Create a new experiment and upload your data:

   1. If you aren't already logged into Cytobank, launch firefox and point your browser to your Cytobank server (e.g. http://www.cytobank.org/cytobank).  
   2. From the Cytobank Inbox, click on the green “Create a New Experiment” button in the upper left.
   4. Enter the information as requested.  Each experiment must have an Experiment Name and Purpose.  The Experiment Name will show up in the Inbox.  You can search all the information you enter here, so the more you enter, the easier it is to find experiments later.
   5. Click the “Create” button at the bottom of the page.
   6. Browse to the folder on your computer with your FCS files.  On a Macintosh computer, you must single click on the folder that contains your FCS files and then click "Choose".  On a Windows computer, you can either single or double click the folder with your FCS file and then select "Open".  For example if your FCS files are in "c:\facsdata\march\leukemia" then single click the leukemia folder to choose it. 

      Optional: An alternative to browsing for a folder is to drag individual FCS files or folders into the center of the upload application window.
   7. Make sure the the files you want to upload are checked and click on "Upload Selected Files".
   8. Once the upload is completed, you will see a page showing a mini Forward Scatter vs. Side Scatter pot for each file and asking to confirm categorization of these files into experimental, compensation or other controls.
   9. Once confirmed you can click on "View Experiment Summary" to see details about the experiment and to share an experiment with another user.  You may also want to invite a friend to open a Cytobank account.
       Optional: You can choose to download your fcs files to start analysis in another program or you can click on "Start an Illustration" from the upload confirmation page to jump directly into analysis.

To share an experiment with another user:

Optional: You may want to invite a friend to open a Cytobank account so that you can share experiments with them.

1. Go to the experiment summary page for an experiment on Cytobank where you have full control (an experiment you uploaded). 

2. Within the text area on the left titled "Share with a User (Full Access):", type the name of someone you would like to share the experiment with.  

3. Once you find the correct user, click their name to share them experiment with them.  If they have email alerts on, they will receive an email saying that you shared the experiment with them and a link to the experiment.

Notes:

- Press "Escape" or delete any text you entered if you do not want to share the experiment with one of the listed users.  

- To remove access for a user, click the "[x]" button after their name in the list of users with full access.

- Primary researchers can always share an experiment.

Projects have two main uses:

- Projects group experiments for sharing.  Projects save time when sharing a lot of experiments with the same users because they allow you to group experiments together and share them as a unit.

- Projects allow you to share experiments with limited permissions.  When you share an experiment directly, you give full access.  When you share a project, you can set the permissions to limit what users can do with your experiment and data files.

To create a project:

1) In the Inbox, under the "Manage Projects" section, click the first link for "Manage my Projects.  (Or go to: https://www.cytobank.org/cytobank/projects).

2) Under the actions, click "New Project".  (Or go to: https://www.cytobank.org/cytobank/projects/new).

3) Enter a Project Name and a Description.  

4) Set the permission levels for project members.  There are two settings:

    - Sharing Level for illustrations:

           "View Only" = Project members can only view the illustrations that have been made.  They cannot make their own illustrations.

           "Illustrations" = Project members can make their own illustrations.

    - Cloning Level for experiment files:

           "Disabled" = Cloning and file download are disabled.  Project members will not be able to download files or clone the experiment.

           "Clone Files Only" = Project members can clone the experiment, but only with files (not with the illustrations).  Project members can download files.

           "Full Clone" = Project members can clone the experiment with both files and illustrations.  Project members can download files.

5) Click the "Create" button at the bottom.

 Optional: You can set a default project in your user profile.  Then, when you create a new experiment and upload data, it will select this project by default.  

Notes:

- If you enable "Full Clone", Project Members will be able to make their own copy of your data which they control fully.  

- Project settings do not over-ride direct sharing.  If you share an experiment with a user, that user has full access to the experiment, regardless of whether it is in a project or not, whether or not the user is on a project, and what permission settings the project has.

- You can change the permissions on a project any time after you create it.

You can set a default project (and others) in your user profile:

1) In the bar at the top of Cytobank, click "Project" to open your user profile.

2) On the left, click "Edit" to edit your profile.

3) Under the default project near the bottom, select a project.

4) Click "Update".

Once you do this, when you create a new experiment and upload data, your default project will be selected.

Notes:

- You can always change when you are uploading a new experiment if that experiment does not belong on that project.  

- If you assign an experiment to the wrong project, you can change it in the experiment summary page.