aiagents4pharma 1.9.0__tar.gz → 1.11.0__tar.gz

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.9.0
+Version: 1.11.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.10
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: copasi_basico==0.78
@@ -48,6 +48,9 @@ Requires-Dist: streamlit-feedback
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
 
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
@@ -56,9 +59,9 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** *(Coming soon)*: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -71,68 +74,77 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Forward simulation of both internal and open-source models (BioModels).
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
+- Extract model information such as species, parameters, units and description.
 
-### 2. Talk2Cells *(Work in Progress)*
+### 2. Talk2Cells _(Work in Progress)_
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 
-### 3. Talk2KnowledgeGraphs *(Work in Progress)*
+### 3. Talk2KnowledgeGraphs _(Work in Progress)_
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2KnowledgeGraphs *(Coming soon)*
+### 4. Talk2Competitors _(Coming soon)_
 
 ## Getting Started
 
-### Prerequisites
-
-- **Python 3.10+**
-- **Git**
-- Required libraries specified in `requirements.txt`
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 ### Installation
+
 #### Option 1: PyPI
-   ```bash
-   pip install aiagents4pharma
-   ```
+
+```bash
+pip install aiagents4pharma
+```
 
 Check out the tutorials on each agent for detailed instrcutions.
 
 #### Option 2: git
+
 1. **Clone the repository:**
+
    ```bash
    git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
    cd AIAgents4Pharma
    ```
 
 2. **Install dependencies:**
+
    ```bash
    pip install .
    ```
 
 3. **Initialize OPENAI_API_KEY**
+
    ```bash
-   export OPENAI_API_KEY = ....
+   export OPENAI_API_KEY=....
    ```
 
 4. **[Optional] Set up login credentials**
+
    ```bash
    vi .streamlit/secrets.toml
    ```
+
    and enter
+
    ```
    password='XXX'
    ```
-   Please note that the passowrd will be same for all the users.
+
+   Please note that the passoword will be same for all the users.
 
 5. **[Optional] Initialize LANGSMITH_API_KEY**
+
    ```bash
    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    ```
-   Please note that this will create a new tracing project in your Langsmith 
-   account with the name `<user_name>@<uuid>`, where `user_name` is the name 
-   you provided in the previous step. If you skip the previous step, it will 
+
+   Please note that this will create a new tracing project in your Langsmith
+   account with the name `<user_name>@<uuid>`, where `user_name` is the name
+   you provided in the previous step. If you skip the previous step, it will
    default to `default`. <uuid> will be the 128 bit unique ID created for the
    session.
 
@@ -164,6 +176,7 @@ We welcome contributions to AIAgents4Pharma! Here’s how you can help:
 5. **Open a pull request**
 
 ### Current Needs
+
 - **Beta testers** for Talk2BioModels.
 - **Developers** with experience in natural language processing, bioinformatics, or knowledge graphs for contributions to AIAgents4Pharma.
 
@@ -174,19 +187,22 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 ## Roadmap
 
 ### Completed
+
 - **Talk2BioModels**: Initial release with core capabilities for interacting with systems biology models.
 
 ### Planned
+
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**
+- **Talk2Competitors**: Interface for exploring articles
 
-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. 
+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.
 
 **Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
 
 ---
 
 ## Feedback
+
 Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/README.md

@@ -2,6 +2,9 @@
 [![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
 [![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
 [![Talk2Competitors](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2competitors.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
 
 <h1 align="center" style="border-bottom: none;">🤖 AIAgents4Pharma</h1>
 
@@ -10,9 +13,9 @@ Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://
 Our toolkit currently consists of three intelligent agents, each designed to simplify and enhance access to specialized data in biology:
 
 - **Talk2BioModels**: Engage directly with mathematical models in systems biology.
-- **Talk2Cells** *(Work in progress)*: Query and analyze sequencing data with ease.
-- **Talk2KnowledgeGraphs** *(Work in progress)*: Access and explore complex biological knowledge graphs for insightful data connections.
-- **Talk2Competitors** *(Coming soon)*: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
+- **Talk2Cells** _(Work in progress)_: Query and analyze sequencing data with ease.
+- **Talk2KnowledgeGraphs** _(Work in progress)_: Access and explore complex biological knowledge graphs for insightful data connections.
+- **Talk2Competitors** _(Coming soon)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero).
 
 ---
 
@@ -25,68 +28,77 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 - Forward simulation of both internal and open-source models (BioModels).
 - Adjust parameters within the model to simulate different conditions.
 - Query simulation results.
+- Extract model information such as species, parameters, units and description.
 
-### 2. Talk2Cells *(Work in Progress)*
+### 2. Talk2Cells _(Work in Progress)_
 
 **Talk2Cells** is being developed to provide direct access to and analysis of sequencing data, such as RNA-Seq or DNA-Seq, using natural language.
 
