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 100 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 unique 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.

   
    

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 100 GB or smaller, click Upload selected files. If the file is larger than 100 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 file appears as a new project version 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. For instructions on previewing and publishing it, refer to Publishing ISA-Tab Files to the CSSI DCC Portal.
    
   
   

   If needed now or later, click Edit to change the project name.