Use Case: The CGI Workflow

How to import the excel-sheet, step-by-step

Presumption

• You have scanned a rack with 96 vials, every rack has a unique rack-id
• The scanner will produce a csv-file
• The csv-file should be merged with sample data and meta-data from rovbase (a web-app to automate is currently being developed)

Before importing the Excel-sheet to SeqDB

• You need to have the rack-id of your rack (scanner)

1. Log into the SeqDB application
2. Landing Page → Storage/ ’Storage Containers’
3. ‘Add New Container’ (96wells) → 'container name' = ‘rack-id’ (i.e '3000142742')

Import the Excel Sheet

1. Landing Page → choose: Import / ’Spreadsheet Import Page’
2. ‘Select importer’ → drop down, choose → ‘NRM Genotype’ (do not check checkbox)
3. ‘Container Type’ → drop down, choose →’96 Well 12*8 plate’
4. ‘Choose file’ → choose the excel-sheet that you want to import → press the submit-button
5. The excel-sheet contains 96 records
6. If the import is successful → You should get the feedback the import was without errors

Verify the Import

Do the following 3 checks ; Collections, Genotypes and Storage

Collections

1. Log into the SeqDB application
2. Landing Page → Collections / ’Specimens’
3. ‘Specimen Records’ → displays ‘102 specimens found’ (If this is your very first batch 96+6exampels = 102)

Genotypes

1. Landing Page → Genotyping / ’Genotypes’
2. You should see your 96 Genotypes in the table

Storage

1. Landing Page → Storage / ’Storage Containers’
2. Click in the table on the record that is your 'Container Name'
3. New page opens : you should see a matrix ([A-H] - [1-12])
4. The id for each cell/vial is your persistent ID (NRM-CGI-A)
5. Click on a random cell/vial
6. New page opens : 'Sample Details'
7. Check if all your details are present.