{"lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "title": "4DN DCIC, HMS", "status": "current", "@id": "/labs/4dn-dcic-lab/", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}, "pi": {"error": "no view permissions"}}, "award": {"@type": ["Award", "Item"], "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE I", "uuid": "b0b9c607-f8b4-4f02-93f4-9895b461334b", "project": "4DN", "name": "1U01CA200059-01", "center_title": "DCIC - DCIC", "@id": "/awards/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.", "status": "current", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "md5sum": "c2c844a0684cc4cfa2434fc2411bd8dd", "status": "released", "accession": "4DNFIG61BI7O", "file_size": 137027, "file_type": "boundaries", "description": "Boundaries calls on Hi-C contact matrices", "extra_files": [{"href": "/files-processed/4DNFIG61BI7O/@@download/4DNFIG61BI7O.beddb", "uuid": "14cce0f3-c74f-4d0b-88c1-98b217712e2a", "md5sum": "f384c5f70fbc719be24fdb96e96985af", "status": "released", "use_for": "visualization", "filename": "4DNFIG61BI7O", "accession": "4DNFIG61BI7O", "upload_key": "14cce0f3-c74f-4d0b-88c1-98b217712e2a/4DNFIG61BI7O.beddb", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "uuid": "76dc8c06-67d8-487b-8fc8-d841752a0b60", "display_title": "beddb", "@id": "/file-formats/beddb/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"status": "released", "@id": "/file-formats/bed/", "file_format": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "display_title": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "higlass_uid": "OHgrfJZ9RwGjWcymSZd09A", "date_created": "2020-09-08T15:21:25.490125+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-04-06T20:13:05.262429+00:00"}, "public_release": "2021-01-25", "schema_version": "3", "static_content": [{"content": {"@type": ["HiglassViewConfig", "UserContent", "Item"], "filetype": "HiglassViewConfig", "description": "", "display_title": "4DNFIG61BI7O - boundaries for G1E-ER4 with mCherry-MD in situ Hi-C DpnII", "status": "released", "lab": {"uuid": "00073229-0955-47af-ab67-6abf4880cb2c", "@id": "/labs/gerd-blobel-lab/", "display_title": "Gerd Blobel, CHOP", "@type": ["Lab", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.00073229-0955-47af-ab67-6abf4880cb2c"]}}, "@id": "/higlass-view-configs/6d98ca80-8518-4506-8181-88b4b299ffd9/", "uuid": "6d98ca80-8518-4506-8181-88b4b299ffd9", "name": "6d98ca80-8518-4506-8181-88b4b299ffd9", "award": {"uuid": "cf0c686c-a3ad-411d-9986-ad42927352c0", "@type": ["Award", "Item"], "status": "current", "display_title": "ENGINEERING AND VISUALIZING GENOME FOLDING AT HIGH SPATIOTEMPORAL RESOLUTION", "@id": "/awards/1U01HL129998-01/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "4DNFIG61BI7O - boundaries for G1E-ER4 with mCherry-MD in situ Hi-C DpnII", "contributing_labs": [{"status": "current", "display_title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@id": "/labs/4dn-dcic-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, {"status": "current", "display_title": "Jennifer Cremins, UPENN", "@type": ["Lab", "Item"], "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "@id": "/labs/jennifer-cremins-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}, "location": "tab:higlass", "description": "auto_generated_higlass_view_config"}], "genome_assembly": "GRCm38", "project_release": "2020-12-17", "contributing_labs": [{"@type": ["Lab", "Item"], "status": "current", "uuid": "b18699f9-e3e9-44e2-8070-d5b044efc09e", "correspondence": [{"contact_email": "amNyZW1pbnNAc2Vhcy51cGVubi5lZHU=", "@id": "/users/8773d50c-1716-4153-9a18-d0f5ff2aa5ee/", "display_title": "Jennifer Phillips-Cremins"}], "@id": "/labs/jennifer-cremins-lab/", "display_title": "Jennifer Cremins, UPENN", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.b18699f9-e3e9-44e2-8070-d5b044efc09e"]}}, {"@type": ["Lab", "Item"], "status": "current", "uuid": "00073229-0955-47af-ab67-6abf4880cb2c", "correspondence": [{"contact_email": "YmxvYmVsQGVtYWlsLmNob3AuZWR1", "@id": "/users/9dcbdd0c-634c-4ec6-b6dc-89efd542c203/", "display_title": "Gerd Blobel"}], "@id": "/labs/gerd-blobel-lab/", "display_title": "Gerd Blobel, CHOP", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.00073229-0955-47af-ab67-6abf4880cb2c"]}}], "source_experiments": ["77d25872-c1f2-4240-8501-5e218d36c313", "f9e81f36-92c5-4a8a-81ed-93eb05c9a904"], "file_classification": "processed file", "@id": "/files-processed/4DNFIG61BI7O/", "@type": ["FileProcessed", "File", "Item"], "uuid": "14cce0f3-c74f-4d0b-88c1-98b217712e2a", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNFIG61BI7O.bed.gz", "external_references": [], "experiments": [], "file_type_detailed": "boundaries (bed)", "track_and_facet_info": {"dataset": "Hi-C on sync.G1E-ER4", "condition": "anaphase/telophase", "experimental_lab": "Gerd Blobel, CHOP", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "DpnII", "biosource_name": "G1E-ER4 with mCherry-MD", "lab_name": "4DN DCIC, HMS", "track_title": "boundaries for G1E-ER4 with mCherry-MD in situ Hi-C DpnII"}, "title": "4DNFIG61BI7O", "href": "/files-processed/4DNFIG61BI7O/@@download/4DNFIG61BI7O.bed.gz", "upload_key": "14cce0f3-c74f-4d0b-88c1-98b217712e2a/4DNFIG61BI7O.bed.