Instructions to use CodeXomics/CodeXomics-ToolAgent-4B-v1 with libraries, inference providers, notebooks, and local apps. Follow these links to get started.

Libraries

How to use CodeXomics/CodeXomics-ToolAgent-4B-v1 with Transformers:

# Use a pipeline as a high-level helper
from transformers import pipeline

pipe = pipeline("text-generation", model="CodeXomics/CodeXomics-ToolAgent-4B-v1")
messages = [
    {
        "role": "user",
        "content": [
            {"type": "image", "url": "https://huggingface.co/datasets/huggingface/documentation-images/resolve/main/p-blog/candy.JPG"},
            {"type": "text", "text": "What animal is on the candy?"}
        ]
    },
]
pipe(text=messages)

# Load model directly
from transformers import AutoProcessor, AutoModelForMultimodalLM

processor = AutoProcessor.from_pretrained("CodeXomics/CodeXomics-ToolAgent-4B-v1")
model = AutoModelForMultimodalLM.from_pretrained("CodeXomics/CodeXomics-ToolAgent-4B-v1", device_map="auto")
messages = [
    {
        "role": "user",
        "content": [
            {"type": "image", "url": "https://huggingface.co/datasets/huggingface/documentation-images/resolve/main/p-blog/candy.JPG"},
            {"type": "text", "text": "What animal is on the candy?"}
        ]
    },
]
inputs = processor.apply_chat_template(
	messages,
	add_generation_prompt=True,
	tokenize=True,
	return_dict=True,
	return_tensors="pt",
).to(model.device)

outputs = model.generate(**inputs, max_new_tokens=40)
print(processor.decode(outputs[0][inputs["input_ids"].shape[-1]:]))

Notebooks
Google Colab
Kaggle
Local Apps Settings

vLLM

How to use CodeXomics/CodeXomics-ToolAgent-4B-v1 with vLLM:

Install from pip and serve model

# Install vLLM from pip:
pip install vllm
# Start the vLLM server:
vllm serve "CodeXomics/CodeXomics-ToolAgent-4B-v1"
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:8000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "CodeXomics/CodeXomics-ToolAgent-4B-v1",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Use Docker

docker model run hf.co/CodeXomics/CodeXomics-ToolAgent-4B-v1

SGLang

How to use CodeXomics/CodeXomics-ToolAgent-4B-v1 with SGLang:

Install from pip and serve model

# Install SGLang from pip:
pip install sglang
# Start the SGLang server:
python3 -m sglang.launch_server \
    --model-path "CodeXomics/CodeXomics-ToolAgent-4B-v1" \
    --host 0.0.0.0 \
    --port 30000
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:30000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "CodeXomics/CodeXomics-ToolAgent-4B-v1",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Use Docker images

docker run --gpus all \
    --shm-size 32g \
    -p 30000:30000 \
    -v ~/.cache/huggingface:/root/.cache/huggingface \
    --env "HF_TOKEN=<secret>" \
    --ipc=host \
    lmsysorg/sglang:latest \
    python3 -m sglang.launch_server \
        --model-path "CodeXomics/CodeXomics-ToolAgent-4B-v1" \
        --host 0.0.0.0 \
        --port 30000
# Call the server using curl (OpenAI-compatible API):
curl -X POST "http://localhost:30000/v1/chat/completions" \
	-H "Content-Type: application/json" \
	--data '{
		"model": "CodeXomics/CodeXomics-ToolAgent-4B-v1",
		"messages": [
			{
				"role": "user",
				"content": "What is the capital of France?"
			}
		]
	}'

Docker Model Runner
How to use CodeXomics/CodeXomics-ToolAgent-4B-v1 with Docker Model Runner:
```
docker model run hf.co/CodeXomics/CodeXomics-ToolAgent-4B-v1
```

CodeXomics commited on 9 days ago

Commit

19db9e9

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1 Parent(s): f6ffa6a

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@@ -22,6 +22,13 @@ performs native function calling against the CodeXomics tool registry (file load
 sequence analysis, annotation, track control, export, BLAST, primer design, database/protein
 retrieval, task management, and UI control).
 ## Fine-tuning
 - Method: QLoRA (rank 16, scale 32.0, dropout 0.05, 4 layers) with MLX-LM 0.31.2 / MLX 0.32.0
@@ -60,8 +67,6 @@ For deployment in CodeXomics, the model is served through Ollama as `qwen3.5:4b-
 ## Limitations
-- Multi-step workflows can occasionally stop before the final verification step, causing minor
-  run-to-run variance on the complex suite (27–29/29 across complete sessions).
 - The model is specialized for CodeXomics genomic workflows; generalization to other tool-calling
   domains was not evaluated.

 sequence analysis, annotation, track control, export, BLAST, primer design, database/protein
 retrieval, task management, and UI control).
+CodeXomics is an AI-native genome browser: a cross-platform desktop application in which
+conversational AI agents drive genome visualization and run real biological analyses, with built-in
+tool execution, a dynamic tool registry, plugin development, and Model Context Protocol (MCP)
+integration. Source code and documentation:
+[github.com/Scilence2022/CodeXomics](https://github.com/Scilence2022/CodeXomics) and
+[scilence2022.github.io/CodeXomics](https://scilence2022.github.io/CodeXomics/).
 ## Fine-tuning
 - Method: QLoRA (rank 16, scale 32.0, dropout 0.05, 4 layers) with MLX-LM 0.31.2 / MLX 0.32.0
 ## Limitations
 - The model is specialized for CodeXomics genomic workflows; generalization to other tool-calling
   domains was not evaluated.