Run planning

Plan, edit, clone, and delete sequencing and cell screening runs in ElemBio Cloud.

Planned runs allow team members to create and manage runs in ElemBio Cloud for use on any connected Element systems. A team member can plan a run in ElemBio Cloud, then select it during run setup. The Planned Runs table displays saved configuration information for planned runs. You can only edit or delete planned runs through ElemBio Cloud.

Run Progression

After an instrument starts processing a planned run, the following rules apply:

• During the run setup and before priming begins, the status of a planned run appears as In Use.
• If you discard a planned run before priming, the In Use status is removed and the run becomes available for selection on the instrument.
• After priming, the run moves from the Planned Runs table to the Active Runs and All Runs pages.
• If you discard the run or the run fails after priming, the run is no longer available as a planned run. To make the run available again, you must re-create the planned run.

Planned runs let you configure a run ahead of time so any connected Element Biosciences system can launch it consistently. Each planned run captures the workflow selection, run manifest, and advanced settings. For workflow-specific setup, see the Sequencing or Cell Screening workflow guides.

Add a planned run

Add a planned run to configure a sequencing or cell screening run before it starts on the instrument. Planned runs let you attach a run manifest, choose a workflow, and save advanced settings so the run can be launched consistently from a connected Element system.

1. On the Planned Runs page, select Plan a Run.
2. Choose the run type (Sequencing or Cell Screening), and then choose the workflow or kit.
3. Enter a unique run name and, optionally, a description.
4. Attach a prepared run manifest if you have one.
5. Complete any run-type-specific fields, and then select Save Run.

For run-type-specific planning steps, see the individual workflow guides under Sequencing or Cell Screening.

Run manifest validation

When you add or edit a planned run, ElemBio Cloud validates any attached run manifest. Validation ensures that the run manifest is compatible with the planned run setup. If the run manifest contains mistakes or invalid data, then ElemBio Cloud displays a list of errors and warnings.

You can save a planned run with warnings, but not with errors. Before you proceed, resolve the errors and re-upload the run manifest. For sequencing run manifests, see Prepare a sequencing manifest. For cell screening run manifests, see Create a cell screening manifest.

Edit a planned run

1. On the Planned Runs page, locate the run that you want to edit.
2. Select the run name. Or, at the end of the row, select the three dots (...), and then select Edit.
3. Update the run information as needed.
4. Select Save Run.

Clone a run

Cloning creates a new planned run from an existing run configuration. There are two paths:

• Clone a planned run that has not started yet.
• Replan an existing run to run the same configuration again.

Either path retains the run configuration, including the selected custom design, target cell assignment manifest, and run manifest, and then opens the new run in the planning form so you can adjust it before saving. If ElemBio Cloud cannot retrieve any of these, then a warning appears and you must re-select or upload the item before you save the cloned run. For each warning and how to resolve it, see Resolve clone warnings.

Clone a planned run

1. On the Planned Runs page, locate the run that you want to clone.
2. At the end of the row, select the three dots (...), and then select Clone.
3. ElemBio Cloud opens the cloned run in the planning form. The run name matches the original run with a -cloned suffix.
4. Update the run information as needed.
5. Select Save Run.

Replan an existing run

Replan an existing run to reuse the configuration of a run that has already been planned or completed.

1. On the All Runs page, locate the run whose configuration you want to reuse.
2. At the end of the row, select the three dots (...), and then select Replan this Run Config.
3. ElemBio Cloud opens the cloned run in the planning form.
4. Update the run information as needed.
5. Select Save Run.

Resolve clone warnings

When ElemBio Cloud cannot carry an item over from the original run, the planning form opens with one or more of the following warnings. More than one can appear at a time.

Warning	Resolution
The manifest from the original run could not be retrieved and was not included in the cloned run.	Upload a run manifest in the planning form.
The Target Cell Assignment Manifest used by the original run could not be found.	Re-select the target cell assignment manifest before you start the cloned run.
The panel from the original run is not in the current panel catalog.	Select a panel before you start the cloned run.

If a run cannot be cloned at all, ElemBio Cloud reports that the run might be too old or use a configuration that is no longer supported. Create the run manually instead.