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/14cce0f3-c74f-4d0b-88c1-98b217712e2a/4DNFIG61BI7O.bed.gz", "tsv_notes": "", "workflow_run_inputs": [{"@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "display_title": "bedtobeddb v2 run 2020-09-08 16:11:55.937544", "status": "released", "@id": "/workflow-runs-awsem/efff9c8c-2019-498c-8af3-f2f76b6b09e2/", "uuid": "efff9c8c-2019-498c-8af3-f2f76b6b09e2", "input_files": [{"workflow_argument_name": "bedfile", "value": {"@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIG61BI7O.bed.gz", "uuid": "14cce0f3-c74f-4d0b-88c1-98b217712e2a", "@id": "/files-processed/4DNFIG61BI7O/", "accession": "4DNFIG61BI7O", "status": "released", "file_format": {"display_title": "bed", "uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "file_format": "bed", "@id": "/file-formats/bed/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "output_files": [{"workflow_argument_name": "beddbfile"}], "workflow": {"display_title": "Converting bed to beddb v2 - 4DNWFLM174GG", "@type": ["Workflow", "Item"], "status": "released", "@id": "/workflows/4DNWFLM174GG/", "uuid": "9d575e99-5ffe-4ea4-b74f-ad40f621cd39", "title": "Converting bed to beddb v2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "workflow_run_outputs": [{"status": "released", "display_title": "insulation-scores-and-boundaries-caller v1 run 2020-09-08 15:21:27.098083", "uuid": "3121723b-b5fc-4b8e-9152-fdfc0fcb5e36", "@type": ["WorkflowRunAwsem", "WorkflowRun", "Item"], "@id": "/workflow-runs-awsem/3121723b-b5fc-4b8e-9152-fdfc0fcb5e36/", "output_files": [{"workflow_argument_name": "bwfile", "value": {"status": "released", "display_title": "4DNFILHZ5VVY.bw", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFILHZ5VVY/", "uuid": "46271c44-5d81-4b39-892c-dcd4af3a12ff", "accession": "4DNFILHZ5VVY", "file_format": {"uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bw", "@id": "/file-formats/bw/", "file_format": "bw", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"workflow_argument_name": "bedfile", "value": {"status": "released", "display_title": "4DNFIG61BI7O.bed.gz", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIG61BI7O/", "uuid": "14cce0f3-c74f-4d0b-88c1-98b217712e2a", "accession": "4DNFIG61BI7O", "file_format": {"uuid": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", "@type": ["FileFormat", "Item"], "status": "released", "display_title": "bed", "@id": "/file-formats/bed/", "file_format": "bed", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "input_files": [{"workflow_argument_name": "mcoolfile", "value": {"display_title": "4DNFIRAHQIGN.mcool", "status": "released", "accession": "4DNFIRAHQIGN", "uuid": "77435de5-d768-4fae-9867-4dbc03f82f92", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIRAHQIGN/", "file_format": {"uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "status": "released", "@id": "/file-formats/mcool/", "display_title": "mcool", "@type": ["FileFormat", "Item"], "file_format": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "workflow": {"@id": "/workflows/4DNWFDKENGO6/", "uuid": "dc9efc2d-baa5-4304-b72b-14610d8d5fc4", "@type": ["Workflow", "Item"], "status": "released", "title": "Getting insulation diamond scores and boundaries from mcool files", "display_title": "Getting insulation diamond scores and boundaries from mcool files - 4DNWFDKENGO6", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_sets": [{"status": "released", "uuid": "dcf39c03-b1f0-47b8-9d1a-de72b8f4164f", "display_title": "4DNESTI1YC1H", "@id": "/experiment-set-replicates/4DNESTI1YC1H/", "accession": "4DNESTI1YC1H", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-07-31T14:46:25.267294+00:00"}}], "source_experiment_sets": [{"status": "released", "@id": "/experiment-set-replicates/4DNESTI1YC1H/", "display_title": "4DNESTI1YC1H", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "dcf39c03-b1f0-47b8-9d1a-de72b8f4164f", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@context": "/terms/", "aggregated-items": {"last_modified": [{"parent": "/files-processed/4DNFIG61BI7O/", "embedded_path": "last_modified", "item": {"date_modified": "2021-04-06T20:13:05.262429+00:00"}}, {"parent": "/experiment-set-replicates/4DNESTI1YC1H/", "embedded_path": "experiment_sets.last_modified", "item": {"date_modified": "2024-07-31T14:46:25.267294+00:00"}}]}, "validation-errors": []}