Remote Run Monitoring
ElemBio Cloud synchronizes with connected systems to update run monitoring information in real time. Runs can be monitored from the following areas:
- Active Runs: Summarizes information for the most recent runs, grouped by instrument.
- All Runs: Displays information for active and historical runs from connected systems.
- Run Details: Displays detailed information for a run.
Active Runs
Cards on the Active Runs page display high-level information about each active and recently completed sequencing or cytoprofiling run. The page orders the cards by instrument and side A or B, resembling the instrument display. A dynamic gauge graphic on each card visualizes the run progress and the number of cycles or batches completed, changing colors for different statuses.
The cards update as follows.
- When a run is in progress, the card information updates in real time.
- The card title indicates if it's a sequencing or cytoprofiling run, and the card links to the Run Details page for the run.
- When a run is no longer in progress, the card displays information for the last run executed. The card footer indicates the side is available, and the card links to the Run Details page for the run.
- The card always displays a badge for the most recent run status.
Example cards on an Active Runs page
Run Statuses
| Status | Gauge Color | Description |
|---|---|---|
| Priming or Primed | Blue | The run is in setup mode. Metrics do not populate before sequencing starts. |
| Running | Blue | The run is actively progressing. Metrics populate as they become available. |
| Pausing or Paused | Orange | The run is pausing or paused for flexible start. Resumption is automatic. |
| Completed | Green | The run successfully completed. The instrument completed data transfer to the selected storage location. |
| Failed | Red | The instrument encountered a critical issue during the run and cannot progress. Data analysis completed up to and including the last successfully cycle or batch, and the instrument transferred available data to the selected storage location. |
| Stopped | Teal | A user stopped the run before it completed. Data analysis completed up to and including the last successfully cycle or batch, and the instrument transferred all data to the selected storage location. |
All Runs
The All Runs sequencing table displays a complete list of sequencing and cytoprofiling runs for active and historical runs. The Run Name links to the Run Details page for the run. Use the available options to filter run data by specific criteria, customize visible columns, and manage your view.
Remove a Run
Remove a run to eliminate the run from view in from ElemBio Cloud. Although a removed run no longer appears, the data remain archived and hidden. If you accidentally remove a run, contact Element Technical Support to restore it.
To remove a run
- On the All Runs page, locate the run you want to remove.
- In the Actions column, select More, and then select Remove.
- When prompted, enter the name of the run.
- Select Remove to remove the run.
Run Details
A Run Details page displays the complete record of a sequencing or cytoprofiling run and associated flow executions.
The page includes the following features:
- Run Overview: Visualizes the current run status in a gauge graphic.
- Run Setup: Displays summary run setup information.
- Run Configuration: Displays detailed run setup information for sequencing and cytoprofiling runs including cartridge, buffer bottle, and flow cell details.
- Analysis Overview: Indicates the status for analysis executions and displays key primary analysis metrics.
- Sequencing: Reads, yield, Q30, and percent reads passing filter (%PF).
- Cytoprofiling: Cell count, cell confluency, and % assigned
- Primary Analysis: Detailed and interactive charts of run metrics.
- Sequencing: Q Scores and PhiX error rates throughout Read 1 (R1) and Read 2 (R2) and onboard indexing metrics
- Cytoprofiling: Differential Expression Level, % Assigned, and Quality Controls
- Run Files: Displays files output from runs that use a compatible provider.
- Analysis Executions: Displays a list of analysis flow executions when you use cloud-hosted flows and enables relaunch.
- CytoCanvas Callout: For cytoprofiling runs, displays a quick way to download the latest version of the CytoCanvas desktop application for transcriptomics, proteomics, and cell phenotypes exploration.
Sensitive Metadata
By default, AVITI OS sends the following metadata to a secure and customer-specific ElemBio Cloud database:
- Run description
- Sample names from the sequencing run manifest, if applicable
- Well labels from the cytoprofilng run manifest, if applicable
The ElemBio Cloud database is separate from the telemetry database. Therefore, telemetry does not collect metadata. If you prefer to keep metadata on-instrument, contact Element Technical Support and request Restrict Metadata mode. When the mode is enabled, a lock appears on the run description in ElemBio Cloud and sample and well names in run manifests are masked as numbers. The numbering reflects the order of samples or wells in the run manifest.
Troubleshooting Run Monitoring
If ElemBio Cloud data seem out-of-sync with instrument data, the instrument might have lost the network connection.
- Reconnect the instrument to the network, and then make sure that the data update in ElemBio Cloud.
- If the issue persists, contact Element Technical Support.