Clarida tutorial: navigating the interface

Tools vs. workflows

Clarida has two kinds of application. Tools are standalone utilities that tackle one specific task. Workflows cover an entire process as a series of steps that together answer a scientific question. This tutorial looks at the qPCR workflow. When you open it, you either start a new experiment or pick one you have run before.

How a workflow is organized

Opening an experiment reveals the workflow as a set of consecutive sections, organized around Clarida's D-DEAR principle: Define → Design → Execute → Analyze → Report. Each section holds content you can interact with — add annotation, view results, and so on — and some sections contain subsections of their own. The sections are laid out in a deliberate order, so working through them from start to finish makes sense for most experiments.

Navigating the workflow — sequential or free

Going A to Z is the natural path, but it is not required. You can make active decisions about how much of the workflow to do inside Clarida. For example, after Design you might choose to run Execute in Clarida — recording how you performed the experiment — or keep your records on paper (or not at all) and skip ahead to data analysis. You can also move backward at any time: if, while analyzing, you notice an issue with your sample or assay annotation, you can return to that earlier section and correct it. Navigation is free.

To open a section, click it directly, or use the quick-navigation links at the bottom of the page. When you are happy to follow the A-to-Z path, scroll to the bottom of the active section and click Next step to open the next one.

No save button — changes record automatically

There is no menu bar, and therefore no save or close button. Every change you make is recorded immediately, and all downstream data are recalculated and updated at once. The experiment is always in a consistent, current state — there is nothing to remember to save.

Section control elements

A set of controls recurs throughout the application, in each section header at the top right:

• a button to open and close the section;
• a focus-mode button that zooms into the active section, removing the surrounding clutter to fill the screen;
• a question-mark button that opens context-specific help and information in the side panel;
• a settings button that opens the settings specific to the active section.

Inside a section such as Design, you will also see quick settings — for example on run layout — that show the choices made for that step at a glance and let you jump straight to the corresponding setting.

Automated, assisted, and manual modes

Many steps can run in one of three modes, trading effort against control:

• Automated — Clarida applies a carefully chosen default that works for many situations, so you can proceed with no clicks and no decisions. Ideal when you are happy to trust the recommended setup.
• Assisted — a middle ground. You get settings that control how the step operates, but they act on the experiment as a whole. For run layout, changing a setting applies it to all runs and all wells.
• Manual — full control, down to the annotation of every individual well, at the cost of doing most of the work yourself.

In short: automated gives you a trusted default with no clicks; assisted balances some control with minimal work; manual gives full control but asks the most of you.