Getting started

Install Ersilia from PyPI. Docker should be installed and running, since models are fetched from DockerHub by default.

# install the Ersilia CLI and Python package
pip install ersilia

# check that the installation worked
ersilia --help

Find a model

Every model in the Ersilia Model Hub has an identifier such as eos4e40. Browse the models and their identifiers in the Ersilia Model Hub catalog, or list them from the terminal:

# list all models available in the Ersilia Model Hub
ersilia catalog --hub

Command line

Fetch and serve a model, run it on a single-column CSV of SMILES, and close it when you’re done:

# download the model (antibiotic activity prediction, Stokes et al. 2020)
ersilia fetch eos4e40

# start the model server in this terminal
ersilia serve eos4e40

# generate 5 example inputs (SMILES) for the model
ersilia example -n 5 -o input.csv

# run predictions and save them to a CSV file
ersilia run -i input.csv -o output.csv

# stop the model server
ersilia close

Each terminal has its own session: a model served in one terminal is used by the commands run in that terminal. When commands do not share a terminal, for example in scripts run through conda run, make or CI steps, give them one session with ERSILIA_SESSION:

# every command below uses the same session, "myproject"
export ERSILIA_SESSION=myproject
conda run -n ersilia ersilia serve eos4e40
conda run -n ersilia ersilia run -i input.csv -o output.csv
conda run -n ersilia ersilia close

Errors are printed to stderr, so they can be told apart from normal output.

See Command-line interface for all commands and options.

Python

from ersilia.api import Model

# create a handle for the model
model = Model("eos4e40")

# download the model
model.fetch()

# serve the model inside the block; it is closed automatically at the end
with model:
    # run predictions on a list of SMILES; returns a pandas DataFrame
    df = model.run(["CCO", "c1ccccc1"])

See Python API for the full API. For installation details and user guides, see the Ersilia Book.