coertquinton edited this page Oct 4, 2017 · 25 revisions

Baobab LIMS

Baobab LIMS is a Laboratory Information Management System (LIMS) designed for the collection, processing and storage of human biospecimens. The system was designed a priori using the Standard operating procedures (SOPs) of the NHLS-Stellenbosch University Biobank. Baobab LIMS comprises modules for biospecimen kit assembly, biospecimen shipping, storage management, analysis requests, reporting and invoicing. Current developed SOPs define the biobanking activities of the Biobank and in an effort to extend the usability of the system, collaborations which incorporate SOPs generated by other Biobanking facilities, are ongoing. The figure demonstrates the workflow of the current system, deduced from SOPs.

Baobab flowchart

Figure 1: Flowchart of activities within the NSB biobank upon which the Baobab LIMS was designed.

Baobab LIMS is both Free and Open Source with some modules being inherited from Bika LIMS. Furthermore, Baobab LIMS can be customized to the specific needs of your laboratory.

Note: For more additional resources, use the following links
https://github.com/SANBI-SA/baobab.lims
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397207

Install your Baobab Distribution

Go to https://<IP server address>/manage_main ( Select ‘Add Plone site’)

steps to add a plone site

Change the Baobab Theme

The Baobab theme can be changed to the graphite theme. The graphite theme has an easy access navigation panel at the top of the page and a site map. baobab theme tab

Follow the instructions below to change your theme;

change baobab theme

Select 'Admin', 'Site setup' in the top right corner. Please note only admin privileges have access. top right menu

site setup

Select 'Add ons'

Add ons

Check the 'Graphite theme' and then click 'Activate'.

This figure represents the homepage of the Graphite theme. The graphite theme can be turned on and and off on the button to the left of the search box on the top menu bar. It is green when enabled and red when disabled.

theme on or off

Graphite homepage theme

Your Baobab distribution

With your installation complete, you can now set up your site. Baobab LIMS requires that your site is set up before you can start to manage clients and projects and certain compulsory information is required for each step. As such, we recommend that you follow this setup section in a stepwise manner.

Go to https://<IP server address>/Demo

This will open the homepage for your distribution.

Set up your mail settings

As the administrator for the site, the mail settings will need to be configured, the page will display the following error.

No email setup error

To set up the mail settings select the ‘Mail control panel’ link in the error message. Alternatively, go to ‘site setup’ under Admin in the top right hand corner and select the ‘Mail’ tab.

site setup

Click 'Mail'

You will be automatically directed to the ‘Mail settings’ page where you will be required to enter the SMTP server address and will be able to set the administrator username and password. Ensure that all the required fields are completed and select ‘save and send test email’.

mail settings page

Following successful set-up, you will receive an email confirming that the email server is working.

test email success

NOTE: For Gmail users, an error may occur due to the security settings on your Gmail account which will prevent sign-in from another device or app.

Please ensure that your Gmail settings permit the site to access your account. Use the following link to understand more; https://support.google.com/accounts/answer/6010255

Set up your laboratory

Mouse over the ‘Laboratory’ Tab and select ‘Laboratory’ Enter the details of the laboratory and press ‘save’. Compulsory fields are indicated by red squares.

edit laboratory

Mouse over ‘Laboratory’ and select ‘Lab Contacts’ Add a lab contact by selecting the ‘add’ button

lab contact

Enter the details of the lab contact and press ‘save’. Compulsory fields are indicated by a red square Select the ‘email, telephone,fax’ tab,enter the email address of the lab contact and press ‘save’.

save lab contact

Set up login details

After saving the contact an edit and a login details tab will become available. Select ‘Login details’.

login details

Enter the details of the user and press ‘save’

save save login details

info login details

An email will be sent to the users email address

user account info

Select the link to activate the account and change the password activate account

Set the new password set new password

Mouse over ‘Laboratory’ and select ‘Lab Departments’ Add a lab department by selecting the ‘add’ button. Compulsory fields are indicated by a red square. add department

Added users are now available to be selected.

Set up your suppliers

Mouse over the ‘management’ tab and select ‘Suppliers’

setup suppliers

Add a supplier by using the ‘Add’ button Enter the details of the supplier and press the ‘save’ . Compulsory fields are indicated by a red square.

add suppliers

Once a supplier has been added, contacts, instruments and inventory orders associated with the supplier can be added. Note that products belonging to the supplier must be added using the ‘Products’ tab. Mouse over the ‘management’ tab and select ‘Products’ Add a product by using the ‘Add’ button

add product

Enter the details of the product and press the ‘save’ . Compulsory fields are indicated by Once products associated to suppliers have been added, the products are now available to be selected in the ‘Suppliers’ tab.

products avaiable Added products are now available to be selected in 'Suppliers'.

