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Users who are logged in Uploading investigation data to the CSSI DCC Portal can upload Investigation-Study-Assay (ISA) data.Templates in this repository are all in Investigation-Study-Assay tab-delimited format (ISA-TAB) format, allowing allows you to curate, manage, and reuse datasets in a standards-compliant way. For more information on the The ISA-TAB format, refer to the ISA-TAB Tab specification

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.Before you upload a template to this repository, you must create and configure describes this standard and how to structure your investigation data to create an Investigation-Study-Assay (ISA) archive. This may involve configuring it using open-source software made software made for this purpose: http://isa-tools.org/
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An ISA -TAB template is an archive file that contains archive is a compressed (.zip) file containing multiple text files and data files. Each tab-delimited text file in an ISA archive describes the structure, meaning the column headers and row values when considered in spreadsheet format, of the Investigationinvestigation, Studystudy, and Assay assay components of the templatearchive. The data files correspond to each assay and are included in the archive in their native format, for example, Microsoft Excel.

In the CSSI DCC Portal, a "template" holds an ISA-TAB template archive file and only specified users can access it. Those users can upload ISA-TAB template archive files to the CSSI DCC Portal template.

Uploading an ISA-TAB Archive File to a Template

You create a template in the CSSI DCC Portal first and then add an ISA-TAB template archive file to it.

Files that you upload to the portal must be in one of the following archive formats: .zip, .rar, .tar, or .gz. Each file must be no larger than 500 MB.

To upload a template

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Select the file you want to upload by either

  • dragging and dropping the ISA-TAB archive file from your computer to the File box, or

  • clicking Add files to navigate to where the file is stored.
    Template files must be in one of the following archive formats: .zip,.rar,.tar,.gz. The file can be no larger than 500 MB.

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  • Upload as new: A new file that has not been uploaded before.
  • Replace existing file: This file replaces an existing one associated with this template.
    Next version: This file becomes the active version of the file associated with the selected template. All previous versions of the template are accessible from the Template List and you can make any of them active or inactive as needed.

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  • Private restricts access only to you, when you are logged in
  • Public makes the file available to both registered and unregistered users.
  • Custom 

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An ISA archive may also contain images and other files.

Uploading investigation data requires a logged-in CSSI DCC user account with permission to upload. For details on requesting permission to upload data, refer to Managing Your Account. 

You can upload a single ISA archive and save it to a folder. If you need an administrator to delete an investigation version from a folder, contact the Center for Strategic Initiatives (CSSI) Data Coordinating Center (https://cssi-dcc.nci.nih.gov/cssiportal/contactus) or click the Contact Us link at the bottom of any DCC page.

The following page family describes how to upload investigation data and request open access for your uploaded data.

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Unpublishing ISA-Tab Files

After publishing a file, you may want to unpublish a version of it to remove that version completely from the CSSI DCC server.

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titleAccess Control and Unpublishing

When you unpublish a file, all access restrictions that may have been applied to it are removed from the investigation. If you decide to publish this investigation later, you must reapply any access restrictions you want.

To unpublish an ISA-Tab file

  1. Open a previously published file.
  2. Next to the version you want to unpublish, click Unpublish.
    The status of this version becomes Unpublication Request Pending. Once an administrator approves the request, the version returns to its unpublished state.

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