Clinical Protocols
A protocol (also called a program) is a reusable plan of activities — workouts, habits, measurements, medications, and biomarker checks — laid out on a schedule. You build a protocol once as a template, then assign it to any client, and it drives what shows up in that client's daily plan. This is how your clinical intent reaches the client every day, not just at the visit.
If you deliver structured programs — a 12-week strength plan, a supplement protocol, a recovery program — this is where you build them. If your care is purely appointment-based, you can keep this light and come back to it later.
Say "Atlas, create a program template for a 6-week post-injury mobility program" and Atlas drafts the template and shows it on a confirmation card; approve it and it lands in your program library, unassigned, ready to assign to any client — the same as one built with Create Program. With a client selected, "Atlas, build a 6-week mobility program for Jordan" drafts and assigns it to that client instead, again only after you approve.
Start from the default library
You do not have to build your first programs. Every organization starts with a library of sixteen ready-made programs on the Programs page, each one written from published evidence, with the citations and an evidence grade attached so you can see what it rests on. Assign one as it is, or open it and change it into your own.
| Area | Default programs |
|---|---|
| Sleep and recovery | Circadian Sleep Reset · Autonomic Recovery (HRV) |
| Metabolic | Glycemic Control Reset · CGM Optimization Program · GLP-1 Therapy Support |
| Cardiovascular | Blood Pressure Reduction · ApoB / Lipid-Lowering · VO2max Builder (Norwegian 4×4) · VO2 Max Builder – Beginner |
| Strength and movement | Strength & Muscle Foundation · Low Back Care |
| Longevity and mind | Longevity Foundations · Mood & Anxiety Resilience · Cognitive Focus |
| Hormone and peptide | Testosterone Therapy Monitoring · Peptide Therapy Support |
Every activity in a default program carries an instruction, the plain-language line the client reads telling them how to do it, and activities meant for several days a week name those days, so the client's plan shows exactly the sessions the program promises.
GLP-1 Therapy Support, Testosterone Therapy Monitoring and Peptide Therapy Support schedule the routine around a medication your prescriber has ordered: the injection reminder, labs, symptom tracking, training and nutrition. They do not contain a compound's dose. The dose belongs on the client's medication record, set by the prescriber. Peptide Therapy Support carries the lowest evidence grade, insufficient, because that is the state of the published research, and it names no specific peptide.
With a client selected, name a library program and say what to change: "Put her on Glycemic Control Reset but drop the fasting, and make strength Monday, Wednesday and Friday." Atlas stages the tailored program on a confirmation card, and nothing is assigned until you approve it. Atlas can remove an activity, change an activity's days, time, length or instruction, and add an activity. It will tell you if you ask for a change it cannot make, and it stages nothing in that case.
The same works on a program a client is already on: "Move her strength sessions to Monday, Wednesday and Friday" or "change the walk to 20 minutes." The change applies from now on and every day the client already completed or logged is kept. Adding a new activity to a running program, or changing a single day, is done on the client's Program tab.
A. Build a protocol template
A template is the reusable version of a program — no client attached yet. You define the activities and when each one should appear, and that schedule is what every assigned client inherits.
Create a template and add its activities. Each activity is one thing the client does, and the type determines how it's tracked:
- Exercises and workouts — with sets, reps, or duration.
- Habits — recurring actions you want the client to build (hydration, sleep, a daily walk).
- Measurements — things the client records (weight, a symptom score).
- Medications and supplements — with dosage and timing. A dose is optional: a supplement saved without one shows its name alone to the client, never "0 mg".
- Biomarker checks — labs or values to track over the program.
The exercises, supplements and biomarkers you pick from come from a built-in catalog. You can ask Atlas what's in it, for example "which magnesium forms can I add?" or "what's the code for fasting glucose?", and it answers from the same catalog you see in the builder.
For each activity, set the default day and time it appears in the client's plan (for example, "strength work every Monday and Thursday morning"). Recurring activities repeat on that schedule; one-off activities appear once.
B. Assign a protocol to a client
Assigning is what turns a template into a live plan. From the client's profile, assign the protocol, and it populates their daily plan on the schedule you defined — the client sees each activity on its day in their app.
