Presets: starting an experiment that is already configured
All methods · October 12, 2026 · Jan Hellemans
How to start an experiment from a preset, build your own, put it on the qPCR start page and change one that is in use, and how presets work: what a preset carries, how the shelf chooses what to show, why a used preset is locked, how Clarida starters and vendor kits differ from your own, and what an experiment keeps from the preset it started from.
Most labs run the same kind of experiment many times: the same assays, the same plate format, the same QC thresholds, the same sections of the workflow and none of the others. Setting that up by hand takes minutes each time, and the minutes are the smaller cost: two people setting up "the same" experiment rarely end up with identical settings.
A preset is that setup, saved once in the Library. Starting an experiment from it gives you an experiment that is already configured: its workflow layout, its settings set, and any samples, assays, markers, mix, protocol and instrument it should start with.
This page has two parts. How to covers starting from a preset, building your own and changing it later. How it works explains what a preset holds and the rules behind it; read it when a step raises a question. The running example is a lab that types SNPs by TaqMan allelic discrimination on 384-well plates, with its own Genotyping 384-well settings set (see Experiment settings sets).
How to
1. Start an experiment from a preset
On the qPCR page, Start a qPCR experiment, the Start from a preset shelf offers one-click starts. Click a card to start at Define, for an experiment you are about to design and run. Its starts it at Import & annotate, for a run that already exists. All presets opens every preset you can use.
Start a blank experiment starts from a preset as well: Clarida's own Clarida default.
See Every experiment starts from a preset, Starting at Define or at Import & annotate, Clarida starters and Vendor kits.
2. Build your own preset
In the sidebar, open Setup → Presets and choose New preset. Give it a Preset name, then work through the two cards below:
- Settings and layout. A new preset starts with Clarida defaults and the All sections layout. Replace settings set and Replace workflow layout pick others from the Library. Our lab picks its Genotyping 384-well settings set and Clarida's Genotyping layout, or its own version of it (see Workflow layouts).
- Contents. Search to add samples, assays, sets, markers, a mix, a cycling protocol or an instrument, in any combination. Our lab adds its markers, which bring their assays with them, its mix, its cycling protocol and its 384-well cycler. Samples stay out, since they change every run.
Create saves the preset.
To build a variant of one of your presets, select it and choose Duplicate preset: the copy starts with everything the original carries, and nothing is saved until you choose Create.
See What a preset carries, Markers bring their assays and Preset, layout and settings set.
3. Put it on your shelf
Select the preset in Setup → Presets and choose Pin to qPCR start. Your first pin keeps the shelf you were seeing and adds to it.
To reorder or remove presets, choose Customize on the shelf. Customize quick start holds up to ten presets under My shelf, with arrows to reorder them. Workspace owners and admins also see Workspace shelf, the list recommended to every member who has not set their own.
See The preset shelf and The Presets library.
4. Check what an experiment started from
Open Define. Under Launched from, the preset card names the preset the experiment was started from, its source and what it contains; beside it, Active settings and layout shows the settings set and layout it started with. In the Experiments list, the Preset column says the same.
See The experiment records its preset and Copies, and where they came from.
5. Change a preset that is in use
Once an experiment has been started from a preset, its contents, layout and settings set are locked; only its name and description stay editable. To change it, choose Duplicate preset, change the copy and Create it. Archive the old one if nobody should start from it any more.
When our lab moves its settings set to v2, its preset shows v2 available on the settings set. The preset has started experiments, so the lab duplicates it and clicks v2 available in the copy to move to v2. An unused preset moves with the same click.
See Locked once used and A preset does not reach back.
How it works
Every experiment starts from a preset
A preset is the starting point of an experiment, and in Clarida every experiment has one. Start a blank experiment starts from Clarida's own Clarida default preset, which carries the All sections layout, Clarida defaults, and nothing else.
The exceptions are experiments imported from qbase+ or from an RDML file, and experiments from before presets existed. They record no preset, and Define says so (No preset) rather than inventing one.
What a preset carries
A preset holds two required parts and any number of optional ones:
- A workflow layout (required) decides which sections the experiment shows, in what order and under which headings. See Workflow layouts.
- A settings set (required) holds the design, analysis, QC and workflow settings the experiment starts with. See Experiment settings sets.
- Contents (optional, in any combination): samples and assays, one by one or as sets; markers, for genotyping, each of which brings the assays its targets belong to; one mix and one cycling protocol; and one instrument, a cycler from your Library, which is preselected for every run of the experiment and can still be changed when you start a run.
A preset without contents is useful in its own right. It fixes how an experiment is analyzed and presented, and leaves what goes on the plate open. Clarida's starters are such presets.
Markers bring their assays
A marker reads its alleles from assay targets and their dyes (see Genotyping), so without those assays it has nothing to measure. Adding a marker to a preset therefore also adds the assays its targets belong to: the whole assay, also when the marker reads only one target of a multiplex. Expanding a marker in the picker says so before you add it, a toast names the assays that came along, and each of them is marked in Contents: Came with marker — removing it removes this too. Removing the marker removes those assays again. An assay you had added yourself is left alone, and stays when the marker goes.
Controls work the same way one level up. A sample with an expected genotype at a marker brings that marker, and with it the marker's assays, so the control always arrives with the genotype to check it against; removing the sample removes them again. When a sample in your preset expects a marker the preset does not include, the preset's details warn A control’s marker is missing and offer Add marker.
