baobablims / baobab.lims

Baobab LIMS is an open-source laboratory information management system (LIMS)

The latest information about Baobab LIMS community can be found on the [Baobab LIMS](https://baobablims.org/).

Baobab LIMS

Baobab LIMS is an open-source laboratory information management system (LIMS) software that will ensure that researchers can track the lifecycle of a biospecimen in the laboratory from receipt to storage and reuse. This software ensures that sufficient metadata is captured.

Baobab is a common name given to nine tree species in different countries in the world, mostly in Africa.

Baobab LIMS written in Plone, a python framework known for its robustness, and inherits some modules from Bika LIMS.

Installation using docker-compose

This is the recommended installation method. It uses Docker and docker-compose which handles the details of installing dependencies for you. On your Linux command line, run:

$ git clone https://github.com/BaobabLims/baobab.lims.git
$ cd baobab.lims
$ docker-compose up -d

Running using Docker

This is a quick way to get a Baobab LIMS site up and running. NOTE: using this installation method, the "volumes" where you store data will not be preserved, so this method is only recommended for testing or development. If you want to use Baobab LIMS long term, we recommend using the docker-compose method described above.

docker run -p 8080:8080 quay.io/baobab-lims/baobab-lims

Access Baobab LIMS on http://localhost:8080:

The first time you run Baobab LIMS, install the Baobab package by going to [http://localhost:8080] and following these instuctions.

• Click on Install a Baobab distribution.
• Check Baobab LIMS option, then click Install the form.
• Authentication: admin:adminsecret
• Go to [http://localhost:8080/manage_main] and select the acl_users item
• Click the users item
• Click on the Password link (next to the admin username) to set the admin user password

Demo with Play with Docker

Play with Docker will give you 4 hours to try Baobab LIMS in the cloud.

DockerHub account needed.

Authentication: admin:adminsecret

Manual Installation

New installation instructions (Recommended installation instructions) Baobab LIMS Standalone installation

Old installation instructions (Don't use these instructions. They will be removed at a later date.) Baobab LIMS Standalone installation

Further Documentation

• User Manual
• Github Wiki
• Online Documentation

baobab.lims's Issues

Change parent of AR to Project Instead of Client

Issue
The parent of ARs is Client type, logically it should be Project

Current
ARs are linked to Client Content Type

Expected
ARs should be linked to Project Content Type

Create participant

Participant unique ID code, sex and age.
Sex values are female, male, unknown or undifferentiated.
Age requires age unit ie. years, months, weeks, days etc

Importing Roles into the LIMS

There is an option to import comma separated data of Roles for each registered biobank staff member. This option is not described in the LIMS manual and should be included.

Deactivate a storage unit must deactivate all the sub, sub,... units

Issue
Deactivating a storage unit not deactivating child units

Current
Deactivating a storage unit not deactivating child units

Expected
Deactivate a storage unit must deactivate all the sub, sub,... units

Shipping

once a biobank receives the kit then an email must go to client to tell her that the kits are received

Add setup guide to sphinx documentation

Add setup guide to sphinx documentation

Kit template field in Kit assembly should be optional

Issue

Kits sometimes are not assembled at NSB, in this case there is no need to use kit template field

Current

Kit template field in kit assembly is required

Expected

Kit template optional. When the field is optional adjust the source code to not use the inventory storage.

Move all aspects of the work from bika to baobab lims

APIs were created and modified in Bika LIMS and must be migrated to Baobab LIMS

Stock Management Done

Report on stock management needed

Analysis services configuration

we should put the NSB biobank analyses here as examples that can be selected because some analyses are standard for many biobanks. For example DNA extraction is routinely used and therefore a biobank staff member should select this analysis from a predefined menu.

options besides VAT

Add GST for certain users. Not everyone uses “VAT”.

Defining Roles of lab managers, clerks etc

where in the lims do you define the role of the lab manager, clerks etc? For example, is there a place where there is a summary of the permissions assigned to each biobank staff member registered in the LIMS.

Error when adding biospecimen

The 'Biospecimens' tab on quick access. This has and 'add' button. If specimen details are edited and saved, an error occurs. There is a sequence for the addition of a biospecimen to a kit, should the user be able to add specimen using quick access.

https://b3abiobank.sanbi.ac.za/DEMO/biospecimens/portal_factory/Sample/sample.2017-08-31.2469698913/base_edit

Track sample volume after AR usage

Issue
No tracking for sample volume in AR

Current
The sample volume is updated manually

Expected
Update sample volume when the sample is used in AR

I need a user friendly error message when creating a Kit without Storage

Issue

I need a user friendly error message when creating a Kit without Storage

Current

A user unfriendly message is generated when the Kit is created without Storage attached.

Expected

A friendly message to the user, informing them to first create a Storage before creating a KIT.

ODK integrations

Continued follow up with Kihara on the integration progress prior to release of v1.4.
Email interactions every 3 days
Once integration completed, TEST

Version release set to end April

suggestion

it could be good if you create a way of sending a feedback to the recipient in the form of a reciept

analysis request

there is a lot of info on this "request" page that we do not need. Please remove this legacy info.

Room temperature

When a room is created in the LIMS storage then the temperature is specified. There is no need to ask for this temperature repeatedly when shelfs and racks are configured. Remove the field "temperature" on subsequent pages after the Room has been configured.

stockmanagement

inventory on stock out-track stock left

Add a transition from kit created to kit received in kit workflow

Issue

NSB receive kits created by clients.

