aiagents4pharma 1.17.0__py3-none-any.whl → 1.17.1__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- aiagents4pharma/__init__.py +0 -1
- aiagents4pharma/talk2biomodels/__init__.py +1 -0
- aiagents4pharma/talk2biomodels/agents/t2b_agent.py +3 -3
- aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/agents/t2b_agent/default.yaml +1 -1
- aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/ask_question/default.yaml +1 -1
- aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/get_annotation/default.yaml +1 -1
- aiagents4pharma/talk2biomodels/tools/ask_question.py +5 -4
- aiagents4pharma/talk2biomodels/tools/get_annotation.py +3 -3
- aiagents4pharma/talk2biomodels/tools/search_models.py +1 -1
- aiagents4pharma-1.17.1.dist-info/METADATA +150 -0
- {aiagents4pharma-1.17.0.dist-info → aiagents4pharma-1.17.1.dist-info}/RECORD +20 -22
- aiagents4pharma/configs/__init__.py +0 -5
- aiagents4pharma/configs/config.yaml +0 -5
- aiagents4pharma-1.17.0.dist-info/METADATA +0 -212
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/__init__.py +0 -0
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/agents/__init__.py +0 -0
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/agents/t2b_agent/__init__.py +0 -0
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/__init__.py +0 -0
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/ask_question/__init__.py +0 -0
- /aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/get_annotation/__init__.py +0 -0
- {aiagents4pharma-1.17.0.dist-info → aiagents4pharma-1.17.1.dist-info}/LICENSE +0 -0
- {aiagents4pharma-1.17.0.dist-info → aiagents4pharma-1.17.1.dist-info}/WHEEL +0 -0
- {aiagents4pharma-1.17.0.dist-info → aiagents4pharma-1.17.1.dist-info}/top_level.txt +0 -0
aiagents4pharma/__init__.py
CHANGED
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@@ -55,10 +55,10 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
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llm = ChatOpenAI(model=llm_model, temperature=0)
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# Load hydra configuration
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logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
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with hydra.initialize(version_base=None, config_path="
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with hydra.initialize(version_base=None, config_path="../configs"):
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cfg = hydra.compose(config_name='config',
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overrides=['
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cfg = cfg.
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overrides=['agents/t2b_agent=default'])
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cfg = cfg.agents.t2b_agent
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logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
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# Create the agent
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model = create_react_agent(
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@@ -66,10 +66,10 @@ class AskQuestionTool(BaseTool):
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question_context,
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experiment_name)
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# Load hydra configuration
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with hydra.initialize(version_base=None, config_path="
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with hydra.initialize(version_base=None, config_path="../configs"):
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cfg = hydra.compose(config_name='config',
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overrides=['
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cfg = cfg.
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overrides=['tools/ask_question=default'])
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cfg = cfg.tools.ask_question
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# Get the context of the question
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# and based on the context, get the data
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# and prompt content to ask the question
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@@ -111,5 +111,6 @@ class AskQuestionTool(BaseTool):
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verbose=True,
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prefix=prompt_content)
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# Invoke the agent with the question
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llm_result = df_agent.invoke(question)
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llm_result = df_agent.invoke(question, stream_mode=None)
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# print (llm_result)
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return llm_result["output"]
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@@ -34,10 +34,10 @@ def extract_relevant_species_names(model_object, arg_data, state):
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Extract relevant species names based on the user question.
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"""
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# Load hydra configuration
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with hydra.initialize(version_base=None, config_path="
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with hydra.initialize(version_base=None, config_path="../configs"):
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cfg = hydra.compose(config_name='config',
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overrides=['
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cfg = cfg.
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overrides=['tools/get_annotation=default'])
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cfg = cfg.tools.get_annotation
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logger.info("Loaded the following system prompt for the LLM"
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" to get a structured output: %s", cfg.prompt)
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@@ -29,7 +29,7 @@ class SearchModelsTool(BaseTool):
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name: str = "search_models"
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description: str = "Search models in the BioMmodels database based on keywords."
