Version 1.0

The following sections are specific to Version 1.x.x of the pysynthbio API.

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 for Version 1.0.

For more examples, check the examples directory in the repository.