Glossary - Cytobank documentation
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  • A Few Terms and Definitions

     

    Some Cytobank terms and concepts may be unfamiliar.  In part, this is because Cytobank is designed to create

    interactive figures by organizing experiment details.

     

    1. ‘Banking’ your data is another way of saying that you are uploading a folder of

      flow cytometry files (representing one experiment) to Cytobank.

    2. In Cytobank analysis, you explain what makes each file and population of cells unique using experiment variables.  Common variables include different stimulation conditions, timepoints, and doses of a stimulus.

    3. The staining panel is a type of experiment variable that describes what was measured

      on every cytometer channel.  Every flow cytometry file must be tagged with just one staining panel.

    4. Dimensions allow you to reorganize experiment variables when creating a figure. Each experiment variable type is its own dimension.

    5.  Illustrations are different views of the data within your experiment. They are similar to panels of a figure you would put together to convey your results.

    6. An md5sum (also known as md5 hash or checksum) is a digital "fingerprint"of a file.  It is a way to verify that the FCS file uploaded from your computer and the FCS file on Cytobank is the same, and it helps ensure data integrity. You'll see it on the successful upload page, one for each file uploaded.

      To check md5sum for a file using a Mac:

      1. In Finder, browse to /Applications/Utilities.
      2. Double-click on the Terminal icon. A Terminal window will appear.
      3. In the Terminal window, type: "openssl md5" (md5 followed by a space).
      4. Drag the downloaded file from the Finder into the Terminal window.
      5. Click in the Terminal window, press the Return key, and compare the checksum displayed to the screen to the one on Cytobank's upload page.

      (Instructions modified from VMware's site)

      To check md5sum for a file using Windows, you will have to download a program to do so. We do not have any particular program we recommend. This page gives some options, though we do not vouch for any recommended here: http://www.openoffice.org/dev_docs/using_md5sums.html#win Remember to check your Windows machine frequently for viruses with a good virus checker.

    7. The QR code is a black-and-white box that appears on a printed illustration. If you hover over the QR code, you'll see identifying information appear, including: the title of the experiment, the name of the illustration (that was given when the illustration was saved), and the URL of the page that generated the illustration.  You can take the picture of a QR code with your iphone or blackberry to get the URL of the illustration.  The quickmark iphone app has worked well for doing this.

    8. A globally recognized avatar (gravatar) is an image that you can use to identify yourself on Cytobank and other sites on the internet.  To set your gravatar through the Profile section or by going directly to www.gravatar.com.