Use Case 2: The DNA LAB Workflow

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. Collection Code
2. Specimen ID ( a unique identifier, only 'Integers' are allowed)
3. Sub ID (an identifier, alphanumeric characters are allowed)
4. Other IDs
5. Genus and Species
6. Permanent collection (Used by the DNA-Lab to link to a voucher-ID)

Sample-Template