Current

Kits are created by the biobank and shipped to the client for drawing specimens from patients

Expected

Create kits and make possible transition to received without going through the shipped state

ODK integration publication

Write a publication on the steps to integrate ODK field collection into Baobab LIMS using novel APIs

Submission by end May 2018

reagents inventry

stock in and stock out

unmanaged storage configuration

Remove “samples” from the drop down menu because we putting stock items here. Do the same for managed storage; remove stock items and leave only samples.

Project/study additions

Add data category with Y/N drop down selection

1. Biological samples
2. Survey Data
3. Imaging data
4. Medical records
5. National registries
6. Genealogical records
7. Physiological/biochemical measurements
8. Other

Include text box with contact details for investigator who may have the information
In project: add age unit and # of sample donors

No need to store created kits in the inventory

Issue
Last jamboree, Himo suggested that there's no need to store the kits because the kits are for shipping or to be processed; opened and store the kit's samples in freezers.

Current
Specifying storage for assembled kits is required

Expected
No need to store the kits

Analysis request AR 1: input required but no input given

https://b3abiobank.sanbi.ac.za/DEMO/clients/client-1/project-1/portal_factory/AnalysisRequest/Request%20new%20analyses/ar_add?ar_count=1

sequence of steps to follow when configuring the LIMS

Point out to the user which modules must be configured first and in which order. For example, start with “client” and “project” so that you know what kit templates to add later.

User manual to Sphinx

Remove the Bika Lims Reference from the installation Form

Issue

BikaLims is referenced in the installation form.

Current

BikaLims is referenced in the installation form.

Expected

Remove the reference to BikaLims on the installation form

latest baobab version

Hi. We need to install the latest version of Baobab to http://training.bibbox.org/ so that it can be tested.

Error with client order

https://b3abiobank.sanbi.ac.za/DEMO/clients/client-1/portal_factory/SupplyOrder/supplyorder.2017-08-31.2643608847/edit?_authenticator=9fe559905a7d2451e94663dc4763cbd738be699f

Federated biobank not possible with Baobab shipping module

One biobank in Sierra Leone will be selected as the site to order all stock items. This biobank will assemble kits on behalf of the other biobanks in Sierra Leone. The current kit assembly and shipping instructions assumes that each biobank will assemble their own kits. In the case of Sierra Leone, one biobank (B2) should inform the centralized biobank (B1) that they need kits to be sent to their clients BUT the client must send the biospecimen-filled kits to their contracted biobank (B2).

Issue with bin/buildout not finding packages

Issue with bin/buildout not finding packages

Development environment is affected as packages (eggs/wheels) not found when bin/buildout is ran.

inventory stock management

how many stock are available now

The state of a Kit biospecimen should default to reserved

Issue

The state of a Kit biospecimen should default to reserved

Current

The default state of a biospecimen (empty) when created in a Kit is "occupied" which is not descriptive enough as the location is merely reserved to be occupied when the kit returns with the biospecimen.

Expected

The default state of the biospecimen when created should be reserved in storage. (Might require change in the worksflow)

Replace the word "department"

During the configuration step there is references to a "department". Change this to "Facility".

Dockerise Baobab Lims

Simplify the installation of Baobab LIMS

Disease list to be added in site set up

Site set up to allow for addition of disease categories

1. Disease ontology eg: ICD, SNOMED
2. Ontology version eg IDC-10
3. Ontology Code
4. Ontology description
5. Disease free -explanation of disease/symptom if disease unknown or insufficient information exists

Disease selection box to be added in project

Update Baobab Version on demo server

Can we please ensure that the b3abiobank.sanbi.ac.za site is updated to version 1.3 so that I can make a new site and send the link to Irena from Poland

Boxes that are full

The biobank staff should get a notification that the storage boxes are full in a specific freezer.

Storage Management

Track expiry date on stock items and send an email notification

Department info during Freezer configuration

There is no need for a "Department" field when you configure the Freezer. This information is already defined one level above.

Same goes for "temperature". This variable is already defined

Create a full docker version for baobab

use of the word "items" in the storage configuration

Change "number of items" to a question "how many?". this new phrase will then be applicable to each configurable section such as rooms, racks etc.

API discovery

ODK requires information about the Baobab APIs (following move from BIKA) such as, the API path, API content fields and Http response status (200 OK)

Configuring boxes

Where you ask for "boxes" during the configuration step, you should replace that with "max number of boxes"

Create storage positions via API

For creating new storage positions under the specific box we need to follow two steps:
1- We can create managed storage with 20 (4x5) positions via API like:
obj_path: /Plone/storage/abc-1/def-1
obj_type: ManagedStorage
XAxis; 4
YAxis: 5
2- After creating Managed Storage(4x5), we can create positions under that. For doing this:
obj_path:/Plone/storage/abc-1/def-1/managedstorage-1
obj_type: StoragePosition

It worked well but if you know easier way so you can share that with us.

Reserve managed storage unit

Reserve a storage unit prior to the commencement of project or receiving of samples. The option exists when creating a new storage unit, so this needs to be an active function.

FROM CLIENT INTERFACE

1. Client must see samples which are associated to their projects
2. Client can select the samples of interest in batch
3. Client can select to send the samples to himself/ herself via
   3.1 Their preferred courier/agent
   3.2 The courier/agent for the Biobank