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. 

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

1. Navigate to the CSSI DCC Portal.
   The home page appears.
   
2. Click Login.
   The Please Sign In page appears.
   
3. Click Register.
   The Registration page appears.
   
4. Provide information in all of the following required fields:
   • First name
   • Last name
   • Institution
   • Email address
   • Password
   • Confirm password
5. 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.
6. Select the I'm not a robot box.
7. Click Register.
   A message box appears.
   
8. Check your inbox for an email with the subject line "CSSI DCC Account Activation." Click the link in the email to complete account activation.
9. 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

1. Navigate to the CSSI DCC Portal.
   The home page appears.
   
2. Click Login.
   The Please Sign In page appears.
   
3. Enter your email address and password you specified when you registered.
4. Click Sign In.
   The CSSI DCC Portal home page appears.

Uploading ISA-Tab Files

Before uploading a file to the CSSI DCC portal, consult the ISA-Tab specification . This specification describes 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.

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

1. Log in to the CSSI DCC Portal.
2. Select Investigations > Upload.
   The Upload ISA TAB Files page appears.
   

3. Click New Project.
   The Project Properties page appears.

   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.

   
   
   

4. Enter a title for your new project. Note that this title and that of the ISA-Tab file that the project contains can be different.

5. Click Save Project.
   The new project is listed under Investigation Projects.
   

   If the File Upload section of the page is not visible, click Open next to the project name to show it.

   
   
   

   If needed now or later, click Edit to change the project name. Depending on your privileges, you may not see the Delete button.

6. 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.

7. If the file is smaller than 10 GB, click Upload selected files.
   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 

   The uploaded 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.
   

   If the file is larger than 10 GB, use Globus instead.

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.

To upload files using Globus

1. If you haven't already, start Globus Connect Personal.
    
2. 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.

3. On the Upload ISA TAB Files page, click .
   If you have not yet logged into Globus, a log in page appears.
   
   

   If you have trouble logging in, go to Globus Support or send an email to support@globus.org.

   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.
   
   

4. Select the starting endpoint (on the left) where the file(s) you want to upload reside(s). Narrow down to the path if necessary.

5. Confirm or change the destination endpoint (on the right).
   

6. Click the arrow button in the direction of the source pointing to the destination to begin the transfer request.
   A message appears on the screen when the transfer request is submitted successfully. You receive an email when the transfer succeeds.
   
   
   The uploaded, unpublished file appears in the Investigation Projects section of the page.
   
   

Validating the Upload

You may encounter an upload error. A sample error message follows:

Missing Data Files: File processed successfully. 1 files referenced in the assay(s) were not found. Click here to view the missing file lists (limited to 1000 entries each).

The CSSI DCC Portal validates uploaded ISA-Tab files using standards and conventions described in the ISA-Tab specification . The ISA tools site provides additional technical information about validating ISA-Tab files.

Publishing ISA-Tab Files to CSSI DCC

1. Upload at least one ISA-Tab file to a project.  
2. 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.   

3. Click the Preview button next to that version.

   

   The Publish Preview page appears.
   
   
   

4. 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.

5. Check your inbox for an email with the subject line "Investigation Published." You can also confirm the published state of your file by checking the value of the Published Version field (the number should equal the number of the version you intended to publish) and the Published field (should be true) on the Upload ISA TAB Files page.
   
   

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, 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.

To view the publish history of an investigation file

1. Browse or search for an investigation.
   The Investigation Details page appears.
   
   
2. Click History to show the timeline.
   
   
   
   • The current version number appears above the timeline. You can hover over the version number to see the date when this version became the current version. In this example, Version 1 became current on 6/9/2017.
     
     
     
     
   • 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. 
     
     
     
     
   • To select a previous version, hover the mouse over the timeline. If the version you want to select is not immediately visible, move the scroll wheel on the mouse down to move left and up to move right until you see a previous version. In this example, a previous version was current only on 6/22/2017.
     
     
     
     
   • Click the previous version to select it. The Investigation Details page appears, showing the selected version number at the top. You can download the full data or selected metadata of this previous version. You cannot download selected data of a previous version.
     

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.

To unpublish an ISA-Tab file

1. Open a previously published file.
2. Next to the version you want to unpublish, click .
   The version returns to its unpublished state.