GS", "accession": "4DNFI563E6GS", "file_size": 24059361, "upload_key": "eb172b70-6864-41af-9b21-7ee6d03dd453/4DNFI563E6GS.pairs.gz.px2", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "@id": "/file-formats/pairs_px2/", "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "content_md5sum": "6b1ab75ae18719515fc038b476cfb2a6"}], "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "file_format": "pairs", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "date_created": "2018-01-23T17:09:33.183379+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-01-11T17:28:37.854190+00:00"}, "content_md5sum": "482ff42416bd796209bfaae0a780d286", "public_release": "2018-03-23", "quality_metric": {"Cis reads (>20kb)": 71041342, "display_title": "QualityMetricPairsqc from 2018-01-26", "Short cis reads (<20kb)": 26189426, "@id": "/quality-metrics-pairsqc/5f302fd1-8fe3-4387-87d2-9b6c196a3191/", "Trans reads": 25591015, "Total reads": 122821783, "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI563E6GS/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "uuid": "5f302fd1-8fe3-4387-87d2-9b6c196a3191", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "122821783", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "57.841", "tooltip": "Percent of filtered reads (=71.04m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.323", "tooltip": "Percent of filtered reads (=26.19m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "20.836", "tooltip": "Percent of filtered reads (=25.59m)", "numberType": "percent"}]}, "schema_version": "3", "genome_assembly": "GRCh38", "project_release": "2018-03-23", "contributing_labs": [{"display_title": "Erez Lieberman Aiden, BCM", "@type": ["Lab", "Item"], "@id": "/labs/erez-liebermanaiden-lab/", "status": "current", "correspondence": [{"contact_email": "ZXJlekBlcmV6LmNvbQ==", "@id": "/users/60938b2e-e120-4c4f-9ddb-001296021df7/", "display_title": "Erez Lieberman Aiden"}], "uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}, "pi": {"error": "no view permissions"}}], "source_experiments": ["e9bf4630-5605-4204-998d-7356f7100e93"], "file_classification": "processed file", "@id": "/files-processed/4DNFI563E6GS/", "@type": ["FileProcessed", "File", "Item"], "uuid": "eb172b70-6864-41af-9b21-7ee6d03dd453", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFI563E6GS.pairs.gz", "external_references": [], "experiments": [{"@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "in situ Hi-C on GM12878 with MboI - 4DNEXHU7XZ7R", "accession": "4DNEXHU7XZ7R", "uuid": "e9bf4630-5605-4204-998d-7356f7100e93", "status": "released", "@id": "/experiments-hi-c/4DNEXHU7XZ7R/", "biosample": {"status": "released", "@id": "/biosamples/4DNBSBUH7SNR/", "modifications_summary": "None", "display_title": "4DNBSBUH7SNR", "biosource_summary": "GM12878", "@type": ["Biosample", "Item"], "treatments_summary": "None", "uuid": "3311492b-735c-4d8a-ae80-ae8369fade45", "accession": "4DNBSBUH7SNR", "biosource": [{"biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "@id": "/biosources/4DNSRVWZS4XO/", "@type": ["Biosource", "Item"], "status": "released", "display_title": "GM12878 - 4DNSRVWZS4XO", "uuid": "0f011b1e-b772-4f2a-8c24-cc55de28a994", "modifications": [], "tissue": {"preferred_name": "B-lymphocyte", "@type": ["OntologyTerm", "Item"], "display_title": "B-lymphocyte", "uuid": "0c98ef0b-9a03-43f3-b409-fb091e62e2f8", "term_id": "CL:0000945", "status": "released", "@id": "/ontology-terms/CL:0000945/", "term_name": "lymphocyte of B lineage", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"display_title": "4DNINGWYEI15", "protected_data": false, "uuid": "3ec2ff42-6f8c-42e9-a1f0-0fa69f482b85", "status": "released", "@id": "/individuals-human/4DNINGWYEI15/", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "cell_line": {"uuid": "b9668b9a-be39-47de-8eab-5bf1b0854417", "@type": ["OntologyTerm", "Item"], "preferred_name": "GM12878", "status": "released", "term_id": "EFO:0002784", "@id": "/ontology-terms/EFO:0002784/", "display_title": "GM12878", "term_name": "GM12878", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "organism": {"@type": ["Organism", "Item"], "name": "human", "@id": "/organisms/9606/", "display_title": "H. sapiens", "status": "released", "scientific_name": "Homo sapiens", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "digestion_enzyme": {"status": "released", "display_title": "MboI", "@id": "/enzymes/MboI/", "name": "MboI", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "@type": ["Enzyme", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_sets": [{"uuid": "b5e7dbe9-6ebe-468e-8d02-45ff6ca04ce8", "experimentset_type": "custom", "display_title": "4DNESEOQUGG3", "accession": "4DNESEOQUGG3", "@id": "/experiment-sets/4DNESEOQUGG3/", "status": "released", "@type": ["ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "aa6f0d82-16c9-4109-a1f8-3fa0636a3560", "experimentset_type": "replicate", "display_title": "4DNES3JX38V5", "accession": "4DNES3JX38V5", "@id": "/experiment-set-replicates/4DNES3JX38V5/", "status": "released", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_type": {"uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "@id": "/experiment-types/in-situ-hi-c/", "display_title": "in