Note: this tutorial assumes that you have already uploaded or created in jinkō a Computational Mode. Should you not have completed this step, you can refer to one of the following links:

• Importing a CM
• Creating a CM 

Introduction 

What it is

A protocol is a simple way to test different experimental conditions, for example different doses of a drug. There is no randomization at this stage: Each protocol arm will be applied to all the patients in your virtual population. In other words, the virtual patients are cloned across each arm allowing for unbiased comparisons. So these are not your traditional real-life trial arms, and, for instance, applying 5 protocol arms to 1,000 patients will lead to 5,000 simulation runs.

What it does

Whereas the virtual population brings variability across patients, with potentially different descriptor values (like weight, age etc…) from one patient to the next, the protocol brings certainty. Indeed, all the patients on one arm will all have the same values for the protocol inputs on that arm. If a descriptor varies from patient to patient in the virtual population but is also set by the protocol arm, the protocol arm takes precedence and all the patients on that arm will have the same value for that descriptor. For instance if the age varies from patient to patient but you set the age in your protocol, then all patients will have the same age on each arm.

Step 1: Initiate a protocol

To start creating Protocol arms, you first need to create a trial simulation, which will be attached to a CM, and go to the Protocol arms section of the trial:

You have then 2 options: 

• select an existing Protocol arms. By default, only the ones attached to the selected CM are displayed - this ensures that the descriptors used will be compatible with your CM, but you can remove the toggle if needed.
• or click on + New set of Protocol arms to create a new one. The newly created PA will be tied to the CM used in your trial. Give your protocol a name and optionally a description

Step 2: Select the input descriptors you want to apply your protocol on

• Press on Select Descriptors . By default those will be filtered for the input descriptors tagged as Protocol Specific. If you want to add other parameters, simply remove the filter by clicking on the small cross. 
• Click on each descriptor in the left box to add them to the right box and select them, or click on >> to transfer all the filtered descriptors at once. 
• Validate once you have selected all of the descriptors you need. You can come back to this step at any time to add or remove additional descriptors. 

Step 3: Set-up your arms

• You can add as many arms as you want. A warning will be raised if two arms are identical. 
• Each arm has an ID that you can edit, but that should be SBML compliant (see documentation here)
• For each arm and each descriptor, you can edit the values taken by all patients on that arm.
• For each arm, you can optionally assign it a Control arm among the other arms. This comes in handy when coupled with Output sets to be able to easily create Quantities of Interest (QoIs) comparing a result on one arm versus its control. For instance if you want to compare the maximum tumor size across two treatment regimens, select one arm as the control of the other. See the creating measure tutorial for more info. 
• Pro tip: You can transpose the protocol if you'd rather see it with the arms at columns and the 

And that's it, you can now go back to your trial and launch it.