https://github.com/biosustain/lifelike
Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
https://github.com/biosustain/lifelike
angular big-data bioinformatics docker helm knowledge-graph python scientific-computing
Last synced: about 1 month ago
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Turning big data into contextualized knowledge. Lifelike is a modern application platform for data extraction, analysis and visualization.
- Host: GitHub
- URL: https://github.com/biosustain/lifelike
- Owner: biosustain
- Created: 2024-01-04T17:18:13.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2026-04-08T21:22:23.000Z (2 months ago)
- Last Synced: 2026-04-08T23:09:10.451Z (2 months ago)
- Topics: angular, big-data, bioinformatics, docker, helm, knowledge-graph, python, scientific-computing
- Language: Python
- Homepage: https://lifelike.bio/
- Size: 195 MB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
#  Lifelike
Lifelike is an open-source project that aims to provide a simple, yet powerful platform for turning structured and unstructured data from a variety of sources into a single, coherent and explorable knowledge graph.
[](https://zenodo.org/badge/latestdoi/437040913)
## Quick start
The easiest way to get started and run a fully functional development environment of Lifelike is to clone this repository and run the `make up` command:
```shell
git clone https://github.com/SBRG/lifelike.git
cd lifelike
make up
```
This will take a few minutes to complete, after which you can start using Lifelike by pointing your browser to [http://localhost:8080](http://localhost:8080).
You can log in using the default admin user `admin@example.com` and password `password`.
## Other installation methods
You can see more details about how to deploy lifelike in a production environment,
or customize the development installation in the following sections.
1. [Docker with Docker Compose](docker)
2. [Kubernetes with Helm chart](helm/lifelike)
## Lifelike main concepts
### Projects
Lifelike organizes content into projects. A project is a filesystem-like collection of resources either uploaded by users or generated by Lifelike based on other resources. Those resources can be all kinds of data, including structured data like spreadsheets, unstructured data like PDF files, images, or text documents.
### Knowledge Domains
Lifelike structures knowledge around domains. A domain is a collection of semantically related entities belonging to a field of study.
### Annotations
Annotations are a powerful way to attach context to your data in knowledge Domains, Lifelike automatically annotates all your data with Domain known entities as well as lets you define your own custom annotations.
### Knowledge Graph
Domain data sources are annotated and stored in a graph database. A knowledge graph consists of nodes and edges. Nodes are domain entities and edges are relations between entities.
### Visualizations
Visualizations are a powerful way to help you to understand the relationships between entities as well as a powerful tool to find new relationships as new data comes in.
Lifelike currently provides the following built-in visualization types:
- Maps
- Enrichment tables
- Sankey diagrams
- Pathway Browser
### Other features
- Multi-user collaborative workbench
- Powerful search engine
## Common development operations
You can run `make help` to see a list of available commands.
```text
$ make help
usage: make [target]
development:
githooks Set up Git commit hooks for linting and code formatting
docker:
up Build and run container(s) for development. [c=]
images Build container(s) for distribution.
status Show container(s) status. [c=]
logs Show container(s) logs. [c=]
restart Restart container(s). [c=]
stop Stop containers(s). [c=]
exec Execute a command inside a container. [c=, cmd=]
test Execute test suite
down Destroy all containers and volumes
reset Destroy and recreate all containers and volumes
diagram Generate an architecture diagram from the Docker Compose files
helm:
helm-lint Run helm lint on Lifelike chart
helm-dependency-update Install or update chart dependencies
helm-schema-gen Generate Helm chart values JSON schema
helm-docs Generate Helm chart README docs
helm-package Generate Lifelike helm chart package
helm-install Install or upgrade Lifelike chart
helm-install-single-node Install or upgrade Lifelike chart using the single-node example values
other:
help Show this help.
```
## Architecture
Lifelike is a distributed system comprised of the following components:
### Core services
- **[Appserver](appserver)**. Backend API service, written in Python using the the Flask framework.
- **[Client](client)**. Frontend Single Page Application, written in Typescript using the Angular framework.
- **[Statistical enrichment](statistical-enrichment)**. Statistics generation microservice, written in Python using the the Flask framework.
- **[Cache invalidator](cache-invalidator)**. Recurrent task runner for bulk large computations and cache data management, written in Python.
- **[Graph data migrator](graph-db)**. Utility service for migrating and versioning knowledge graph database, using the Liquibase database migration tool.
### Backing services
- **PostgreSQL** as a RDBMS.
- **ArangoDB** as a graph database.
- **Elasticsearch** as a full-text search engine.
- **Redis** as a key-value cache store.
- **PDFParser** as a document parsing library.
- **Sendgrid** as an email messaging service.
## License
Lifelike is distributed under a [modified MIT license](LICENSE).
