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Use Case 2: The DNA LAB Workflow

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Ingi Erli edited this page Jan 23, 2020 · 26 revisions

History of this page

Date SeqDB-version changes name
2020-01-23 3.37-SNAPSHOT derived from use-case 1 Ingimar E

Constraints

  1. You must have an Account to be able to use the system.
  2. The system can only be used within the NRM-network.

Step-by-Step on how to Import to SeqDB

Import is done through 2 Excel-files

Pre-requirements (Configurations) - before starting import

You must configure the following in SeqDB before you start importing your samples.

See : 'Administration','Groups','Storage'

Administration -> People and Account

Adding staff and linking that person to an account (3 types of Account: 'Admin'/'User' and 'Guest')

People

  1. press 'Add Users'
  2. mandatory-fields are = 'First Name' & 'Last Name'

Account

  1. 'Add Account'
  2. mandatory-fields are = 'Account Name', Password and expiry-date and link-to-User

Groups

  1. Create a group

for instance: the Labb has 'DNA-LAB' and CGI has 'DNA-CGI'

'Specimen Collection'

  1. 'Add new Specimen Collection'
  2. mandatory-fields are = Group and 'Collection Code'

For instance: the DNA-LAB has 'NRM-BOT' for the Botany-institution and 'NRM-ZOO' for the Zoology-institution

Storage

First you create the 'Container Type',if you do not have any, and then you add a 'Storage Container'

1: 'Storage Container Type'

The 'Container Type' needs to be linked to your Group

Note: The 'Container Type' only needs to be added once for each type!

  1. Press 'Add a new Container Type'
  2. Mandatory-fields = 'Group','Container Type Name','Container Type' and 'Columns'&'Rows'
  3. For a Micronic rack: Columns=12 and Rows=8 (Total number of wells = 96)

Note: The DNA-LAB has the settings: 'Columns=12 and Rows=8'

2: 'Storage Container'

You add a new container for each rack.

Container Name equals to the rack-id (code expressed in a number and a barcode, on the short-side)

  1. Press 'Add New Container'
  2. Mandatory-fields = 'Group','Container name' (Fill by order of 'Row')
  3. Mandatory-fields = link to a 'Container Type'

Additional Configuration

The 'Project Tag'

If you would like to use the 'Project Tags' in the Template - then you need to create a 'Project' in SeqDB before importing.

Import

You need the 2 Excel-templates; One for the Specimens and one for The Samples

You need to import the Specimen-file before the Sample-file

You need to strictly adhere to the templates, otherwise the import will break

1: Specimen-file

Fill in the minimum content, some fields are mandatory

'Spreadsheet Import Page'

  1. Select Importer, Choose 'Specimen' in the drop-down list
  2. DO-NOT-CHECK the 'Bulk EDIT?'-radiobutton
  3. Choose your Group in the drop-down list
  4. Browse for the Spreadsheet
  5. press the 'Submit'-button

2: Sample-file

  1. Select Importer, Choose 'Sample' in the drop-down list
  2. No-Group is needed
  3. Browse for the Spreadsheet
  4. press the 'Submit'-button

Templates

Specimen-Template

Using the Dario-example from the DNA-lab

Mandatory-fields:

  1. (A) 'Collection Code'
  2. (B) NOTE: 'Specimen ID' (a unique identifier, only 'Integers' are allowed - for linking to the Sample-file)
  3. (C) NOTE: 'Sub ID' (an identifier, alphanumeric characters are allowed - for linking to the Sample-file)
  4. (D) 'Other IDs'
  5. (E) 'Genus'
  6. (F) 'Species'
  7. (G) 'Permanent collection' (Used by the DNA-Lab to link to the voucher-ID)
  8. (H) ONLY-IF-USED, NON-Mandatory : 'Project Tags'

Sample-Template

This file contains the rack-ID and the vile position within the rack.

The information about the rack : 'Container Name', 'Tube Id' and Position is resulting from the scanner.

Rest of the data is linkage-information, for linking to the specimen-file.

Mandatory-fields:

  1. (A) 'Sample Group Name' (which equals to 'Group')
  2. (B) 'Sample Name'
  3. (C) 'Version' (set to 'auto')
  4. (D) 'Collection Code Group'(which equals to 'Group' - set Excel to 'formula')
  5. (E) 'Collection Code'
  6. (F) 'Specimen Source Type , Write S for Specimen or MS for Mixed Specimen'
  7. (G) NOTE: 'Specimen or Mixed Specimen Identifier (links to 'Specimen ID' in the Specimen-file)
  8. (H) NOTE: 'Sub ID' (links to 'Sub ID' in the Specimen-file)
  9. (I) 'Container Group Name'
  10. (J) 'Container Name' (the identifier of the container - from the scanner csv-file)
  11. (K) 'Tube ID' (the identifier - from the scanner csv-file)
  12. (L) 'Position' (position in the rack; Syntax ex. 'A1' -> ranging from A1 to H12)
  13. (M) ONLY-IF-USED, NON-Mandatory : 'Project Tags' 14: (N) 'Specimen Replicate Version' (Set To 'A')
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