Uploading investigation data to the CSSI DCC Portal allows you to curate, manage, and reuse datasets in a standards-compliant way. The ISA-Tab specification describes this standard and how to structure your investigation data to create an Investigation-Study-Assay tab-delimited (ISA-Tab) archive file. This may involve configuring it using open-source software made for this purpose.

An ISA-Tab archive file is a compressed (.zip) file containing multiple text files and data files. Each tab-delimited text file in an ISA-Tab file describes the structure, meaning the column headers and row values when considered in spreadsheet format, of the investigation, study, and assay components of the archive. The data files correspond to each assay and are included in the archive in their native format, for example, Microsoft Excel. An ISA-Tab archive file may also contain images and other files.

Only users who have registered for and logged in to the CSSI DCC Portal can upload investigation data. During registration, you must also select the I would like to upload Investigation data checkbox and be approved. For more information, refer to Registering to Use the CSSI DCC Portal.

You can upload a single ISA-Tab archive file and save it to a folder. If you need an administrator to delete an investigation version from a folder, click the Contact Us link at the bottom of the screen.

Uploading ISA-Tab Files

Uploading Large Files with Globus

Globus is a service that enables large file transfers securely. You must have an account with Globus before you use it to upload investigation files to CSSI DCC. If you do not already have an account, you are prompted to create one when you start the upload process.

To upload files using Globus

Begin uploading your ISA-Tab file by creating a project in CSSI DCC and selecting a file. For more information on this process, go to Uploading ISA-Tab Files.
On the Upload ISA TAB Files page, click .
If you have not yet logged into Globus, a log in page appears.

For more information about using Globus, consult their documentation and/or support .
After you successfully log in, the Globus Transfer Files page appears. One of the Endpoints you configured is already populated, though you can change it.
Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.
Confirm or change the destination endpoint (on the right).
Click the right arrow button that points to the destination to begin the transfer request. A message briefly appears on the screen when the transfer request is submitted successfully. When the transfer succeeds, Globus sends a notification email message.
To view the resulting list of files in the destination endpoint, click refresh list on the right.

Once an administrator approves the upload request, the uploaded, not-yet-published file appears as a new project version in the Investigation Projects section of the page.
Since you have not yet published the uploaded file, you must publish it to use it in CSSI DCC. For instructions on previewing and publishing it, refer to Publishing ISA-Tab Files to the CSSI DCC Portal.

Understanding Upload Errors

Controlling Access to Investigation Data

Making an Investigation Open Access

Editing or Removing the Embargo Date for an Investigation

Viewing Open Access History

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.

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

Open a previously published file.
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.