When an activity is meant to happen at a visit — a personal-training session, an in-clinic measurement — link it to the booked appointment. The appointment's real time then overrides the activity's default time, so the client sees one session, not a duplicate.
C. Track progress
As the client completes activities in their app, their progress and adherence show up on their plan, and you can adjust the protocol as they go. Completions are recorded through the platform's single source of truth, so what you see, what the client sees, and what reports show all agree.
D. Set real targets — and let them track themselves
Activities can carry measurable goals instead of instructions buried in a note, and the platform measures them for you. On any walking activity you can set a daily step goal; on cardio, a heart-rate range, a zone target with minutes-in-zone (for example, "90 minutes in Zone 2"), a calorie burn, or a distance; on exercises, sets measured as reps or as timed holds ("3 × 90-second plank"). You can set these when you build the template, when you assign it, or later while editing.
When the client's wearable shows the goal was reached, step and zone activities complete themselves — the client doesn't have to remember to check a box. When you open a completed activity on the client's Program tab, you see target versus actual side by side, with a checkmark when the goal was met, so a follow-up conversation starts from real numbers.
Ask "Atlas, how is this client doing against their Zone 2 target?" from the client's chart — Atlas reads the same targets and results you see.
E. Activity days must fall inside the protocol's dates
A protocol runs between a start and an end date, and each recurring activity runs on the weekdays you pick for it. Those two settings have to agree: an activity scheduled for Saturday inside a protocol that runs Monday to Friday has no day to land on, so it produces nothing at all — and the client never sees it.
When you assign a protocol, anything in that position is now named back to you straight away: "Protocol assigned, but one activity won't appear for the client — Zone 5 Cardio runs on Sat, which never falls between 2026-09-14 and 2026-09-18." The protocol is still assigned; the rest of it works normally. Fix it by editing the protocol to widen the date range or move the activity to a day inside it, and the activity starts appearing on the client's plan.
Service visits behave differently and are not affected. A booked visit is scheduled as a set number of appointments rather than a weekly recurrence, so it has no weekdays to match against.
F. Medication phases and dose ramps
For medication that ramps over time (a titration), create one activity per phase and give each an Active window — the date range that phase runs. Week-based shortcuts ("Week 1", "Weeks 2–4") calculate the dates from the protocol's start for you. Only the current phase appears in the client's plan, and the next phase takes over automatically on its start date. Nothing shows up early, and past phases keep their history.
G. Meals with a choice
A meal activity can offer several options from your meal library — "Green Giant or Super Veggie" — each with its full recipe, ingredients, and macros. The client sees all options in their app and records which one they ate, so your nutrition data reflects reality rather than assumptions.
H. Questionnaires on a schedule
Attach a standardized questionnaire — such as the Oswestry Disability Index — to a client's protocol with a cadence (weekly, every two weeks, monthly). Each cycle is delivered automatically, every submission is scored automatically, and the score trend appears right on the protocol so you can see whether the plan is working between visits.
Questionnaires attached to a template stay with it: save the program, reopen it later, and the questionnaire and its cadence are still listed, and the assignment wizard pre-loads them for every client the program is assigned to.
I. Know who's falling off the plan
Every day the platform reviews each active protocol's last seven days of adherence. When a client drops below half of their planned activities, an alert lands in your dashboard's Needs attention queue and the protocol is flagged on their chart — so you find out before the missed follow-up, not after.
Two details worth knowing so the absence of an alert means something. A protocol is only assessed once it is at least seven days old — judging adherence on day two would flag almost everyone, so new protocols are left alone until there is a real week to measure. And the alert fires once, when a client crosses into at-risk, not every day they stay there; it is a signal that something changed, not a daily reminder. The current figure is always on the protocol itself if you want to check on someone without waiting to be told.
An activity like "4 physical-therapy visits" tracks visits attended against the goal, shows the next booked visit, and gives you a one-click Book visit button in the protocol details — it never fills the calendar with placeholder rows.
Your protocols checklist
- At least one protocol template built with a real schedule of activities
- Template assigned to a test client and visible in that client's plan
- Progress tracking confirmed (mark an activity complete and see it reflect)
Next steps
- Staff & Permissions → — invite your team and set what each role can do.