{"lab": {"correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "status": "current", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "@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"]}}, "body": "#### Do I need an account to download files?\nFile download from the 4DN data portal now requires authentication, even if the file is public.\nAccounts can be created by anyone, including those not part of the 4DN Network.\nUse your Github or Google account, or create a new one as explained in the [Account Creation User Guide](/help/user-guide/account-creation).\n\n#### How do I download files?\nTo download a single file, login (if you haven't already), go to the File page and click the Download button. The file will start downloading immediately.\n\nTo download many files (bulk download), select and filter the file(s) from either the [browse Experiment Sets](/browse/?experimentset_type=replicate&type=ExperimentSetReplicate) page, the [search Files](/search/?type=File) page, or from the page of an Experiment Set containing the desired files.\nThen click on the Download button to generate a metadata.tsv file with download URLs for the selected files.\nThese can be downloaded from the command line using cURL (include your access key, as explained [here](/help/user-guide/downloading-files)).\n\n#### Can I use unpublished 4DN data sets in my publication?\nUnpublished data sets are generated by the 4DN Network and made freely available to the scientific community.\nIf you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication.\nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884))\nand the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand acknowledge the 4DN lab which generated the data. Please \ndirect any questions to the Data Coordination and Integration Center at [support@4dnucleome.org](mailto:support@4dnucleome.org).\n\n#### Should I cite the 4DN data portal if I use it in my research?\n\nIf you have used the 4DN data portal or datasets obtained \nfrom us during your research, we urge you to cite us in your \npublished work.\n\n[https://www.nature.com/articles/s41467-022-29697-4](https://www.nature.com/articles/s41467-022-29697-4)\n\nReiff, S.B., et al. (2022) The 4D Nucleome Data Portal as \na resource for searching and visualizing curated nucleomics \ndata. *Nature Commun.* 13(1):2365. \n[doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)", "name": "help.user-guide.faq.download", "award": {"name": "2U01CA200059-06", "center_title": "DCIC - Park", "status": "current", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "project": "4DN", "@type": ["Award", "Item"], "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, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "@id": "/awards/2U01CA200059-06/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "Downloading and using data from the 4DN data portal", "status": "released", "aliases": ["4dn-dcic-lab:static_section_faq_how_to_download"], "options": {"filetype": "md", "collapsible": true, "default_open": true}, "date_created": "2021-03-23T00:05:26.854756+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2022-05-13T15:29:02.505009+00:00"}, "schema_version": "2", "@id": "/static-sections/f44b5da6-3d6d-49ff-9a67-ca1bb9a7341e/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "f44b5da6-3d6d-49ff-9a67-ca1bb9a7341e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.e4a22298-1da4-4e59-8a65-9e661f47fb48"]}, "display_title": "Downloading and using data from the 4DN data portal", "external_references": [], "content": "#### Do I need an account to download files?\nFile download from the 4DN data portal now requires authentication, even if the file is public.\nAccounts can be created by anyone, including those not part of the 4DN Network.\nUse your Github or Google account, or create a new one as explained in the [Account Creation User Guide](/help/user-guide/account-creation).\n\n#### How do I download files?\nTo download a single file, login (if you haven't already), go to the File page and click the Download button. The file will start downloading immediately.\n\nTo download many files (bulk download), select and filter the file(s) from either the [browse Experiment Sets](/browse/?experimentset_type=replicate&type=ExperimentSetReplicate) page, the [search Files](/search/?type=File) page, or from the page of an Experiment Set containing the desired files.\nThen click on the Download button to generate a metadata.tsv file with download URLs for the selected files.\nThese can be downloaded from the command line using cURL (include your access key, as explained [here](/help/user-guide/downloading-files)).\n\n#### Can I use unpublished 4DN data sets in my publication?\nUnpublished data sets are generated by the 4DN Network and made freely available to the scientific community.\nIf you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication.\nIn your manuscript, please cite the 4DN White Paper \n([doi:10.1038/nature23884](https://doi.org/10.1038/nature23884))\nand the 4DN Data Portal paper ([doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)), \nand acknowledge the 4DN lab which generated the data. Please \ndirect any questions to the Data Coordination and Integration Center at [support@4dnucleome.org](mailto:support@4dnucleome.org).\n\n#### Should I cite the 4DN data portal if I use it in my research?\n\nIf you have used the 4DN data portal or datasets obtained \nfrom us during your research, we urge you to cite us in your \npublished work.\n\n[https://www.nature.com/articles/s41467-022-29697-4](https://www.nature.com/articles/s41467-022-29697-4)\n\nReiff, S.B., et al. (2022) The 4D Nucleome Data Portal as \na resource for searching and visualizing curated nucleomics \ndata. *Nature Commun.* 13(1):2365. \n[doi:10.1038/s41467-022-29697-4](https://doi.org/10.1038/s41467-022-29697-4)", "filetype": "md", "content_as_html": "

Do I need an account to download files?

\n

File download from the 4DN data portal now requires authentication, even if the file is public.\nAccounts can be created by anyone, including those not part of the 4DN Network.\nUse your Github or Google account, or create a new one as explained in the Account Creation User Guide.

\n

How do I download files?

\n

To download a single file, login (if you haven't already), go to the File page and click the Download button. The file will start downloading immediately.

\n

To download many files (bulk download), select and filter the file(s) from either the browse Experiment Sets page, the search Files page, or from the page of an Experiment Set containing the desired files.\nThen click on the Download button to generate a metadata.tsv file with download URLs for the selected files.\nThese can be downloaded from the command line using cURL (include your access key, as explained here).

\n

Can I use unpublished 4DN data sets in my publication?

\n

Unpublished data sets are generated by the 4DN Network and made freely available to the scientific community.\nIf you are intending to use these data for a publication, we ask that you please contact the data generating lab to discuss possible coordinated publication.\nIn your manuscript, please cite the 4DN White Paper \n(doi:10.1038/nature23884)\nand the 4DN Data Portal paper (doi:10.1038/s41467-022-29697-4), \nand acknowledge the 4DN lab which generated the data. Please \ndirect any questions to the Data Coordination and Integration Center at support@4dnucleome.org.

\n

Should I cite the 4DN data portal if I use it in my research?

\n

If you have used the 4DN data portal or datasets obtained \nfrom us during your research, we urge you to cite us in your \npublished work.

\n

https://www.nature.com/articles/s41467-022-29697-4

\n

Reiff, S.B., et al. (2022) The 4D Nucleome Data Portal as \na resource for searching and visualizing curated nucleomics \ndata. Nature Commun. 13(1):2365.
\ndoi:10.1038/s41467-022-29697-4

", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}