Bioreactor dashboard

I have deployed the project on AWS, view at https://bit.ly/bioreactor-dashboard

Motivation:

This is a hobby project to create a web-based dashboard(Python & Dash) to visualize real-time process data originating from a bioreactors(simulated via containerized Postgres DB). This project also leverages advanced concepts like Containerization(Docker & Docker compose) and packaging applications using Python entry points

This project idea and skeleton is obtained from internet.

What all have I done?

● Built a Python-Dash interactive web-based data visualization application to monitor metrics like temperature, pH, pressure, oxygen% of a Bioreactor streaming from Postgres DB.

● Stylized application using HTML and CSS, further Implemented interactive features for users to select the time window and hot reloading.

● Configured application to run as python package automatically leveraging python entry points

● Containerized the application and Postgres DB and further leveraged Docker-compose to abstract and run the application underneath.

Whats used?

Python, Pandas, Dash, HTML, CSS, Docker, Docker-compose, Postgres

Functionality

The dashboard plots each of the metrics(Temperature, pH, Distilled Oxygen, and Pressure) over time.

The features include select time window along both axes or in box, double click to reset, auto-refresh the page, download plot as png, pan, zoom

How to run?

(skip if you have it) install docker from https://docs.docker.com/engine/install/

$ git clone https://github.com/rasi5050/Bioreactor_Dashboard.git

$ cd Bioreactor_Dashboard

$ docker-compose up

Edit

11/18/2023: When I tried to deploy app on AWS, it thowed error from postgres docker container. Errors suggest that its due to permissions on /pgdata supplied along with the project. Since I was not able to find the root cause, I have found alternate method to run the application by zipping the orginal files and unzipping on the destination.

If you cannot run app normally, follow as below

$ unzip Bioreactor_Dashboard.zip

$ cd Bioreactor_Dashboard

$ docker-compose up

Navigate your browser to http://localhost:8888/. That's it!

Whats happening behind:

In the directory, you'll find a Dockerfile that defines the image the code will be copied into and installed in. Specifically, the source code will be installed into a Python 3.10 virtual environment as a package via pip, along with all dependencies specified in a requirements.txt file.

You'll also find a compose.yaml file that defines the container that'll be used to run the code. Specifically, to serve the web-based dashboard in a local browser at http://localhost:8888/, Docker is configured to start the container by executing run-app, the expected entrypoint for the application.

The database

The data visualized will be in a Postgres database, also configured in compose.yaml. Credentials to access this database is provided in the following environment variables accessed through local.env:

POSTGRES_HOST provides the host
POSTGRES_PORT provides the port
POSTGRES_USER provides the user
POSTGRES_PASSWORD provides the password
POSTGRES_DB provides the database

The data

The tables in the database:

brx1=# \dt
                      List of relations
 Schema |           Name           | Type  |      Owner       
--------+--------------------------+-------+------------------
 public | CM_HAM_DO_AI1/Temp_value | table | process_trending
 public | CM_HAM_PH_AI1/pH_value   | table | process_trending
 public | CM_PID_DO/Process_DO     | table | process_trending
 public | CM_PRESSURE/Output       | table | process_trending

Each table has the same schema, like so:

brx1=# \d public."CM_HAM_DO_AI1/Temp_value"
                Table "public.CM_HAM_DO_AI1/Temp_value"
 Column |            Type             | Collation | Nullable | Default 
--------+-----------------------------+-----------+----------+---------
 time   | timestamp without time zone |           |          | 
 value  | double precision            |           |          |

Each table contains the following data:

Table	Name	Units
CM_HAM_DO_AI1/Temp_value	Temperature	Celsius
CM_HAM_PH_AI1/pH_value	pH	n/a
CM_PID_DO/Process_DO	Distilled Oxygen	%
CM_PRESSURE/Output	Pressure	psi

Screenshots

Happy learning! Happy to connect on Linkedin

rasi5050 / bioreactor_dashboard Goto Github PK