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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
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An ISA -Tab archive file is a compressed (.ZIPzip) file containing multiple text files and data files. Each tab-delimited text file in an ISA -Tab file archive 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, see Chapter 3: Uploading and Publishing Investigation Data.
Registering to Use the CSSI DCC Portal
Before you can log in for the first time, you must register.
To register on the CSSI DCC Portal
- Navigate to the CSSI DCC Portal.
The home page appears.
- Click Login.
The Please Sign In page appears.
- Click Register.
The Registration page appears.
- Provide information in all of the following required fields:
- First name
- Last name
- Institution
- Email address
- Password
- Confirm password
- If you want to upload investigation data to the CSSI DCC portal in the future, select the I would like to upload investigation data box. Doing so ensures that your future submissions are correctly tracked.
- Select the I'm not a robot box.
- Click Register.
A message box appears.
- Check your inbox for an email with the subject line "CSSI DCC Account Activation." Click the link in the email to complete account activation.
- Get started using the CSSI DCC Portal.
Logging In to the CSSI DCC Portal
Before you can upload investigation data, you must register and then log in.
You do not need to log in to browse, search, and download investigation data.
To log in to the CSSI DCC Portal
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Changing Your Password
- Log in to the CSSI DCC portal.
Your email address appears in the upper-right corner of the screen. - Click the arrow next to your email address to open the window and then click Change Password.
The Change Password window appears. - Your current password is already supplied. Enter your new password twice and click Change Password.
A message appears confirming that you have changed your password. - Click the arrow next to your email address to open the window and then click Change Password.
The Change Password window appears. - Your current password is already supplied. Enter your new password twice and click Change Password.
A message appears confirming that you have changed your password.
Uploading ISA-Tab Files
Before uploading a file to the CSSI DCC portal, consult the ISA-Tab specification
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ISA-Tab files that you upload must be in .zip format. Use Globus to upload files larger than 10 GB.
To upload ISA-Tab files
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Click New Project.
The Project Properties page appears.
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A project is simply a container for the ISA-Tab file. It allows you to track multiple versions of ISA-Tab file uploads to this project. It is a best practice for each investigation to have its own project. |
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Click Save Project.
The new project is listed under Investigation Projects.
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If the File Upload section of the page is not visible, click Open next to the project name to show it. |
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If needed now or later, click Edit to change the project name. Depending on your privileges, you may not see the Delete button. |
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Select the file you want to upload to this project in one of the following ways:
Drag and drop the ISA-Tab archive file from your computer to the Drop your files here box surrounded by the dashed lines:
Click the Drop your files here box image and browse to where the file is stored.
The file is listed in the File Upload area and the status is listed as Ready.
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If the file is smaller than 10 GB, click Upload selected files. If the file is larger than 10 GB, use Globus instead.
The file begins processing and the status moves through the following stages:
- Uploading
- Processing Queued
- Queued
- Preparing uploaded files
- Parsing ISA TAB Metadata
- Preparing Data Files
- Validating assay files and file sizes
- File processed successfully
Success: file processed successfully
Once an administrator approves the upload request, the uploaded, unpublished file appears in the Investigation Projects section of the page. It is not yet published, so you must now publish it to use it in CSSI DCC.
Uploading Large Files with Globus
Globus is a service that enables large file transfers securely. You must have an account with Globus and install
Globus Connect Personal to 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. Multiexcerpt include MultiExcerptName ExitDisclaimer nopanel true PageWithExcerpt wikicontent:Exit Disclaimer to Include
To upload files using Globus
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On the Upload ISA TAB Files page, click .
If you have not yet logged into Globus, a log in page appears.
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If you have trouble logging in, go to Globus Support
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After you successfully log in, the Globus Transfer Files page appears. One of the Endpoints you configured when you installed Globus Connect Personal is already populated, though you can change it.
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Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.
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Confirm or change the destination endpoint (on the right).
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Click the right arrow button that points to the destination to begin the transfer request.
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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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Publishing ISA-Tab Files to CSSI DCC
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Upload at least one ISA-Tab file to a project.
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If you have uploaded multiple versions of the file to the project, decide which version of the ISA-Tab file you want to publish to CSSI DCC.
Click the Preview button next to that version.
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Review the uploaded file by exploring the investigation details. If you are satisfied with the content of this version, request its publication by clicking Publish this Version. If you are not satisfied or the upload generated an error, click Return to go back to your project and upload a new version of the ISA-Tab file.
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You may encounter an upload error. A sample error message follows:
The CSSI DCC Portal validates uploaded ISA-Tab files using standards and conventions described in the ISA-Tab specification
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Viewing Publish History
The first time you upload an ISA-Tab file to a new project, it is the first version of that file.
While you should associate only one investigation with a project, you can upload multiple versions of an investigation file to that project, and then publish or unpublish a version as many times as you like. You may want to do this if you change your investigation data or need to fix it due to an upload error. Each time you upload a new investigation file to a project and publish it, the version number increases by one.
CSSI DCC tracks the history of each file you publish by date and time. Use the publish history timeline to switch between current and previous versions of the investigation file. You can download the full data or selected metadata of a previous version. You can only see the publish history for investigation files you have uploaded.
To view the publish history of an investigation file
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When a file has multiple versions, they appear on the timeline as well. The version that is currently selected is always green. In the example below, the current version is selected, so it appears in green. The current version is also open-ended to the future until you publish another version.
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The white space between versions, as in the example below, indicate times when no version of the investigation file was published. |
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Unpublishing ISA-Tab Files
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