-### 3. Talk2KnowledgeGraphs *(Work in Progress)*
+### 3. Talk2KnowledgeGraphs _(Work in Progress)_
 
 **Talk2KnowledgeGraphs** is an agent designed to enable interaction with biological knowledge graphs (KGs). KGs integrate vast amounts of structured biological data into a format that highlights relationships between entities, such as proteins, genes, and diseases.
 
-### 4. Talk2KnowledgeGraphs *(Coming soon)*
+### 4. Talk2Competitors _(Coming soon)_
 
 ## Getting Started
 
-### Prerequisites
-
-- **Python 3.10+**
-- **Git**
-- Required libraries specified in `requirements.txt`
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
 
 ### Installation
+
 #### Option 1: PyPI
-   ```bash
-   pip install aiagents4pharma
-   ```
+
+```bash
+pip install aiagents4pharma
+```
 
 Check out the tutorials on each agent for detailed instrcutions.
 
 #### Option 2: git
+
 1. **Clone the repository:**
+
    ```bash
    git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
    cd AIAgents4Pharma
    ```
 
 2. **Install dependencies:**
+
    ```bash
    pip install .
    ```
 
 3. **Initialize OPENAI_API_KEY**
+
    ```bash
-   export OPENAI_API_KEY = ....
+   export OPENAI_API_KEY=....
    ```
 
 4. **[Optional] Set up login credentials**
+
    ```bash
    vi .streamlit/secrets.toml
    ```
+
    and enter
+
    ```
    password='XXX'
    ```
-   Please note that the passowrd will be same for all the users.
+
+   Please note that the passoword will be same for all the users.
 
 5. **[Optional] Initialize LANGSMITH_API_KEY**
+
    ```bash
    export LANGCHAIN_TRACING_V2=true
    export LANGCHAIN_API_KEY=<your-api-key>
    ```
-   Please note that this will create a new tracing project in your Langsmith 
-   account with the name `<user_name>@<uuid>`, where `user_name` is the name 
-   you provided in the previous step. If you skip the previous step, it will 
+
+   Please note that this will create a new tracing project in your Langsmith
+   account with the name `<user_name>@<uuid>`, where `user_name` is the name
+   you provided in the previous step. If you skip the previous step, it will
    default to `default`. <uuid> will be the 128 bit unique ID created for the
    session.
 
@@ -118,6 +130,7 @@ We welcome contributions to AIAgents4Pharma! Here’s how you can help:
 5. **Open a pull request**
 
 ### Current Needs
+
 - **Beta testers** for Talk2BioModels.
 - **Developers** with experience in natural language processing, bioinformatics, or knowledge graphs for contributions to AIAgents4Pharma.
 
@@ -128,19 +141,22 @@ Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
 ## Roadmap
 
 ### Completed
+
 - **Talk2BioModels**: Initial release with core capabilities for interacting with systems biology models.
 
 ### Planned
+
 - **User Interface**: Interactive web UI for all agents.
 - **Talk2Cells**: Integration of sequencing data analysis tools.
 - **Talk2KnowledgeGraphs**: Interface for biological knowledge graph interaction.
-- **Talk2Competitors**
+- **Talk2Competitors**: Interface for exploring articles
 
-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. 
+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.
 
 **Get Started** with AIAgents4Pharma today and transform the way you interact with biological data.
 
 ---
 
 ## Feedback
+
 Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use the `Isssues` tab 😀

aiagents4pharma-1.11.0/aiagents4pharma/__init__.py

@@ -0,0 +1,11 @@
+"""
+This file is used to import aiagents4pharma modules.
+"""
+
+from . import (
+    configs,
+    talk2biomodels,
+    talk2cells,
+    talk2competitors,
+    talk2knowledgegraphs,
+)

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -16,6 +16,7 @@ from ..tools.get_modelinfo import GetModelInfoTool
 from ..tools.simulate_model import SimulateModelTool
 from ..tools.custom_plotter import CustomPlotterTool
 from ..tools.ask_question import AskQuestionTool
+from ..tools.parameter_scan import ParameterScanTool
 from ..states.state_talk2biomodels import Talk2Biomodels
 
 # Initialize logger
@@ -35,17 +36,13 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
         return response
 
     # Define the tools
-    simulate_model = SimulateModelTool()
-    custom_plotter = CustomPlotterTool()
-    ask_question = AskQuestionTool()
-    search_model = SearchModelsTool()
-    get_modelinfo = GetModelInfoTool()
     tools = ToolNode([
-                    simulate_model,
-                    ask_question,
-                    custom_plotter,
-                    search_model,
-                    get_modelinfo
+                    SimulateModelTool(),
+                    AskQuestionTool(),
+                    CustomPlotterTool(),
+                    SearchModelsTool(),
+                    GetModelInfoTool(),
+                    ParameterScanTool()
                     ])
 
