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Daylily-Informatics / bloom

Templated Abstract Polymorphic (and opinionated) LIMS
Mozilla Public License 2.0
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Bloom : Templated Abstract Polymorphic (and opinionated) LIMS

a conceptual gambit in collaboration with chatGPT4 /// POC v0.9.6

BLOOM LIMS Build Tests, MacOS, Ubuntu & CentOS BLOOM LIMS Build Tests, MacOS, Ubuntu & CentOS BLOOM CENTOS

Built from first principles and drawing upon 30 years experience scaling laboratory process. Constructed with as few object model shortcuts as I could manage ( I believe these shortcuts are among the main reasons LIMS nearly universally dissapoint ). Supporting both arbitrary and prescribed interacting objects. Intended for use: by small to factory scale laboratories, in regulated environments, for both research & operations usecases. Bloom can handle multiple areas LIS tend to touch: acessioning, lab processes, specimen/sample management, equipment, regulatory and compliance.

Spoilers

bloom early peeks

Oauth2 Authentication w/All Major Social Providers

and flexible whitelisting, etc...

Graph Object View (add, remove, edit, take actions, explore)

Interactive, Dynamic Metrics

bloom-lims-graph

Accessioning Modalities

Nested Assay / Queue / Workset

bloom-lims-trad-view

Intantiate Objects From Available Templates

bloom-lims-instantiated-abstracts

Object Detail

bloom-lims-obj-view

Specialized Object Detail Views

Labware (ie: a 96w plate)

bloom natively will support arbitrarily defined labware, a 96w plate is just one example. Anything that nested arrays of arrays can describe can be configured as a type of labware with next to no effort!

bloom-lims-obj-view

Exhaustive & Comprehensive Audit Trails (+soft deletes only)

bloom-lims-audit

Bells And Whistles

Integrated Barcode Label Printing For All Objects

Workflows Available

Accessioning

Pacage receipt -> kits registration (multiple) -> specimen registration (multiple) -> requisition capture & association -> adding specimens to assay queues. Fedex tracking details fetched, barcode printing available.

Plasma Isolation -> DNA Extraction -> DNA Quant

managing all object relationships, tracking all details, printing labels, etc.

Installation

Prerequisites

Hardware Supported

see build test badges above for all supported platforms

Conda

~/miniconda3/bin/conda init
bash  # newly created shells should not auto load the conda (base) env.

Supabase

Very Quickest Start

assumes you have completed the prerequisites

# Clone the repository
git clone git@github.com:Daylily-Informatics/bloom_lims.git
cd bloom_lims

# This will attempt to build the conda env, install postgres, the database, build the schema and start postgres
source bloom_lims/env/install_postgres.sh 

# conda activate BLOOM if is has not happened already.

# Start the Bloom LIMS UI
source run_bloomui.sh

(optional) Install & Run pgadmin4 Database Admin UI


# RUN TESTS
pytest

# START THE UIs (on localhost:8080)
source bloom_lims/env/install_pgadmin.sh

Integrations

CRMs

If they have APIs, integration to fetch things like physician or patient identifiers/metadata is straight forward.

Zebra Barcode Label Printing

FedEx Tracking API Integration

ie: Salesforce

Design Principles

Enterprise UIDs

Each Object Has A UUID & UUIDs Are Immutable & UUIDs Are Not Reused Or Applied To Other Objects

The UID Identifies The Object Class And The UUID w/in The Class

Exhaustive Metadata About An Object May Be Queried Using The Enterprise UUID.

Metadata may also be printed on labels along with the UUID.

Trust The Database To Manage The UUIDs

Clear And Concise Data Model

TSV's not CSV's

All LIMS Data Editable w/CRUD UI

Easily configurable object definitions as well as actions (ie workflows, etc)

Other

Use Cases

LIMS Actions (must have)

Many To Many Relationships Among All Objects

All other relationships are subsets of this, and designing parts of the LIMS which disallow many to many will result in an inflexible system.

Objects May Be Involved In Multiple Workflows Simultaneously

Support For Predefined and Arbitrary Workflows

Objects may all be: root (singleton, parent & able to become a child at some point), child(singleton, parent and possibly terminal) of one another

Zero Loss Of Data (comprehensive audit trails, soft deletes) && 100% Audit Coverage

Deployment & Maintanence

You may deploy bloom wherever it will run. This does mean you are responsible for all aspects of the deployment, including security, backups (AND recovery), performance optimization, monitoring, etc. This need not be daunting. I am available for consulting on there topics.

Testing


conda activate BLOOM
pytest

Regulatory & Compliance

CLIA

CAP

HIPAA

Support

Authors

License

References // Acknowledgments

Dev Tools

note: all commands below are expected to be run from a shell with conda activated. conda activate BLOOM

Drop The Entire Database(loose all data!) > Rebuild The Database / Re-seed With All Accessible json Templates

The steps are wrapped in a script, please see clear_and_rebuild_postgres.sh.

It is executed as follows:

source clear_and_rebuild_postgres.sh

Stop pgsql

Remove the db

Rebuild the schema

Build LIMS Workflows With Autogen Objects

Similar to pytest, but more extensive. Largely useful in development work. The following will auto-gen 'n=2' passes of the lims schema

Run the bloom UI

Run the pgadmin UI

Start Interactive Shell w/Core Bloom Objects Instantiated

python bloom_shell.py

Random Notes

File System Case Sensitivity

MacOS is Not Case Sensitive

echo "test" >test.log
echo "TEST" >TEST.LOG
more test.log
TEST
more TEST.log
TEST

Ubuntu Is Case Sensitive

echo "test" > test.log
echo "TEST" > TEST.LOG
more test.log
test
TEST.LOG
TEST

Assume Case Insensitivity In All File Names

Bloom UUIDs and EUIDs Are Safe As File Names

A widely adopted UUID spec (and used by postgres), rfc4122, treates uc and lc as the same character. Bloom EUIDs only contain uc characters in a prefix followed by integers.