pysynthbio 2.2.0

A package to retrieve data and models from Synthesize Bio's API

pysynthbio

The Pythonic API calling package for Synthesize Bio

Installation

To start using pysynthbio, first you need to have an account with synthesize.bio. Go here to create one

Then on your machine you can install using pip:

pip install pysynthbio

To ensure it installed you can run pip show pysynthbio.

Installing from a GitHub Release

Alternatively, you can install a specific version directly from its GitHub Release page. This is useful for testing pre-releases or specific tagged versions.

1. Go to the Releases page of the repository.

2. Find the release tag you want to install (e.g., v2.2.0).

3. Expand the "Assets" section for that release.

4. Download the .whl (wheel) file or the .tar.gz (source distribution) file. The wheel file is generally preferred if available for your platform.

5. Install the downloaded file using pip, replacing <path_to_downloaded_file> with the actual path to the file:

   # Example using a downloaded wheel file
   pip install /path/to/pysynthbio-2.2.0-py3-none-any.whl
   
   # Example using a downloaded source distribution
   pip install /path/to/pysynthbio-2.2.0.tar.gz
   

Usage

Get your API key

Go to https://app.synthesize.bio/profile to generate an API key. Then set this key as an environment variable named SYNTHESIZE_API_KEY to authenticate your API requests.

Form a request

First, import the necessary functions from the package:

import pysynthbio

Discover Valid Modalities

To see which output modalities are supported by the current model, use get_valid_modalities. This function returns a set of strings representing the allowed values for the output_modality key in your query.

supported_modalities = pysynthbio.get_valid_modalities()
print(supported_modalities)
# Output might look like: {'bulk_rna-seq', 'lincs', 'sra', ...}

Generate Example Queries

The structure of the query required by the API is fixed for the current supported model (v1.0). You can use get_valid_query to get a correctly structured example dictionary.

# Get the example query structure
example_query = pysynthbio.get_valid_query()

Get Predictions

Use predict_query to send a query to the API and get expression predictions. You'll typically use get_valid_query to help structure your request. This function also requires the API key.

# You can modify the example_query or create your own following the structure
my_query = pysynthbio.get_valid_query() # Example: using the default valid query
# Modify my_query as needed...

results = pysynthbio.predict_query(
    query=my_query,
    as_counts=True # Get results as estimated counts (default). Set to False for logCPM.
)

# Access results:
metadata_df = results["metadata"]
expression_df = results["expression"]

This covers the basic workflow: understanding the required query structure and making predictions.