situ Hi-C", "title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2020-08-24T21:57:47.692273+00:00"}}], "file_type_detailed": "contact list-replicate (pairs)", "track_and_facet_info": {"experimental_lab": "Erez Lieberman Aiden, BCM", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on GM12878 cells - protocol variations", "condition": "Preferred protocol - in situ Hi-C on GM12878 with MboI and bio-dATP", "replicate_info": "Biorep 1, Techrep 4", "biosource_name": "GM12878", "lab_name": "4DN DCIC, HMS"}, "title": "4DNFI563E6GS", "href": "/files-processed/4DNFI563E6GS/@@download/4DNFI563E6GS.pairs.gz", "upload_key": "eb172b70-6864-41af-9b21-7ee6d03dd453/4DNFI563E6GS.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/eb172b70-6864-41af-9b21-7ee6d03dd453/4DNFI563E6GS.pairs.gz", "tsv_notes": "", "workflow_run_inputs": [{"status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/d82d3537-92b8-4665-8403-d7324172511c/", "uuid": "d82d3537-92b8-4665-8403-d7324172511c", "display_title": "pairsqc-single 0.2.5 run 2018-01-26 14:59:05.659153", "output_files": [{"workflow_argument_name": "report", "value_qc": {"uuid": "5f302fd1-8fe3-4387-87d2-9b6c196a3191", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI563E6GS/pairsqc_report.html", "display_title": "QualityMetricPairsqc from 2018-01-26", "@id": "/quality-metrics-pairsqc/5f302fd1-8fe3-4387-87d2-9b6c196a3191/", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "input_pairs", "value": {"uuid": "eb172b70-6864-41af-9b21-7ee6d03dd453", "accession": "4DNFI563E6GS", "status": "released", "display_title": "4DNFI563E6GS.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI563E6GS/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "status": "released", "display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "PairsQC 0.2.5", "uuid": "ae3a87cb-3fa2-469e-97c7-540fc2d0a117", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWF36CF3A1/", "display_title": "PairsQC 0.2.5 - 4DNWF36CF3A1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/d5df644e-fc94-47d3-b520-77b72cfd8e72/", "uuid": "d5df644e-fc94-47d3-b520-77b72cfd8e72", "display_title": "hi-c-processing-pairs 0.2.6 run 2018-04-23 16:01:30.423889", "output_files": [{"workflow_argument_name": "merged_pairs", "value": {"display_title": "4DNFIYECESRC.pairs.gz", "@id": "/files-processed/4DNFIYECESRC/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIYECESRC", "status": "released", "uuid": "7eb7dbc1-0bdc-404a-b47d-46058e669890", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "display_title": "pairs", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "hic", "value": {"display_title": "4DNFI1UEG1HD.hic", "@id": "/files-processed/4DNFI1UEG1HD/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI1UEG1HD", "status": "released", "uuid": "a98ca64a-861a-4a8c-92e9-586af457b1fb", "file_format": {"uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "file_format": "hic", "display_title": "hic", "@type": ["FileFormat", "Item"], "@id": "/file-formats/hic/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "mcool", "value": {"display_title": "4DNFIXP4QG5B.mcool", "@id": "/files-processed/4DNFIXP4QG5B/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIXP4QG5B", "status": "released", "uuid": "d6abea45-b0bb-4154-9854-1d3075b98097", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "file_format": "mcool", "display_title": "mcool", "@type": ["FileFormat", "Item"], "@id": "/file-formats/mcool/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "cooler_normvector", "value": {"display_title": "4DNFI341QQ4F.normvector.juicerformat.gz", "@id": "/files-processed/4DNFI341QQ4F/", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI341QQ4F", "status": "released", "uuid": "34936c09-689e-4da1-a2c9-d8d6cebbe9ec", "file_format": {"uuid": "d13d06cf-218e-4f61-55f0-94f226118b2c", "file_format": "normvector_juicerformat", "display_title": "normvector_juicerformat", "@type": ["FileFormat", "Item"], "@id": "/file-formats/normvector_juicerformat/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "chromsizes", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "accession": "4DNFI823LSII", "status": "released", "display_title": "4DNFI823LSII.chrom.sizes", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823LSII/", "filename": "hg38.mainonly.chrom.sizes", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/chromsizes/", "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "c0b86b98-dfce-4313-be62-c4b7e3ec3023", "accession": "4DNFIIT7LQ6M", "status": "released", "display_title": "4DNFIIT7LQ6M.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIIT7LQ6M/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "2cfcd1d2-02c4-489f-9c5d-ffcfd8a004f5", "accession": "4DNFIFQL2K6N", "status": "released", "display_title": "4DNFIFQL2K6N.