Let’s get you started using FlowJo Envoy with a few simple steps. Kiss those long email chains goodbye!

Step 1: Sign in to FlowJo Envoy

If you have purchasedFlowJo Envoy or signed up for a free trial, sign in using your FlowJo Cloud credentials. If you don’t have a FlowJo Cloud account, don’t worry, it’s a quick and easy process to get your authentication details. To obtain an account, simply click Create Account to access FlowJo Cloud, and fill out the form.

Step 2: Create a Project

Projects are the highest level in your file hierarchy. We suggest you name your project using a broad over-arching theme. You might even name it after your grant proposal. You can have multiple projects, and each project can contain one or more studies, so don’t get too caught up in what belongs and what doesn’t. To create a project:

1. If necessary, click the Workflows tab at the top of your FlowJo Envoy window to display Workflow Filter view. (This is the first screen you see when you sign in.)
2. Near the top right of the view, click the Action button. This button looks like three horizontal lines.
   
3. From the drop-down menu that appears, click New.
   
4. The New dialog box appears, asking you to supply a name and description for the project you are about to create. In the Enter a Name field, type the name of the project (think big!). You can also type a description in the Enter a Description field (this is optional).
   
5. Click Save.
6. The new project appears in the Project list, which is located at the upper left of Workflow Filter view.
7. Congratulations! You’ve created your first project.

Step 3: Create a Study

As the name implies, studies are subtopics you research within the broader project category. For example, you might have a project that focuses on the uptake and release of glucose or ketones. A study within that project might be the kinetics of the glucose transporter (GLUT). You create a study in a similar way to how you created a project:

1. Click the project you created in the previous step to highlight it.
2. Click the Action button, and select New from the drop-down menu.
3. In the New dialog box, click the Project field, and select Study.
4. In the Enter a Name field, type a name for the study.
5. Click Save.
6. The study appears in the Study list, located under the Project list. Because your project was selected when you created this study, the new study is automatically made part of that project.
7. Way to go! You’ve just created your first study.

Step 4: Create a Workflow

Workflows are the heart and soul of FlowJo Envoy! It is here that your data live and thrive, providing that critical piece of deduction to your manuscript or grant proposal. Best of all, it stays in the context of what was done, who did it, and when. No more guesswork to get the 411 on the data.

Workflows can be thought of as individual experiments, composed of one or more steps (we’ll get to those soon). When naming a workflow, consider what you are doing in the experiment. Is it a sorting experiment by flow, a sequencing run, PCR for genotyping or cloning? For example, I might name my workflow “T-cell isolation and sort” or “Sub-cloning TD-60 Serine mutants to pUC-19.”

To create a workflow:

1. Highlight the study you created in the previous step.
2. Click the Action button, and select New from the drop-down menu. The New dialog box appears.
3. In the New dialog box, click the Project field, and select Workflow.
4. In the Enter a Name field, type a name for the workflow.
5. Click Save.
6. The workflow appears in the Workflow list, which is located near the top right of the view. For now, it appears as an empty rectangle, outlined in gray.
   
7.  Awesome! You’ve got a workflow. Let’s add some steps to get ourselves organized.

Step 5: Create Steps within your Workflow

Steps are individual components within a workflow. If you think about it, a single experiment in the lab often involves different protocols for different stages of sample preparation and data acquisition. Often, an experiment involves sample processing by more than one individual. Steps in Workflows represent these highly variable components, and permit you to assign them to other colleagues, and upload protocols, data, results, or anything else pertinent to the experiment.

Let’s get started creating some steps for a hypothetical sort-and-sequence experiment:

1. Double-click the workflow you created in the previous step.
2. This opens a screen called Workflow Detail view. This view works like a dashboard, with the labeled workflow toward the top of your screen.
3. At the right of the workflow, click the large plus sign. 
4. The New dialog box appears, asking you to name the step.
   
