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

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.

     ISA-TAB files that you upload must be in .zip format. The file can be no larger than 20 GB.

7. Click Upload files.
   The status of the file becomes Ready.
   
   
8. Click Upload 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
     

     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 usingstandards and conventions described in the ISA-TAB specification . The ISA tools site provides additional technical information about validating ISA-TAB files.
      

       
9. Refresh the page to see the new upload listed in the Investigation Projects section of the page. 
   

 You are now ready to publish the ISA-TAB file to CSSI DCC.

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.