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args_schema: Type[BaseModel] = SearchModelsInput
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return_direct: bool =
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return_direct: bool = False
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def _run(self,
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query: str,
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@@ -0,0 +1,150 @@
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Metadata-Version: 2.2
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Name: aiagents4pharma
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Version: 1.17.1
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Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
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Classifier: Programming Language :: Python :: 3
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.12
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: copasi_basico==0.78
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Requires-Dist: coverage==7.6.4
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Requires-Dist: einops==0.8.0
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Requires-Dist: gdown==5.2.0
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Requires-Dist: huggingface_hub==0.26.5
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Requires-Dist: hydra-core==1.3.2
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Requires-Dist: joblib==1.4.2
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Requires-Dist: langchain==0.3.7
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Requires-Dist: langchain-community==0.3.5
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Requires-Dist: langchain-core==0.3.31
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Requires-Dist: langchain-experimental==0.3.3
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Requires-Dist: langchain-openai==0.2.5
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Requires-Dist: langchain_ollama==0.2.2
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Requires-Dist: langgraph==0.2.66
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Requires-Dist: matplotlib==3.9.2
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Requires-Dist: openai==1.59.4
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Requires-Dist: ollama==0.4.6
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Requires-Dist: pandas==2.2.3
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Requires-Dist: plotly==5.24.1
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Requires-Dist: pydantic==2.9.2
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Requires-Dist: pylint==3.3.1
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Requires-Dist: pypdf==5.2.0
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Requires-Dist: pytest==8.3.3
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Requires-Dist: pytest-asyncio==0.25.2
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Requires-Dist: streamlit==1.39.0
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Requires-Dist: sentence_transformers==3.3.1
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Requires-Dist: tabulate==0.9.0
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Requires-Dist: torch==2.2.2
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Requires-Dist: torch_geometric==2.6.1
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Requires-Dist: tqdm==4.66.6
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Requires-Dist: transformers==4.48.0
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Requires-Dist: mkdocs==1.6.1
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Requires-Dist: mkdocs-jupyter==0.25.1
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Requires-Dist: mkdocs-material==9.5.47
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Requires-Dist: mkdocstrings-python==1.12.2
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Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
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Requires-Dist: mkdocstrings==0.27.0
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Requires-Dist: streamlit-feedback
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
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[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
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## Introduction
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Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
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Our toolkit currently consists of the following agents:
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- **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology.
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- **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
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- **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
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- **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease.
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## Getting Started
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### Installation
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#### Option 1: PyPI
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```bash
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pip install aiagents4pharma
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```
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Check out the tutorials on each agent for detailed instrcutions.
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#### Option 2: git
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1. **Clone the repository:**
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```bash
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git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
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cd AIAgents4Pharma
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```
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2. **Install dependencies:**
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```bash
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pip install .
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```
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3. **Initialize OPENAI_API_KEY**
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```bash
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export OPENAI_API_KEY=....
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```
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4. **[Optional] Initialize LANGSMITH_API_KEY**
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```bash
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export LANGCHAIN_TRACING_V2=true
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export LANGCHAIN_API_KEY=<your-api-key>
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```
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_Please note that this will create a new tracing project in your Langsmith
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account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars),
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`KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will
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default to the name `default`. `xxxx` will be the 4-digit ID created for the
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session._
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5. **Launch the app:**
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```bash
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streamlit run app/frontend/streamlit_app_<agent>.py
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```
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_Replace <agent> with the agent name you are interested to launch._
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For detailed instructions on each agent, please refer to their respective modules.
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---
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## Contributing
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We welcome contributions to AIAgents4Pharma! Here’s how you can help:
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1. **Fork the repository**
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2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`)
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3. **Commit your changes** (`git commit -m 'feat: Add new feature'`)
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4. **Push to the branch** (`git push origin feat/feature-name`)
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5. **Open a pull request** and reach out to any one of us below via Discussions:
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_Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_
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- **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey)
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- **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey)
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- **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey)
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### Current Needs
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- **Beta testers** for Talk2BioModels and Talk2Scholars.
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- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma.
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Feel free to reach out to us via Discussions.
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Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
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---
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## Feedback
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Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀
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aiagents4pharma/__init__.py,sha256=
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aiagents4pharma/
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aiagents4pharma/configs/config.yaml,sha256=e0w2GOBVWcoPDtX-z4S6yKbv2rja5PfGRBhmTPVIXNU,161
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aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=safyFKhkd5Wlirl9dMZIHWDLTpY2oLw9wjIM7ZtLIHk,88
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aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
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aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=eLrJIezoPJ6_DvrSYsi3eALl03o0hJhntej3ESoeKKg,551
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aiagents4pharma/configs/talk2biomodels/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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aiagents4pharma/configs/talk2biomodels/tools/ask_question/default.yaml,sha256=yy-Sq1u4dBlTFi_UeoWYoHkWRDWueJWVNK_rcUCC5bw,1747
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aiagents4pharma/configs/talk2biomodels/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
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aiagents4pharma/configs/talk2biomodels/tools/get_annotation/default.yaml,sha256=8vUlzU5Y3BPggId5bVMo9B23VG4mp2ziTglb4LmLCsc,319
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aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
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aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=CXlqDRqG_cxb1TUEL6960s2ActFiXblYPraagDDGQpo,3416
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<h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
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Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
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### Planned
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198
|
-
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199
|
-
- **User Interface**: Interactive web UI for all agents.
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|
200
|
-
- **Talk2Cells**: Integration of sequencing data analysis tools.
|
|
201
|
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- **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
|
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202
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- **Talk2Scholars**: Interface for exploring articles
|
|
203
|
-
|
|
204
|
-
We’re excited to bring AIAgents4Pharma to the bioinformatics and pharmaceutical research community. Together, let’s make data-driven biological research more accessible and insightful.
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205
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-
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206
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**Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
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|
207
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-
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208
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---
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209
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210
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## Feedback
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211
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212
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Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀
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/aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/agents/t2b_agent/__init__.py
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/aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/ask_question/__init__.py
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/aiagents4pharma/{configs/talk2biomodels → talk2biomodels/configs}/tools/get_annotation/__init__.py
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