Only your workspace's Library markers can be added, and only when their targets belong to Library assays. A marker made inside a single experiment is refused.
Starting an experiment links your markers rather than copying them: the experiment uses the Library marker, with its alleles and cut-offs, and Marker Setup shows it with a Mine pill. Its method is changed in the Library, where the change applies wherever the marker is used. A vendor kit's markers are copied into the experiment instead, together with the kit's assays.
Preset, layout and settings set
The three are separate Library items, and each answers a different question:
| Item | The question it answers |
|---|---|
| Layout | What the experiment shows |
| Settings set | How the experiment computes |
| Preset | Which layout, which settings, and what for |
A preset refers to its layout and its settings set; it does not contain copies of them. One layout or one settings set can therefore serve many presets. Our lab could keep a second preset for validation runs, with the same layout and settings set and a different set of markers.
The preset shelf
The Start from a preset shelf on the qPCR page holds up to ten presets and shows as many as fit the screen. Which presets it holds is decided at three levels, and the most specific one that is set wins:
- Your own shelf, once you have pinned presets or saved My shelf.
- Otherwise, your workspace's shelf, if its owners or admins have saved one.
- Otherwise, your starred presets, most recently used first, topped up with Clarida's starters.
A level you or your workspace configured is never topped up from a lower one. A workspace shelf is a recommendation: any member can replace it with a shelf of their own, and Clear my list brings it back. A preset that stops being available to you, because it was archived or a kit was withdrawn, drops off the shelf by itself.
Stars and pins are different things. A star marks a favorite, and feeds the shelf only when nothing else is configured; a pin puts a preset on your shelf in the position you choose.
Starting at Define or at Import & annotate
Each preset offers two starts. Define is the beginning of the workflow, for an experiment you are about to design and run; on the shelf it is a click on the card, in a preset's details Start new experiment from Define. Import & annotate is for data that already exists; on the shelf and in the details it is , Start new experiment from Import.
Either way the experiment receives the same layout, settings and contents. Only the page it opens on differs.
The second start opens Import & annotate wherever the preset's layout places it, also when the layout moved it out of Analyze into a group of its own. A layout that leaves Import & annotate out opens the nearest section above it that the layout does show.
The Presets library
Setup → Presets lists every preset you can use: your workspace's own, Clarida's, and kits shared with your workspace, each with a pill saying whose it is. Selecting one shows what it contains, its layout and settings set, the experiments started from it, and its actions: start, pin, star, and for your own presets duplicate, edit, archive or delete.
Locked once used
Once an experiment has been started from a preset, its contents, layout and settings set are locked. The name and description stay editable. To change anything else, duplicate the preset and edit the copy.
The reason is the record. An experiment states which preset it started from, and that statement only means something if the preset still says what it said then. A preset nobody has started from yet stays fully editable, and can move to a newer version of its settings set with one click on v2 available.
For the same reason a used preset cannot be deleted, only archived, and an unused one is deleted rather than archived. An archived preset leaves the shelf and the Library list, and experiments started from it name it as (archived).
Clarida starters
Clarida ships a starter preset for each of its workflow layouts: relative quantification, reference gene finder, plate homogeneity check, detection and genotyping, most of them also in an analysis-only version. Each carries its layout and Clarida defaults, and no contents. They are what the shelf shows before anyone has configured it. All sections has no starter of its own: the Clarida default preset behind Start a blank experiment already pairs it with Clarida defaults.
Clarida's presets are read-only to you. To adapt one, build a new preset with the same layout and settings set, then change what you need.
Vendor kits
A kit vendor can publish its kits as presets, to partner workspaces (Partners) or to everyone (Public). A kit preset carries the vendor's assays, controls, mix and cycling protocol, together with its catalog number and links to the protocol and the product page.
A kit is used as published. You can start from it, star it, pin it and inspect every part of it, but you cannot edit it or duplicate it. Its contents are the vendor's validated design, and a modified kit is no longer the kit its validation describes.
The experiment records its preset
The preset an experiment started from is part of its history. Define shows it under Launched from, beside the settings set and layout, and the Experiments list has a Preset column. Both lead to the preset in the Library.
Two experiments that name the same preset started from the same layout, the same settings and the same contents, without anyone comparing settings.
Copies, and where they came from
At the start, the preset's settings set and layout are copied into the experiment. Changing a setting in the experiment changes the experiment, not the settings set in the Library.
Contents behave according to whose they are. Items from your own Library are linked to the experiment as your Library's items. Items from a vendor kit are copied into it, so the experiment stays complete whatever the vendor later does with the kit.
Each sample, assay, mix and marker in the experiment shows where it came from with a pill: Mine, Clarida or the vendor's name, as long as it is unchanged. Editing it inside the experiment makes it the experiment's own. The pill gives way to Add to library, which saves your version as a new Library item, and to Reset to your library's version, or to the vendor's. Reset lists what will change before it does anything, and leaves wells and imported data alone.
For a kit, the difference matters: an edited assay is no longer the vendor's validated version, and its row no longer carries the vendor's name.
A preset does not reach back
Nothing done to a preset afterwards changes an experiment already started from it. The settings and layout were copied at the start, and a used preset is locked in any case. A changed preset is a duplicate, and only experiments started from the duplicate use it.
For our lab, moving to a new marker panel means duplicating its preset, swapping the markers, and starting the next run from the copy. Last month's experiments still name the old preset and still read as they did.