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Each data set contains three files--investigation, study, and assay--that conform to the ISA-Tab structure and naming conventions. Within this structure are fields that are standard for each type of file, though null values are allowed; that is, not every data set includes values for each field. The portal allows you to filter these fields in an interactive way so that you can visualize the data in a pie chart or list.

You can search investigations, studies, and assays using any keyword. You can download selected files, the entire data archive, or only the metadata associated with a study. You can also upload and publish your own investigation data to the portal.

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1. On the Browse Investigations page, click .
   The Select menu appears to the left of the pie charts.
   

2. Expand fields by clicking the plus signs. Note that in the STUDY PROTOCOLS and Study Assays section, the field values of Study Protocol Name, Study Assay Technology Type, and Study Assay Measurement Type are already selected. These field values are the ones that appear in the three default pie charts on the Browse Investigations page. If you clear these check boxes, those pie charts disappear from the page. When you reset all of the pie charts or select Browse > Investigations, however, they reappear.

   
   

3. Click any of the field values to select them. For example, select Study Protocol Type.
   The pie charts immediately update to include one for Study Protocol Type.
   
   
   Correspondingly, the Investigations list updates to show Study Protocol Type in the fields available for the investigation.
   
   
   
   You could also opt to clear all of the check boxes except for Study Protocol Type. In this case, that is the only pie chart that would appear.
   
   
   
   The field also disappears from the Investigations list.
   
   

    
4. When you have selected or cleared as many fields as you want from the pie charts, click .
   The Select menu moves back to its original position.

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Select the boxes next to the objects you want to visualize and filter. If you download these objects, all of these objects will be included in the download.

Visualizing and Filtering Study Data

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Metadata describes the structure of the data collected in an investigation and translates to the file columns, field definitions, and placeholders that appear in a spreadsheet. It is in Investigation-Study-Assay tab-delimited format (ISA-Tab), which is based on the ISA-Tab specification

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You do not have to log in before downloading the full data from an investigation. If you are not logged in, when you request the full data, you are prompted to provide your email address. You will receive a link at that address you can use to access and download the data. If you are logged in, you have the option of using Globus to download the file.

To download full data

1. Open the investigation you want to download.
   The Investigation Details page appears.
   

2. Click the Download Full Data button.
   The Request Data Files dialog appears. It offers different options depending on whether or not you are logged in to CSSI DCC.

   • If you are not logged in, enter your email address and then click Download. A link to the archive will be emailed to you.
     

   • If you are logged in, you have two options: 1) transfer the file with Globus, which is useful when the file is very large, or 2) download the file to your computer now.
     
     If you choose to transfer the file with Globus, click the checkbox and then click Download. The Transfer Files page in Globus opens. For more information about transferring files with Globus, see Uploading Files with Globus or Globus Support

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     .
     
     If you choose to download the file now, just click Download.
     Your browser prompts you to open or save full_archive.zip.

     Info
     It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_full.zip.

     For example, the following dialog box appears in Google Chrome.
     
     
     Follow your browser's instructions to open or save the file.

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To download selected metadata

1. Filter a study or an assay until you reach a selection of investigation data you are interested in downloading.

2. On the Investigation Details page, click Download Selected Metadata.
   Your browser prompts you to open or save the .zip file. Follow your browser's instructions to open or save the file.
   

   Info
   It may be useful to rename the .zip file as you save it to include the name of the investigation so that you can identify it more easily. For example, miRNA_metadata.zip.

   Info
   title Archive File Contents
   The archive file is in compressed format. When you download it, it may be a single compressed folder or .zip file. When you open it, you see at minimum three text files at the root of the folder or file. An example of these follow.     a_10290.txt    i_10290.txt    s_10290.txt The text files describe the investigation, study or studies, and assay or assays. In this example, 10290 represents the file identifier but in practice, each file identifier may be named differently, even in the same investigation. Only the a, i, or s prefix is required. If you download full data or selected data, the archive may also contain other files or folders as appropriate for the investigation; for example, images. If you download metadata, the archive only includes the a, i, and s files.

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Downloading Large Files with Globus

Globus is a service that enables large file transfers securely. You must have an account with Globus and install

To download files using Globus

1. If you haven't already, start Globus Connect Personal.
2. Filter a study or an assay until you reach a the investigation data you are interested in downloading.
   The Request Data Files page appears. It looks slightly different if you are downloading the investigation's full data or selected data.
3.   If you are downloading the investigation's full data,   click the Transfer with Globus checkbox and then click Download.
   
     Yo u You are prompted to log into Globus. Skip to step 5 to continue this procedure.
4. If you are downloading selected data from the investigation, do the following.
   

   1. Click the Transfer with Globus checkbox.
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   2. Click Request Download.
      The Globus Upload window appears, asking you to confirm your Globus ID.
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   3. Enter your Globus ID (an email address) and click Confirm.
      The Download Requested window appears.

      

   4. Click Ok. Periodically check your email inbox for the link to the file on Globus. Click the link in the email.
      
5. Review the Transfer Files page. This page appears no matter whether you are downloading full or selected data.
   One of the Endpoints you configured when you installed Globus Connect Personal is already populated, though you can change it.
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6.   Select the starting endpoint (on the right) where the file(s) you want to download reside(s). Narrow down to the path if necessary.
7. Confirm or change the destination endpoint (on the left). 
8. Click the left arrow button that points to the destination to begin the transfer request. 
   A message appears on the screen when the transfer request is submitted successfully.
   

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   You will receive an email when the request is granted and the transfer succeeds.