Set up your instruments

Mouse over the ‘Instruments’ tab and select ‘Instrument types’

instruments tab

Add an instrument type by using the ‘Add’ button add instrument button

Enter the details of the instrument type and press the ‘save’ . Compulsory fields are indicated by

add instrument The instrument type and the supplier can be selected from data which was previously added.

Once an instrument has been added, a notification of expired calibration certification will appear and additional tabs will become available for editing.

certificate expired

Select the ‘Calibration Certificates’ tab and add a certification specifically related to the instrument using the ‘Add’ button. Enter the details of an instruments calibration and press ‘save’. Compulsory fields are indicated by a red square. If the calibration dates are current, the notification which occurred, will automatically be removed.

Set up your storage types

Mouse over the ‘Management’ tab and select ‘Storage Types’ storage types tabs

Add a storage type by using the ‘Add’ button add storage

Enter the details of the storage type (e.g. a freezer) and press the ‘save’. Compulsory fields are indicated by a red square.

Set up your storage

Mouse over the ‘Management’ tab and select ‘Storage’ setup storage

Prefix text: such as room, shelf, box Leading zeros: denotes the prefix number ID sequence start: the number on which the prefix should start Number of items: How many units with the prefix must be created Storage unit type: become available once defined in the ‘Storage types’ Department: becomes available once defined in the ‘departments’ section in ‘set up your laboratory’

Enter the details of the storage and press ‘create storage units’

Once a storage has been created, the storage unit can be selected and a hierarchical storage system can be created for each unit. Example: Room > Freezer > Shelf > Box > Position storage hierarchy

Select the ‘Room’ initially created. Enter the details of a new storage unit and press ‘create storage unit’

Select a freezer storage unit that has been created. Enter the details of a new storage unit and press ‘create storage unit’ storage info

Select a shelf storage unit that has been created. Enter the details of a new storage unit and press ‘create storage unit’ storage info

At each level of a storage unit creating, space can be managed (ie. Spaces are assigned) or unmanaged (ie. Spaces are not allocated prior to storage).

Managed storage

Managed storage is used specifically for the storage maintenance of biospecimens. The process of creating managed storage is as follows; Navigate to the storage unit created in the previous step and select the ‘managed storage’ tab. managed storage

Enter the details required to create managed storage and press ‘create storage’. By selecting the created storage unit, a list of created positions will be shown. In addition, a graphical display is available. storage box

storage occupancy

By selecting a storage unit (a position within a box), the item may be reserved. When the item is reserved, the state of the item will change and this change will also be reflected in the graphical representation.

storage box selected

storage occupancy

The storage position can be freed by selecting the position and pressing ‘liberate’.

storage position liberate

Unmanaged storage Unmanaged storage refers to locations for items such as inventory stock items that will be used in kit assembly. The process of creating unmanaged storage is as follows; Navigate to the storage unit created previously and select the ‘add new storage’ button. Navigate to the ‘unmanaged storage’ tab and enter the details of the storage. In the example below, Room01 contains 3 shelves for storage of inventory items. The shelves are labeled from 1 to 3 and will contain stock items.

unmanaged storage

Set up your analysis category

Mouse over the ‘Workflow’ tab and select ‘Analysis category’ analysis category tab

Add an analysis category by using the ‘Add’ button analysis category add button

Enter the details of the analysis category and press the ‘save’. Compulsory fields are indicated by a red square

Set up your Sample Type

Mouse over the ‘Samples’ tab and select ‘Sample Types’ samples tab

Add a sample type by using the ‘Add’ button samples types add button

Enter the details of the sample type and press the ‘save’. Compulsory fields are indicated by a red square

Set up your other parameters

Once all the above categories have been set up, all other categories can be set up. These can be managed by simply selecting the category and adding information using the ‘Add’ button. Enter details related to the category and press the ‘save’ button. Compulsory fields are indicated by red square.

Other categories to be set up include;

Workflow tab

  1. Methods
  2. Calculations
  3. Analysis specifications
  4. Analysis services
  5. AR priorities

Samples tab

  1. Biospecimens
  2. Sampling deviations

Management tab

  1. Stock items
  2. Kit templates

Instruments tab

  1. Methods
  2. Calculations

Accounting tab

  1. Statements
  2. Price list

Other tab

  1. Attachment types
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