ginkgo-ai-client 0.9.0
Client for the public Ginkgo AI API
Requires Python: >=3.7

# Ginkgo's AI model API client

**Work in progress: this repo was just made public and we are still working on integration**

A python client for [Ginkgo's AI model API](https://models.ginkgobioworks.ai/), to run inference on public and Ginkgo-proprietary models.
Learn more in the [Model API announcement](https://www.ginkgobioworks.com/2024/09/17/ginkgo-model-api-ai-research/).

## Prerequisites

Register at https://models.ginkgobioworks.ai/ to get credits and an API KEY (of the form `xxxxxxx-xxxx-xxxx-xxxx-xxxxxxxx`).
Store the API KEY in the `GINKGOAI_API_KEY` environment variable.

## Installation

Install the python client with pip:

```bash
pip install ginkgo-ai-client
```

## Usage:

**Note: This is an alpha version of the client and its interface may vary in the future.**

**Example : masked inference with Ginkgo's AA0 model**

The client requires an API key (and defaults to `os.environ.get("GINKGOAI_API_KEY")` if none is explicitly provided)

```python
from ginkgo_ai_client import GinkgoAIClient, MaskedInferenceQuery

client = GinkgoAIClient()
model = "ginkgo-aa0-650M"

query = MaskedInferenceQuery(sequence="MPK<mask><mask>RRL", model=model)
prediction = client.send_request(query)
# prediction.sequence == "MPKRRRRL"
```

It is also possible to send multiple queries at once, and even recommended in most cases as these will be processed in parallel, with appropriate scaling from our servers. The `send_batch_request` method returns a list of results in the same order as the queries:

```python
sequences = ["MPK<mask><mask>RRL", "M<mask>RL", "MLLM<mask><mask>R"]
queries = [MaskedInferenceQuery(sequence=seq, model=model) for seq in sequences]
predictions = client.send_batch_request(queries)
# predictions[0].sequence == "MPKRRRRL"
```

For large datasets (say, 100,000 queries), one can also send multiple batches of requests, then iterate over the results as they are ready. Note that the order in which the results are returned is not guaranteed to be the same as the order of the queries, therefore you should make sure the queries have a `query_name` attribute that will be used to identify the results.

```python
from ginkgo_ai_client import MeanEmbeddingQuery
queries = MeanEmbeddingQuery.iter_from_fasta("sequences.fasta", model=model)
for batch_results in client.send_requests_by_batches(queries, batch_size=1000):
    for result in batch_results:
        print(result.query_name, result.embedding)
```

Changing the `model` parameter to `esm2-650M` or `esm2-3b` in this example will perform
masked inference with the ESM2 model.

**Example : embedding computation with Ginkgo's 3'UTR language model**

```python
from ginkgo_ai_client import GinkgoAIClient, MeanEmbeddingQuery

client = GinkgoAIClient()
model = "ginkgo-maskedlm-3utr-v1"

# SINGLE QUERY

query = MeanEmbeddingQuery(sequence="ATTGCG", model=model)
prediction = client.send_request(query)
# prediction.embedding == [1.05, -2.34, ...]

# BATCH QUERY

sequences = ["ATTGCG", "CAATGC", "GCGCACATGT"]
queries = [MeanEmbeddingQuery(sequence=seq, model=model) for seq in sequences]
predictions = client.send_batch_request(queries)
# predictions[0].embedding == [1.05, -2.34, ...]
```

## Available models

See the [example folder](examples/) and [reference docs](https://ginkgobioworks.github.io/ginkgo-ai-client/) for more details on usage and parameters.

| Model       | Description                            | Reference                                                                                    | Supported queries                 | Versions |
| ----------- | -------------------------------------- | -------------------------------------------------------------------------------------------- | --------------------------------- | -------- |
| ESM2        | Large Protein language model from Meta | [Github](https://github.com/facebookresearch/esm?tab=readme-ov-file#esmfold)                 | Embeddings, masked inference      | 3B, 650M |
| AA0         | Ginkgo's protein language model        | [Announcement](https://www.ginkgobioworks.com/2024/09/17/aa-0-protein-llm-technical-review/) | Embeddings, masked inference      | 650M     |
| 3UTR        | Ginkgo's 3'UTR language model          | [Preprint](https://www.biorxiv.org/content/10.1101/2024.10.07.616676v1)                      | Embeddings, masked inference      | v1       |
| Promoter-0  | Ginkgo's promoter activity model       | Coming soon                                                                                  | Promoter activity accross tissues | v1       |
| ABdiffusion | Antibody diffusion model               | Coming soon                                                                                  | Unmasking                         | v1       |
| LCDNA       | Long-context DNA diffusion model       | Coming soon                                                                                  | Unmasking                         | v1       |

## License

This project is licensed under the MIT License. See the `LICENSE` file for details.

## Releases

To release a new version to PyPI:

- Make sure the changelog is up to date and the top section reads `Unreleased`.
- Increment the version with the `bumpversion` workflow in Actions - it will update the version everywhere in the repo and create a tag.
- If all looks good, create a release for the tag, it will automatically publish to PyPI.