AI4Green is an Electronic Laboratory Notebook which combines data storage and sharing while promoting green and sustainable chemistry.
We highly recommend using Chromium-based browsers such as Google Chrome for accessing AI4Green.
See the video tutorials on how to use AI4Green.
Visit ai4green.app for more information and to register for a free account.
Download Docker Desktop for your distribution.
From your terminal pull and run the ai4green image:
docker run --rm -p 80:80 ai4green/ai4green
An instance of AI4Green is now running locally on your machine.
This can be accessed via your browser at 127.0.0.1:80/home/. If port 80 is already in use, you may change this by running e.g. -p 2000:80 from Docker then accessing the app at the corresponding port.
Within the docker image there is an admin account with the following credentials:
Username: admin
Password: admin_login
The database is built with SQLite and contains information from 100,000 compounds from PubChem. It is not possible to interrogate or update the database using this docker image. Note that this option is primarily for evaluation. All data is lost when the container is stopped.
The source code can be downloaded from this repository. Place the contents in a folder named AI4Green.
Windows users should run from following commands from Anaconda Prompt and Mac OS/Linux users from terminal.
We recommend using Anaconda to set up the python environment, available at anaconda.com.
cd AI4Green
conda env create -f environment.yaml
conda activate ai4green
conda install -c conda-forge rdkit
python -m pip install -r requirements.txt
Configuration of AI4Green is controlled by AI4Green/Webapp/config.py, the default values can be overridden by setting environment variables.
SQLALCHEMY_DATABASE_URI: Postgres database connection string.
COMPOUND_LIMIT: Sets the limit for the number of compounds extracted from PubChem. Note that a large database can cause smaller servers to crash.
MAIL: Ai4Green is configured to send email alerts triggered by actions such as managing and creating Workgroups. Functionality such as password reset requires email support.
We use Flask-Mail, which can be set up by providing the email address and password. Note that you may need to configure your email account to allow messages to be sent from the application.
MARVIN_JS_API_KEY: API key for Marvin JS is specified here.
A set of predefined users, workgroups, and workbooks are seeded to the database on creation, these are defined in seed_data.yaml
Please note that you must define admin credentials before setting up the database.
predefined_users:
You must predefine an admin account before setting up the database. Username, email, password, and fullname should be provided.
Information is provided at postgresql.org/download on how to set up Postgres on your distribution.
Note that Window users may have to add Postgres to their system variables. To use PGAdmin, the port, username and password should match the connection string in AI4Green/config.py.
Run flask db upgrade to make database migrations.
Run flask download-pubchem to download the PubChem database.
The user is prompted to select whether to use an existing download or PubChem database or download the latest version.
Finally, the user decides whether to add PubChem Compound data to the existing database (i.e. retain User, Workgroup, Workbook and Reaction data) or create a new database.
flask download-pubchem can be rerun at any time to update the database.
Run flask seed-db to seed data from the download.
Run flask update-pubchem to update your database from the latest pubchem download.
(Optional) Run flask seed-users to seed the seed_data.yaml values. Otherwise, you can create a new user through the CLI, run flask add-user and follow the prompts.
The flask app can now be run locally.
conda activate ai4green
cd AI4Green/Webapp
flask run
AI4Green can now be accessed via your browser at 127.0.0.1/home/.
It is possible to deploy an instance of AI4Green to a remote server for increased data security and privacy. A system administrator should be able to set up a version which is available on an organisation's internal server.
There are several useful guides on how to deploy a web application with a Postgres database on cloud services For example, Microsoft Azure provide a collection of useful guides.
For developers running the application locally.
- Poetry
- Docker
- Install the dependencies:
poetry install - Install pre-commit hooks:
pre-commit install - Start Postgres docker:
docker-compose up -d - Change directory to Webapp
cd Webapp - Use the CLI to update the database, follow step 5
- Run the app
flask run
Database changes are handled using Flask-Migrate and you should read their documentation for usage.
Briefly, to create a new migration after you have made changes in sources/models/
flask db migrate -m "Migration name" # create the migration
flask db upgrade # update the databaseAn error with Anaconda on Windows 10 has been reported, when using the conda install command. Details of this error and a solution can be found here.
It is a known issue that PubChem sometimes change the format of their data between the releases, which causes an error extracting that data. A previous version of the PubChem compound data can be obtained by emailing ai4green@nottingham.ac.uk.
If there is a problem with Marvin JS or you are deploying AI4Green to another url rather than running it locally, you may need a new Marvin JS API key and register the domain. You can find these at pro.chemicalize.com/app. Please note you will have to register for a ChemAxon account to use this service. The Marvin JS api key can then be replaced in AI4Green/Webapp/config.py.