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Workflows & Processes

Workflows & Processes

Complete guide to LIMS business processes and workflows

This documentation covers all the key workflows in the Sinteni LIMS, from ordering kits to receiving final analysis reports. Each workflow shows the steps, actors involved, and system actions.

Customer Actions
Order, submit, receive
Lab Tech Actions
Process, analyze, report
System Automation
Notifications, tracking

Kit Order Workflow

The kit order workflow covers the complete process from a customer ordering sample collection kits to receiving them at their location.

1

Customer Places Order

Customer

Customer logs in, navigates to Kit Orders, and submits a request for sample collection plates.

System: Creates kit order record, assigns order number, sends confirmation email
2

Lab Prepares Kit

Lab Tech

Lab technician reviews order, generates plate barcodes, and prepares shipping materials.

Actions: Print barcodes, generate shipping label, package kit
3

Mark Ready to Ship

Lab Tech

Lab tech marks order as ready, triggering UPS pickup scheduling.

System: Creates UPS shipment, generates tracking number, schedules pickup
4

Shipping & Tracking

System

Package is shipped via UPS. System automatically tracks delivery status.

Automation: Celery Beat checks UPS tracking every 4 hours, updates status on delivery
5

Kit Delivered

Customer

Customer receives kit. Can optionally confirm receipt manually if UPS tracking is delayed.

System: Updates order to "Delivered", enables sample submission

Sample Submission Workflow

After receiving their kit, customers prepare and submit their samples for analysis.

1

Prepare Samples

Customer

Customer collects samples and places them in the provided plates according to their plate map.

2

Create Plate Map

Customer

Customer downloads Excel template and fills in sample details (well position, name, species).

Required: Well position, sample name, species. Optional: additional metadata
3

Upload Plate Map

Customer

Customer uploads the completed Excel file through the Submit Samples page.

System: Parses Excel, creates sample records, validates well positions
4

Ship Samples

Customer

Customer uses the provided return label to ship plates back to the lab.

Lab Processing Workflows

The lab supports three main workflow paths. Lab technicians select the appropriate workflow based on sample type and analysis requirements.

🧪

Clean Extraction Path

Standard extraction with quantification and normalization. Leads to Whole Genome Profile or Multispecies Arrays.

âš¡

Quick Extraction Path

Rapid extraction for diagnostic assays. Can include marker development for new assays.

🧬

NGS Path

Next Generation Sequencing workflow for comprehensive genomic analysis.

🧪 Clean Extraction Path

Initial Steps:

1. Clean Extraction 2. Quantification 3. Normalization
Whole Genome Profile (13 steps)
  1. Restriction (20 µl)
  2. Ligation (30 µl)
  3. Multiplex & Clean Up
  4. Amplification
  5. Clean Up #2
  6. Gel Quality Check #1
  7. Size Selection
  8. Clean Up #3
  9. Final Gel Quality Check
  10. Sent Out for Sequencing
  11. Received from Sequencing
  12. Sequence Alignment
  13. Results
Multispecies Arrays (11 steps)
  1. Amplify DNA
  2. Incubate DNA
  3. Fragment DNA
  4. Precipitate DNA
  5. Resuspend DNA
  6. Hybridize DNA to BeadChip
  7. Wash BeadChip
  8. Extend and Stain BeadChip
  9. Image BeadChip
  10. Sample Analysis
  11. Results

âš¡ Quick Extraction Path

Initial Step:

1. Quick Extraction
Diagnostic Assay Development (4 steps)
  1. Marker Development
  2. Marker Validation
  3. PCR
  4. Results

→ Leads to Diagnostic Assay

Diagnostic Assay (7 steps)
  1. Quick Extract
  2. Dilution
  3. Consolidation
  4. Assay Mixture
  5. Assay Delivery
  6. PCR
  7. Results

🧬 NGS Path (9 steps)

  1. Library Preparation
  2. Library QC
  3. Library Pooling
  4. Sequencing Setup
  5. Sequencing
  6. Data Transfer
  7. Demultiplexing
  8. QC & Analysis
  9. Results

Report Delivery

Final reports are delivered to customers through the portal with email notification.

Notification

  • • Customer receives email when report is ready
  • • Email contains link to download
  • • Summary of samples processed

Download

  • • Access Reports page in portal
  • • Download complete report package
  • • Multiple format options available

Billing Process

Billing is handled through QuickBooks integration after sample processing is complete.

1

Order Completion

When all workflow steps are complete, order is marked as finished.

2

Invoice Generation

System creates invoice in QuickBooks based on sample count and type.

3

Customer Payment

Customer receives invoice email with payment link via QuickBooks.

4

Payment Confirmation

Payment status syncs from QuickBooks, visible in LIMS portal.

Status Reference

Kit Order Statuses

ordered
Initial state
processing
Being prepared
ready_to_ship
Awaiting pickup
shipped
In transit
delivered
Received

Sample Statuses

submitted
Awaiting approval
approved
Ready for processing
in_processing
Being analyzed
completed
Results ready

Workflow Step Statuses

pending
Not started
in_progress
Currently active
completed
Finished
failed
Error occurred