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIFQL2K6N/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "eb172b70-6864-41af-9b21-7ee6d03dd453", "accession": "4DNFI563E6GS", "status": "released", "display_title": "4DNFI563E6GS.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI563E6GS/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "e7720768-1968-4c8f-a4a2-2c04257bf1cf", "accession": "4DNFIG59MQN6", "status": "released", "display_title": "4DNFIG59MQN6.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIG59MQN6/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "9837ced5-abe3-4327-8c5e-16d3c4a29ba3", "accession": "4DNFIDN4BQ8Z", "status": "released", "display_title": "4DNFIDN4BQ8Z.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIDN4BQ8Z/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0745981e-ba3d-4b41-a50b-a742f56e857d", "accession": "4DNFIHW7O3BR", "status": "released", "display_title": "4DNFIHW7O3BR.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIHW7O3BR/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "850b91fe-9a6d-4622-b4ab-8a96226ea353", "accession": "4DNFIZGHJ9EM", "status": "released", "display_title": "4DNFIZGHJ9EM.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIZGHJ9EM/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0a763174-74a8-45a5-b569-a6f681ce3fb5", "accession": "4DNFIATMYDMG", "status": "released", "display_title": "4DNFIATMYDMG.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIATMYDMG/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "ae9f6f00-a695-47c8-8b2e-94077cd05ef9", "accession": "4DNFIROARX7U", "status": "released", "display_title": "4DNFIROARX7U.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIROARX7U/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "02be967e-fc41-44a3-97cb-ac96818a4f08", "accession": "4DNFIWBALW9K", "status": "released", "display_title": "4DNFIWBALW9K.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIWBALW9K/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "11f4b520-b2c7-4660-8ab3-821a98fa2bf5", "accession": "4DNFIA38JZQ6", "status": "released", "display_title": "4DNFIA38JZQ6.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIA38JZQ6/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "d9a1405b-ab75-4a6b-b513-db383a5eb62d", "accession": "4DNFIW97L8UQ", "status": "released", "display_title": "4DNFIW97L8UQ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIW97L8UQ/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "0015115c-bf78-460f-8e40-3425a341be6e", "accession": "4DNFI7ICGXY9", "status": "released", "display_title": "4DNFI7ICGXY9.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI7ICGXY9/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "e4136ecc-d406-41fb-bb92-c354eaf34acf", "accession": "4DNFICBVHXUA", "status": "released", "display_title": "4DNFICBVHXUA.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFICBVHXUA/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "4db8ad45-b77b-40b5-bbba-8538857aa5f3", "accession": "4DNFI24MDDBZ", "status": "released", "display_title": "4DNFI24MDDBZ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI24MDDBZ/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "cb9d0032-680f-4979-94e7-34c9260c4b39", "accession": "4DNFIUOVQH68", "status": "released", "display_title": "4DNFIUOVQH68.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIUOVQH68/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "4dffed8a-0383-490e-84d5-e19856405419", "accession": "4DNFIF71VGQ3", "status": "released", "display_title": "4DNFIF71VGQ3.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIF71VGQ3/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "7f13cf57-f867-4a3a-89d4-f797f7936c1b", "accession": "4DNFI3O82QVV", "status": "released", "display_title": "4DNFI3O82QVV.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI3O82QVV/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "acc6e566-7f3e-40cb-9a77-7051ac73a1c9", "accession": "4DNFI6FXMIGS", "status": "released", "display_title": "4DNFI6FXMIGS.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI6FXMIGS/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "c5b8415a-d554-4183-ac6b-175f80314551", "accession": "4DNFI1W46362", "status": "released", "display_title": "4DNFI1W46362.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1W46362/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "185be2b9-7526-4bca-ae50-cdbe96960742", "accession": "4DNFIYBWQG4A", "status": "released", "display_title": "4DNFIYBWQG4A.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIYBWQG4A/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "bc416c53-f620-4e4b-9b9d-549ab0f3ee52", "accession": "4DNFIQ65WNKK", "status": "released", "display_title": "4DNFIQ65WNKK.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIQ65WNKK/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "893f17d2-3a08-4687-b56e-5bd8a8ea68be", "accession": "4DNFIIS73OJN", "status": "released", "display_title": "4DNFIIS73OJN.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIIS73OJN/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "3904484f-4035-4af0-bc01-79a0742ee1e5", "accession": "4DNFIXR9BRGT", "status": "released", "display_title": "4DNFIXR9BRGT.