Use Case: The CGI Workflow

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

History:

version 3.32 , 2019-08-22

https://seqdb.nrm.se

• Only accessible from within NRM-firewall
• Big change: No predefined 'Storage Container Types' - you will have to create the 1st one (12colx8row)
• Error 1: When pressing 'Genotypes' -> Javastack-trace 'org.hibernate.exception.SQLGrammarException: could not extract ResultSet'

Presumption

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

Before importing the Excel-sheet to SeqDB

• You need to have the rack-id of your rack (scanner)
• check that the Genus species does not contain Swedish character such as; 'Ä' / 'Å' or 'Ö'

1. Log into the SeqDB application
2. Landing Page → 'Storage'/'Storage Container Types ' [ver. 3.32]
   • 2.1 'Add New Container Type ' → select group , 'Type Name'&'Type ' + 'Columns'&'Rows '
3. Landing Page → Storage/ 'Storage Containers '
   • 3.1 ‘Add New Container ’ (96wells)
   • 3.2 ‘Select Options ’ → select the appropriate group , i.e ' NRM-CGI '
   • 3.3 'Container Name ' = ‘rack-id ’ (should be the same as the micronic-id , i.e. '3000142742')
   • 3.4 'Select a Container Type ' , see the previous step - use one of the containers that you have created.
   • 3.5 if appropriate choose a 'Storage Unit ' (2019-08-22: not using this attribute)

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

note on version 3.32 -> need to create the 'Container type'

• Number of Column :12
• Number of Rows : 8

Q: Collection code = NRM-CGI ? needed or not ?

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.