PCR Protocols

What a PCR protocol is

Each protocol opens in a popup with two panels stacked on top of each other.

• The Thermal Gradient panel up top is a left-to-right row of colored square blocks, one per step. Each block shows the temperature and duration of that step. A purple dashed rectangle wraps the cycled section and carries a small x30 badge for the repeat count.
• The Reaction Recipe panel below has one row per ingredient with a stock concentration and a per-reaction volume in microliters. The bottom Total row is a manual entry where you type the target reaction volume. It looks identical to the ingredient rows above it (no input border, no edit affordance), so click into the volume cell and type your target volume.

It is the same library-plus-variation pattern as Methods. ResearchOS keeps the saved protocol in your library and copies its gradient and reagent values onto each experiment that attaches it.

The four zones of a program

Reading the gradient panel left to right, every protocol moves through four zones in this order. The default that a brand-new protocol starts with shows all four, so a new protocol is also the quickest way to see the layout. A protocol can contain more than one cycled block when the chemistry calls for it (for example, a touch-down PCR with two consecutive cycle rectangles at different annealing temperatures). Each cycled block has its own repeat count and its own set of steps, all within the same gradient.

• An initial step is one or more blocks that run once before the cycled section. Typically this is initial denaturation around 95 °C for three minutes, painted red.
• The cycled block is a group of blocks wrapped in a purple dashed rectangle, repeated end-to-end by the count on the purple badge above it (30 by default). The usual three are denaturation, annealing, and extension. Steps inside this block carry a faint purple ring so you can tell at a glance which blocks are inside the cycle.
• A final step is one or more blocks after the cycled block that run once. Typically final extension at 72 °C for five minutes.
• The hold is a single block at the right end with the duration Indef., parking the thermocycler at a low temperature (12 °C by default) until you come back to it. Painted blue.

Block color is keyed to temperature across six bands, blue (≤ 15 °C), cyan (≤ 30 °C), green (≤ 50 °C), amber (≤ 70 °C), orange (≤ 85 °C), and red (above 85 °C). A step typed in at the wrong temperature is visually obvious because its color doesn't match its neighbors.

Build a protocol step by step

1. Go to Methods and click + New Method. In the type picker that opens, choose the PCR type. That drops you into the protocol editor. Type a name into the Method Name field at the top of the popup.
2. The gradient panel opens with a sensible default loaded in (initial denaturation, the three-step cycle at 30 repeats, final extension, and a hold). Click the Edit Cycle button on the toolbar to enter editing mode. The blocks start jiggling to signal that they are now interactive.
3. Edit any block. Double-click a block to open the Edit Step popup. It has three fields, Step Name (e.g. Annealing), Temperature (°C) as a number input, and Duration as free text (e.g. 20 sec, 2 min). The Hold checkbox next to the duration field locks duration to Indef. for the parking step.
4. Reorder. Single-click a block to select it (a blue ring appears) and a pair of ← → arrow buttons drop in above the block. The arrows swap the block with its neighbor. The arrows step around the cycled block rather than into it. A block outside the cycle stays outside, and a block inside the cycle stays inside.
5. Move a step in or out of the cycle. When a block inside the cycled rectangle is selected, a red Remove from Cycle button appears next to the arrows. When a block outside the cycle is selected, a purple Add to Cycle button appears with a dropdown listing each cycle by position and repeat count (e.g., Cycle 1 (x30), Cycle 2 (x30)). Cycles have no name field, so the positional label is the only identifier. Pick a cycle and the block jumps into its rectangle.
6. Adjust the repeat count. Click the purple x30 badge above the cycled rectangle to open the Edit Cycle Repeats popup. Type a new number (1–100) and save.
7. Add or remove blocks. The toolbar has + Add Step (opens a StepEditPopup pre-populated with "New Step", 60 °C, 30 sec, where the block only lands in the gradient after you click Save) and + Add Cycle (opens an Add Empty Cycle confirmation modal with Cancel and Add buttons, where the new empty cycled rectangle only appears after you click Add, and you fill it by adding steps and using Add to Cycle). To delete, switch on the red Gradient Eraser and click any block to remove it. The purple Cycle Eraser works differently. Click a x30 badge and it removes just the cycle rectangle, leaving its steps behind as ordinary final steps. In normal (non- eraser) mode, clicking the same x30 badge opens the Edit Cycle Repeats popup so you can change the repeat count. Clear All wipes the whole gradient back to empty.
8. Hit Done Editing to leave editing mode. The jiggle stops and the toolbar collapses.
9. Scroll down to Reaction Recipe. Fill in each row with a stock concentration (e.g. 10x) and a per-reaction volume in microliters. Use + Add Row at the bottom of the table to add ingredients, and the x on each row to remove one. The Total row at the bottom is a manual entry. Type your target reaction volume there so it sits next to the ingredient rows and you can eyeball whether the ingredients add up.
10. Type any free-text Notes (lot numbers, master mix quirks, the day's primer pair). Click Create Method. The card appears in your protocol library and shows up in the Attach a method picker on any experiment.

Attaching a protocol to an experiment

From an experiment popup, the Attach a method picker shows every method and protocol in your library, your own and any in the public folder. Pick a PCR protocol and ResearchOS copies the gradient and the reagent table onto that experiment.

From that point on, the experiment carries its own copy. Bump the annealing temperature by a degree, add another microliter of primer, knock the cycle count down to 28 for a low-template run. The experiment records the variation and the library protocol stays exactly as you left it. The next experiment that attaches the same protocol starts from the unedited values.

Checking off ingredients at the bench

When you open a PCR protocol on an experiment (via the Method tab), the Reaction Recipe table gains a checkoff column on the left. Each ingredient row has a small checkbox. Tick it as you pipette each reagent into your tube. Checked rows turn green and a progress bar at the top of the table advances from left to right as you work through the recipe, with an X/Y checked count beside it. The Total row has no checkbox and is left out of that count (it's a math row, not an ingredient). Checkoff state is per-experiment and does not affect the library protocol.

Sharing

A PCR protocol is a method like any other, and it shares the same Private/Public pill as every other method type. Open the protocol and click the Private pill in the header to open the share popup. Select All Lab Users and click Apply. The pill flips to Public and the protocol appears in every labmate's method picker. See Methods Library for the full sharing model.