Tour of the screens¶

This page walks through what you see and where to click, in the order most people use during a run. Technical paths (for bookmarks or IT) are noted in italics at the end of each section.

Welcome (home)¶

What it is: The landing page after you sign in. It introduces ROBIN in plain language and explains that it analyses nanopore BAM data in real time.

What to do here:

• View All Samples — opens the big table of runs (see below).
• Open Workflow Monitor — opens the Activity Monitor view so you can see whether the pipeline is busy and how far it has progressed.
• Manage watched folders — for advanced users who need to add or remove input folders (see Watched folders).
• Generate Sample ID — opens a small form to create a library ID from a test ID and optional patient fields.
• View Documentation — opens the public documentation site in a new tab.

You may also see a News area with updates from the team.

Bookmark path: home is the site root, e.g. http://your-server:8081/.

All samples (sample list)¶

What it is: A searchable table of every sample ROBIN is tracking—your main hub for finding a run. The browser title may read Sample Tracking Overview.

Example only: the library IDs in this screenshot are anonymised samples from a quality-control exercise; your own list will show your runs.

What you’ll see:

• A short intro: Tracked nanopore runs and workflow state in one place…
• A heading All tracked samples and a legend such as A=Active P=Pending T=Total C=Completed F=Failed so you can read the status columns.
• Buttons like Select all / Clear selection if you need to run bulk actions (your team may use these for SNP or other batch jobs).
• In Actions, click View to open that sample’s detail page (clicking elsewhere on the row does not open it).

If a sample never appears, check that MinKNOW is writing BAMs where ROBIN expects them and that the run has started—your bioinformatics contact can confirm.

Bookmark path: /live_data.

Activity Monitor (workflow monitor)¶

What it is: A dashboard for overall pipeline health: whether work is running, how long it has been up, and counts of completed or failed jobs. The browser title may read Workflow Monitor.

What you’ll see:

• Workflow monitor with the subtitle Real-time workflow monitoring and control.
• A Workflow status card with a status line (for example “Running”), Started and Duration, a progress bar, and Run counts (such as completed / failed / skipped).
• File processing — overall and per-sample progress when files are being handled.
• Queue status — counts for preprocessing, analysis, classification, and other queues.
• Active jobs — a searchable table of jobs when work is running (it can show “no data” when idle).
• Live logs — scrollable output with Clear and Export for monitoring or sharing with support.

Use this when you want a quick “is ROBIN still working?” answer without opening a specific sample.

Bookmark path: /robin.

One sample (detail page)¶

What it is: The page for a single library ID—this is where Run summary, Classification details, Analysis details, optional MNP-Flex results, and reports appear. Deeper tools on a follow-on screen (/details) are shown in Sample details (extra tools) below.

Open it from All tracked samples by clicking View on the row you want. That opens this sample page (/live_data/<your-sample-id>), not the Workflow Monitor (/robin); the monitor is described in Activity Monitor above.

OneSample.png: this repo image is another capture of the Workflow Monitor (/robin)—the same layout as Activity.png—not the /live_data/<id> page after View. The main sample screen is covered in Reading your results.

If ROBIN doesn’t recognise an ID yet, you may see Unknown sample and a short message that the library hasn’t been seen this session; the app will send you back to the list after a few seconds, or you can use Back to samples.

Full walkthrough: Reading your results.

Bookmark pattern: /live_data/<your-sample-id>.

Sample details (extra tools)¶

What it is: A secondary page with deeper tools for that sample: where files live on disk, links into IGV, sample identifiers, SNP tables, fusion pairs, and target genes, depending on your configuration.

Example only: any sample IDs or paths in this screenshot are from anonymised quality-control data; your page will reflect your run and configuration.

Use Back to sample to return to the main sample page.

What’s on the page: step-by-step description of each block (paths, IGV, SNP, fusion pairs, target genes) is in Reading your results → Sample details page.

Bookmark pattern: /live_data/<your-sample-id>/details.

Watched folders¶

What it is: Lets you add or remove directories that contain BAM files so ROBIN can watch them for new data. The browser title may read Watched Folders.

Example only: folder and work-directory paths in this screenshot are from a development machine; yours will match your deployment.

What you’ll see:

• Currently watched — each path with Remove to stop watching it.
• Add folder — type a path or use Browse, then Add folder.
• Work directory — where ROBIN is using as the main output/work area (read-only context on this screen).

Note: On some setups this only works when ROBIN was started in a mode that supports folder management. If you see a message that Ray or the workflow is required, ask your administrator—this is not something most clinical users change during a run.

Bookmark path: /watched_folders.

Sample ID generator¶

What it is: A form to build a sample identifier from:

• Test ID (required)
• Optional: first name, last name, date of birth, hospital number

Use the same value in MinKNOW: After you Generate sample ID, copy that Sample ID (MD5) and enter it as the sample ID for your sequencing run in MinKNOW (the field used to name the library and outputs). ROBIN expects BAMs and folders to use this identifier, so it can match the run to the manifest and tracking list automatically. Do not invent a different ID in MinKNOW if you already generated one here—use the generated ID verbatim.

The browser title may read Generate Sample Identifier.

What you’ll see:

• Short help text explaining required vs optional fields.
• Generate sample ID — computes the identifier and fills the Sample ID (MD5) field.
• Copy to clipboard — copies the generated ID when one exists.

How it works:

1. Identifier string — ROBIN builds a single line by joining, in order, Test ID, First name, Last name, and Date of birth, separated by pipe characters (|). Any optional field you leave blank is treated as an empty string between the pipes. The date of birth is formatted as YYYY-MM-DD when you pick a date.
2. MD5 hash — The Sample ID is the MD5 digest (hexadecimal) of that UTF-8 string. It is deterministic: the same inputs always produce the same ID.
3. Hospital number — This is not included in the MD5 string. It is stored separately when ROBIN writes a sample identifier manifest next to your sample output (see below).
4. After generating — If a work directory is configured, ROBIN creates a folder named with the new sample ID and writes a small manifest file there: Test ID is stored in plain text; first name, last name, date of birth, and hospital number (if provided) are stored encrypted so they can be recovered in a controlled way. If no work directory is set, you still get the MD5 ID, but the manifest step may not run—watch the on-screen notification.

Use this when your lab’s workflow expects a consistent naming scheme before or during a run.

Bookmark path: /sample_id_generator.

Next¶

• Reading your results — understand each block on the sample page.
• Troubleshooting — if something doesn’t look right.