Delete a planned run

1. On the Planned Runs page, locate the run that you want to delete.
2. At the end of the row, select the three dots (...), and then select Delete.
3. When prompted, enter the name of the planned run.
4. Select Delete to immediately remove the run.

Planned run compatibility with Element systems

A planned run appears on a connected instrument only when the configuration matches the instrument type, OS version, and add-ons. Review the sequencing and cell screening tables for the requirements of each configuration.

Sequencing

Planned runs appear in AVITI OS based on compatibility with the system. Factors that affect compatibility are the instrument OS version, system type, and available add-ons. When you add or edit a planned run, a statement at the bottom of the form identifies the run compatibility requirements.

The following table defines the compatibility requirements for different configurations of a planned sequencing run:

Note:

Some of the following configurations are available in AVITI Dx™ IVD Mode; however, loading a planned run from ElemBio Cloud is available only in AVITI Dx RUO Mode.

Planned Run Configuration	Instrument Compatibility	Compatible AVITI OS Version	Add-On Requirement
Two Library Pools	AVITI™ LT™ AVITI AVITI24™ AVITI Dx (RUO Mode)	2.3.0 or later	Individually Addressable Lanes
Low-Diversity High-Multiplex w/ 2 × 300 Cloudbreak™ + Adept™ library	AVITI AVITI24 AVITI Dx (RUO Mode)	2.4.0 or later	No add-on required
Low-Diversity High-Multiplex w/ other kits or library types	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	2.5.0 or later	No add-on required
Cloudbreak Freestyle™ Sequencing Kit	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	2.5.0 or later	No add-on required
Cloudbreak UltraQ™ Sequencing Kit	AVITI AVITI24 AVITI Dx (RUO Mode)	2.6.0 or later	No add-on required
Custom Recipe	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	2.6.0 or later	Add-on required for AVITI OS 3.0.0 or earlier
Filter Mask	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	2.6.0 or later	Filter Mask
High Density or Expert Mode HD (including 2 × 300 Cloudbreak sequencing kit)	AVITI AVITI24 AVITI Dx (RUO Mode)	2.6.0 to 3.3.0 3.4.0 or later only with 2 × 300 Cloudbreak sequencing kit	Earlier than 3.0.0 - Add-on required 3.0.0 or later - No add-on required
PMG Shift	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	3.0.0 or later	PMG Shift
Trinity™ Sequencing Kit	AVITI AVITI24 AVITI Dx (RUO Mode)	3.0.0 or later	No add-on required
Cloudbreak 2 × 75 Low Sequencing Kit	AVITI LT AVITI AVITI24 AVITI Dx (RUO Mode)	3.1.0 or later	No add-on required
Trinity Sequencing Kit with Third Party	AVITI AVITI24 AVITI Dx (RUO Mode)	3.4.0 or later	No add-on required
Trinity Sequencing Kit with Two Library Pools	AVITI AVITI24 AVITI Dx (RUO Mode)	4.1.0 or later	Individually Addressable Lanes

Cell screening

Cell screening planned runs appear in AVITI OS based on compatibility with the system. When you add or edit a planned run, a statement at the bottom of the run planning form identifies the run compatibility requirements.

Planned Run Configuration	Instrument Compatibility	Compatible AVITI OS Version	Add-On Requirement
12-well	AVITI24	4.1.0+	No add-on required
Cytos™ Cell Culture Optimization Run	AVITI24	4.1.0+	No add-on required
Cytos Custom Workflow that uses: Cytos Protein Kit Cytos OPS Kit Cytos 3' Transcriptome Kit Cytos MPS Kit	AVITI24	4.1.0+	No add-on required
Custom Recipe	AVITI24	4.1.0+	No add-on required
Save Raw Imaging Projections	AVITI24	4.1.0+	No add-on required
Save Per Target Background Images	AVITI24	4.1.0+	No add-on required
Illumination Correction	AVITI24	4.1.0+	No add-on required

See also

• Run planning for sequencing
• Set up a protein screening planned run
• Set up an OPS planned run
• Set up a 3' Transcriptome planned run
• Set up an MPS planned run
• Set up a cell culture optimization planned run