5. Enter a name for the step. (Consider what you will do first in your experiment: Sample Collection, Plate Seeding, and so on.)
6. Click Save.
7. You’ve just created the first step in your experiment. Let’s create a few more steps that describe the experiment in its entirety.
8. If you closed the step creation window, click the large “+” to re-open it. Enter a new name for the next step in your experiment (such as Sample Staining, Library Preparation, Master Mix, and so on).
9. Click Save. Notice that this step is placed after your initial step.
10. Go ahead and create another step, remaining within the Step creation menu to add to your growing workflow. (This one might be data acquisition, analysis, or review).
11. On the step creation menu, click the “x” (Cancel button) to exit.
12. The workflow appears in the center pane along with several steps contained within the larger rectangle.

Step 6: Assign Colleagues to Steps

Our experiments in the lab often involve other colleagues processing or acquiring samples, analyzing or reviewing data. Step assignments in FlowJo Envoy help keep you and your colleagues organized and on top of your work. We can assign steps in FlowJo Envoy to alert our colleagues of just when to begin work on the next step in an experiment, or when data can be analyzed. Assigning a step to a colleague alerts them (via email) that it’s their turn to begin work on the experiment, when a preceding step has been completed.

1. Double-click a Workflow to return to the dashboard view. If you’re already there, skip this step.
2. Click the first step within the Workflow.
3. Notice the box underneath and slightly towards the right end of the Workflow. This is the step state and assignment box.
4. Click the “+” button next to the name listed on the “Assigned to” line. By default this shows your name (the creator of the workflow).
5. A drop-down list of names should appears. These list shows the names of users associated with your FlowJo Envoy account, most likely colleagues of yours in the lab.
6. Click any of the other steps, and change their assignment to the appropriate colleagues.

Step 7: Start the Workflow

Setting up our workflows and steps are great, but the really cool stuff happens when we start a Workflow. Don’t miss out! Let’s begin our Workflow.

1. Double-click a Workflow to return to the dashboard view. If you’re already there, skip this step.
2. Locate the button labeled “Start Workflow” in the bottom left of the Workflow dashboard.
3. Click  the “Start Workflow” button.
4. Your Workflow should now come to life! The first step in your workflow is outlined in green. This indicates the step is active; we’ll discuss step states in the next section.

Step 8: Update the State of a Step

Steps not only outline the configuration of an experiment, they also communicate to you (and others) exactly where you are in a given experiment. No need for your PI to ask “where are the data?” it’s right there in the workflow dashboard!

Steps can have one of four states assigned to them: Pending, Active, Blocked or Completed. Let’s return to our Workflow and change the state of our first step.

1. Ensure you’re in Workflow detail view.
2. Click the step highlighted in green within the Workflow.
3. Notice the box underneath and slightly towards the right end of the Workflow. This is the step state and assignment box.
4. Check the larger open square to indicate the step has been completed. Note how the step is now filled in green. This indicates that the step has been completed. The subsequent step also highlights in green, indicating that the next step is active.
5. Double-click the subsequent step.
6. Note the “Block this Step” and the adjacent pause button, at the bottom of the state and assignment box.
7. Click the pause button next to the “Block this Step” line.**
8. Note how the workflow state indicator on the upper left of the dashboard changes from “Running” and a green indicator to “Blocked” and a red indicator. The step outline also reverts to gray.
9. Unblock the step by clicking the “Play” button next to the “Unblock this Step” line.

**You can use the notifications pane to tell colleagues why the Step is blocked. Maybe there are insufficient reagents, the machine is down or a bulb has blown. Try typing @yourcolleague’s name to directly notify them about the problem.

Step 9: Upload Protocols, Data, or Results

We’ve learned how to create projects, studies, workflows, make step assignments, and change the state of a step or workflow. The last thing we ought to get a handle on is uploading the pertinent data and other files related to our experiment. You can assign data, protocols, workspaces or other results to a step or entire workflow. The more we have here, the greater the context enrichment of the data. To upload data and other files to a step:

1. Ensure you’re in Workflow Detail view.
2. Double-click the step you would like to assign data or files to.
3. To begin uploading, do either of the following:
   • Drag and drop files to the box below the File list labeled “Drag files here or Browse to upload.”
   • As the label implies, you can also click Browse to upload using your file system and upload any file or folder containing data, documents, workspaces or other files.
     The data begins to upload.
4. When the upload is complete, the File list displays the files of data you uploaded. The data and/or derivatives are associated with the step.