In the current version, the flow module has been used successfully by only one lab. It is likely that you will encounter an issue because of your unique flowjo workspace that will prevent you from being able to analyze your data. If you do have a problem, please let me know, and I'll try to fix it for the next version. Also, be aware that flow data in the current version (1.5) will not be compatible with the next version (1.6). Any analysis that you do of flow data in this version will need to be redone in the next version.

1. To begin, enable the "flow" tab on the folder (on the left side panel, there's a link under "Manage Project" and under that "Customize Tabs". Click that, then check the box next to "Flow", and make "Flow" the default tab.
2. On the main flow page, there will be a link to set the pipeline root for the folder. The pipeline root specifies where on the server flow files might be found. You could set it to either "c:" or "/", or something more specific.
3. Back on the flow tab, there will be a link to upload FCS files. Navigate through the file system and find a directory containing containing FCS files. There will be a button to upload the fcs files. Pressing it will enable you to choose which directories to upload. This will read the keywords from the FCS files, and give you a link to "flow experiment runs" on the flow tab.
4. To analyze the flow data, you need to create an "Analysis Script". There's a button to do this.
5. If your data needs to be compensated, then you will need to "define the compensation keywords". Then, you upload a flowjo workspace, and it lets you choose which keywords identifies the compensation wells. There are several things that may go wrong at this point. The "choose compensation keywords" page only lets you choose keywords that uniquely identify one FCS file in the workspace. Therefore, if the workspace contains data from two runs (plates), then you will not be able to choose the keywords that you need to. Also, interval gates are not supported in 1.5.
6. To analyze flow data, upload a flowjo workspace containing your gate definitions. If this workspace uses gates that require compensated parameters, ("<FL-4>") then you will have had to do step 5. In version 1.6, you will be able to upload a compensation matrix that you created in FlowJo.

(I'm assuming here that you do have a FlowJo workspace. It is theoretically possible to create an analysis script without using flowjo, but no one has done it yet. If you would like to try, let me know.)