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIXR9BRGT/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "74559d84-9a6e-4644-83a4-076e3c24d823", "accession": "4DNFI34KOJMZ", "status": "released", "display_title": "4DNFI34KOJMZ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI34KOJMZ/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "fb72da8c-60bb-410c-b8d7-2be7b796bc06", "accession": "4DNFIU585JSM", "status": "released", "display_title": "4DNFIU585JSM.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIU585JSM/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "input_pairs", "value": {"uuid": "e323ef4e-2241-4e6a-8f0b-05bd2fadcbae", "accession": "4DNFI1CMC4NQ", "status": "released", "display_title": "4DNFI1CMC4NQ.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFI1CMC4NQ/", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/pairs/", "file_format": "pairs", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "restriction_file", "value": {"uuid": "4a6d10ee-2edb-4402-a98f-0edb1d582084", "accession": "4DNFI823L812", "status": "released", "display_title": "4DNFI823L812.txt", "@type": ["FileReference", "File", "Item"], "@id": "/files-reference/4DNFI823L812/", "filename": "hg38_MboI.txt", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "@id": "/file-formats/juicer_format_restriction_site_file/", "file_format": "juicer_format_restriction_site_file", "display_title": "juicer_format_restriction_site_file", "uuid": "d13d06cf-218e-4f61-55f0-94f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6", "uuid": "c9e0e6f7-b0ed-4a42-9466-cadc2dd84df0", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWFTKI1QLK/", "display_title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists 0.2.6 - 4DNWFTKI1QLK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"error": "no view permissions"}, {"error": "no view permissions"}], "workflow_run_outputs": [{"status": "released", "@id": "/workflow-runs-awsem/14fda39d-48a0-4e95-8e82-fb3e48f2f92a/", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "uuid": "14fda39d-48a0-4e95-8e82-fb3e48f2f92a", "display_title": "hi-c-processing-bam 0.2.6 run 2018-01-23 17:09:33.542770", "input_files": [{"workflow_argument_name": "input_bams", "value": {"@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIPQ4K13M", "@id": "/files-processed/4DNFIPQ4K13M/", "status": "released", "uuid": "8784151c-3068-404a-ad9a-712d98b5b8aa", "display_title": "4DNFIPQ4K13M.bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "file_format": "bam", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}, {"workflow_argument_name": "chromsize", "value": {"@type": ["FileReference", "File", "Item"], "accession": "4DNFI823LSII", "@id": "/files-reference/4DNFI823LSII/", "status": "released", "uuid": "4a6d10ee-2edb-4402-a98f-0edb1d58f5e9", "display_title": "4DNFI823LSII.chrom.sizes", "filename": "hg38.mainonly.chrom.sizes", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "file_format": "chromsizes", "display_title": "chromsizes", "uuid": "d13d06cf-218e-4f61-55f0-93f226248b2c", "@id": "/file-formats/chromsizes/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}}], "output_files": [{"workflow_argument_name": "annotated_bam", "value": {"@id": "/files-processed/4DNFIR4LSSNY/", "status": "released", "display_title": "4DNFIR4LSSNY.bam", "uuid": "39dba462-934c-4ea7-89a5-ee289b775bef", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIR4LSSNY", "file_format": {"display_title": "bam", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "filtered_pairs", "value": {"@id": "/files-processed/4DNFI563E6GS/", "status": "released", "display_title": "4DNFI563E6GS.pairs.gz", "uuid": "eb172b70-6864-41af-9b21-7ee6d03dd453", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI563E6GS", "file_format": {"display_title": "pairs", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@type": ["Workflow", "Item"], "display_title": "Hi-C Post-alignment Processing 0.2.6 - 4DNWFT69RBY4", "@id": "/workflows/4DNWFT69RBY4/", "status": "released", "title": "Hi-C Post-alignment Processing 0.2.6", "uuid": "023bfb3e-9a8b-42b9-a9d4-216079526f68", "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/4DNFI563E6GS/4DNFI563E6GS.plot_table.out", "source_experiment_sets": [{"uuid": "b5e7dbe9-6ebe-468e-8d02-45ff6ca04ce8", "display_title": "4DNESEOQUGG3", "@type": ["ExperimentSet", "Item"], "status": "released", "@id": "/experiment-sets/4DNESEOQUGG3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "aa6f0d82-16c9-4109-a1f8-3fa0636a3560", "display_title": "4DNES3JX38V5", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "status": "released", "@id": "/experiment-set-replicates/4DNES3JX38V5/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/experiments-hi-c/4DNEXHU7XZ7R/", "embedded_path": "experiments.last_modified", "item": {"date_modified": "2020-08-24T21:57:47.692273+00:00"}}, {"parent": "/files-processed/4DNFI563E6GS/", "embedded_path": "last_modified", "item": {"date_modified": "2022-01-11T17:28:37.854190+00:00"}}]}, "validation-errors": []}