An Example COXEN Session

  1. Log in to COXEN.org.

    • Enter the email address and password associated with your account.
    • If you haven't yet registered for an account, click on the "Request Account" link and follow the instructions.
    • If you've forgotton your password, click on the "Password Reminder" link to have your password emailed to you.

    Login Example

  2. Once logged in, follow the "Datasets" link.

    Logged in, now click on Datasets

  3. Click the "Create New Dataset" link.

    Empty Dataset Page

  4. Name the dataset with a short, descriptive name, and specify the relevant clinical information.
    • Currently only Affymetrix HG-U133A chips are supported, but we hope to expand this soon.
    • You may also enter more detailed descriptive information about the conditions of the test.
    • Once everything is entered to your satisfaction, click "Save".

    Dataset Creation Page

  5. After your dataset has been created you will be returned to the Datasets page, which will contain the dataset you just created.
    • Clicking the + to the left of the dataset name will expand the listing, showing any files associated with the dataset.
    • Clicking the dataset name will take you back to the dataset creation page, allowing you to alter any of the associated metadata.
    • Clicking delete will delete any datasets with a checked box.
    • Click upload to upload your files.

    You've created your dataset

  6. Upload your .CEL files.
    • You can upload files individually, or in .zip or .tar.gz archives.
    • There is a limit to how much you can upload with direct http connections. The limit depends on your connection speed and configuration options. In general, we recommend using FTP if your file is larger than 20MB. Depending on which web browser you use, the browser may support ftp upload. Check your browser documentation for details. If your browser does not support ftp upload, you can use an ftp client to connect to the ftp server.

    Upload page

  7. After your files have been uploaded, you should be able to see them in your dataset.
    • Push + to expand the dataset listing; - collapses it.
    • Clicking delete will delete any datasets with a checked box and all files contained within the dataset.
    • Clicking delete will delete any individual files with a checked box.
    • Click analyze to run the COXEN algorithm on the files in your dataset.

    Your files are done

  8. Click analyze to confirm you wish to analyze the specified files. You will be emailed twice, once on initiation of computation, once upon completion.

    Analyzing

  9. When the computations have been completed, you will be prompted to return to the datasets page.
    • If everything went well, the result files will be found in the corresponding dataset.
    • For information on how to interpret the COXEN results, click here.

    Results are back