Use Case 1: The DNA LAB Workflow

How to import the excel-sheets (2 sheets)

The 2 files are mandatory.

1. 'specimen'-file
2. 'sample'-file

The files should be imported in that order; First the specimen-file and then the sample-file.

Presumption

• You have scanned a rack with 96 vials, every rack has a unique rack-id and every vial in the rack has an individual ID.
• The scanner will produce a csv-file

Before importing the Excel-sheets to SeqDB

• You need to have the rack-id of your rack (scanner)
• An excel template can be used to generate the "sample" and "specimen" files for import using DNA extract information and their respective rack and vial identifiers from the scanner csv-file

Using the Excel template (NRM-DNA file builder)

• DNA extract information is typed/copied into the "Extract information" tab, in row order: A01, A02... H11, H12
• Container number, tube position and tube ID number are pasted into the "Scanner data" tab
• The "Sample file" tab and the "Specimen file" tab are copied onto new excel documents 'as values' for importing to SeqDB
• The format of Column "E" in the new sample file (extraction date) may need to be adjusted to "Date yyyy-mm-dd"

Additional preparation in SeqDB

1. If you do not have a 'group' in SeqDB, then create a new group. Example: "NRM-DNA" is the group for the permanent DNA archive collection.
   • this group should reference the group in the sample- and specimen-file
2. If you do not have the 'Specimen Collection' present, then create the 'Specimen Collection'. Example: RODESP is the collection identifier for Rodrigo Esparza-Salas' DNA collection.
   • this 'Specimen Collection' should reference the 'Specimen Collection' in the sample- and specimen-file

Create a Group

1. Log in to the SeqDB application
2. In the header, select 'Account' (a drop-down menu), select 'View Groups'
3. Press the ‘Add New Group’-button
   • Check the 'sample'-file, what is the 'Collection Code Group'?
   • Fill in the 'Group Name' with the 'Collection Code Group',check all the 'Default Rights'
   • Press the 'Save'-button (If OK, you should see the info ‘Group has been added successfully’)

Add a 'Specimen Collection'

1. Log in to the SeqDB application
2. Landing Page → Collections/'Specimen Collections'
3. Press the 'Add New Specimen Collection'-button -> new page 'Specimen Collection Details'
   • Choose the appropriate 'Group Options' from the dropdown list ( see column 'Collection Code Group' in the sample-file
   • Fill in the 'Collection Code', the 'Collection Code' should match the column 'Collection Code' in the sample-file
   • Not mandatory: Fill in the rest of the fields
   • Press the 'Save'-button (If OK, you should see the info 'Specimen Collection has been added successfully.')

Don't forget to insert a 'storage container'

-fyll i senare enligt notering.

Importing the 2 Excel-sheets to SeqDB

Import the Specimen Excel-Spreadsheet

1. Log in to the SeqDB application
2. Landing Page → Import/'Spreadsheet Import Page'
3. Follow Step 1, Step 2 and Step 3
   • Step 1: 'Select the Importer': Specimen (Do not check the 'Bulk Edit' checkbox)
   • Step 2: 'Select Group': Choose the appropriate group ( that you created earlier. e.g. RODESP)
   • Step 3: 'Choose file': Choose your 'Specimen Excel File'
     • If OK , You should see the ‘info’ at the top → 'xx records imported successfully'
4. Verify the import
   • xxx
   • check specimens ...

Pre-Requirements: Import the Sample Excel-Spreadsheet

1. Check if Check if the 'container type' = '96 Well 12x8 Plate' is created or not.

   • Landing Page → Import/'Spreadsheet Import Page'
   • Storage / 'Storage Container Types'

2. If the container does not exist then

   • click button : 'Add New Container Type'
   • Create container type with the following values: 'Container Type Name' = '96 Well 12x8 Plate', 'Container Type' = 'Plate', 'Number of Columns' = 12, 'Number of Rows' = 8

3. Add a container with the correct name (name should be the same as 'rack-id')

   • Landing Page → Import/'Spreadsheet Import Page'
   • Storage / 'Storage Containers'

4. Press the 'Add New Container'-Button

   • find the 'Container Name' in your Sample Excel file, use this number
   • Group options: choose the approriate group in the dropdown-menu
   • Default-values: No Need to change the radiobuttons (column / row)
   • Select a Container Type : ‘96 Well 12x8 Plate’ in the dropdown-menu
   • NOT-USED-NOW: Drop down for 'select container type' ( should be the 'Freezer) + 3 fields ( Compartment/Shelf Number and Rack Number)
   • Press the 'Save'-Button
     • If OK , You should see the ‘info’ at the top → ’Container has been added successfully.’

Import the Sample Excel-Spreadsheet

1. Log in to the SeqDB application
2. Landing Page → Import/'Spreadsheet Import Page'
3. Follow Step 1, Step 2 and Step 3
   • Step 1: 'Select the Importer': Sample (Do not check the 'Bulk Edit' checkbox)
   • Step 2: 'Select Group': Choose the appropriate group ( see the column xxx in the yyy-file)
     • Leave empty : DO NOT choose any ‘Container Type’
   • Step 3: 'Choose file': Choose your 'Specimen Excel File'
     • If OK , You should see the ‘info’ at the top → 'xx records imported successfully'
4. Verify the import
   • xxx
   • check samples ...
   • yyy