     # Define the model

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/models/basico_model.py

@@ -48,52 +48,49 @@ class BasicoModel(SysBioModel):
             self.name = basico.model_info.get_model_name(model=self.copasi_model)
         return self
 
-    def simulate(self,
-                 parameters: Optional[Dict[str, Union[float, int]]] = None,
-                 duration: Union[int, float] = 10,
-                 interval: int = 10
-                 ) -> pd.DataFrame:
+    def update_parameters(self, parameters: Dict[str, Union[float, int]]) -> None:
+        """
+        Update model parameters with new values.
+        """
+        # Update parameters in the model
+        for param_name, param_value in parameters.items():
+            # check if the param_name is not None
+            if param_name is None:
+                continue
+            # if param is a kinetic parameter
+            df_all_params = basico.model_info.get_parameters(model=self.copasi_model)
+            if param_name in df_all_params.index.tolist():
+                basico.model_info.set_parameters(name=param_name,
+                                            exact=True,
+                                            initial_value=param_value,
+                                            model=self.copasi_model)
+            # if param is a species
+            else:
+                basico.model_info.set_species(name=param_name,
+                                            exact=True,
+                                            initial_concentration=param_value,
+                                            model=self.copasi_model)
+
+    def simulate(self, duration: Union[int, float] = 10, interval: int = 10) -> pd.DataFrame:
         """
         Simulate the COPASI model over a specified range of time points.
         
         Args:
-            parameters: Dictionary of model parameters to update before simulation.
             duration: Duration of the simulation in time units.
             interval: Interval between time points in the simulation.
         
         Returns:
             Pandas DataFrame with time-course simulation results.
         """
-
-        # Update parameters in the model
-        if parameters:
-            for param_name, param_value in parameters.items():
-                # check if the param_name is not None
-                if param_name is None:
-                    continue
-                # if param is a kinectic parameter
-                df_all_params = basico.model_info.get_parameters(model=self.copasi_model)
-                if param_name in df_all_params.index.tolist():
-                    basico.model_info.set_parameters(name=param_name,
-                                                exact=True,
-                                                initial_value=param_value,
-                                                model=self.copasi_model)
-                # if param is a species
-                else:
-                    basico.model_info.set_species(name=param_name,
-                                                exact=True,
-                                                initial_concentration=param_value,
-                                                model=self.copasi_model)
-
         # Run the simulation and return results
         df_result = basico.run_time_course(model=self.copasi_model,
                                         intervals=interval,
                                         duration=duration)
-        # Replace curly braces in column headers with square brackets
-        # Because curly braces in the world of LLMS are used for
-        # structured output
-        df_result.columns = df_result.columns.str.replace('{', '[', regex=False).\
-                    str.replace('}', ']', regex=False)
+        # # Replace curly braces in column headers with square brackets
+        # # Because curly braces in the world of LLMS are used for
+        # # structured output
+        # df_result.columns = df_result.columns.str.replace('{', '[', regex=False).\
+        #             str.replace('}', ']', regex=False)
         # Reset the index
         df_result.reset_index(inplace=True)
         # Store the simulation results

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/models/sys_bio_model.py

@@ -35,18 +35,21 @@ class SysBioModel(ABC, BaseModel):
         Returns:
             dict: Dictionary with model metadata
         """
+    @abstractmethod
+    def update_parameters(self, parameters: Dict[str, Union[float, int]]) -> None:
+        """
+        Abstract method to update model parameters.
+
+        Args:
+            parameters: Dictionary of parameter values.
+        """
 
     @abstractmethod
-    def simulate(self,
-                 parameters: Dict[str, Union[float, int]],
-                 duration: Union[int, float]) -> List[float]:
+    def simulate(self, duration: Union[int, float]) -> List[float]:
         """
         Abstract method to run a simulation of the model.
-        This method should be implemented to simulate model 
-        behavior based on the provided parameters.
 
         Args:
-            parameters: Dictionary of parameter values.
             duration: Duration of the simulation.
 
         Returns:

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -12,13 +12,13 @@ class Talk2Biomodels(AgentState):
     """
     The state for the Talk2BioModels agent.
     """
-    model_id: Annotated[list, operator.add]
-    # sbml_file_path: str
+    llm_model: str
     # A StateGraph may receive a concurrent updates
     # which is not supported by the StateGraph.
     # Therefore, we need to use Annotated to specify
     # the operator for the sbml_file_path field.
     # https://langchain-ai.github.io/langgraph/troubleshooting/errors/INVALID_CONCURRENT_GRAPH_UPDATE/
+    model_id: Annotated[list, operator.add]
     sbml_file_path: Annotated[list, operator.add]
     dic_simulated_data: Annotated[list[dict], operator.add]
-    llm_model: str
+    dic_scanned_data: Annotated[list[dict], operator.add]

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tests/test_basico_model.py

@@ -19,13 +19,14 @@ def test_with_biomodel_id(model):
     Test initialization of BasicoModel with biomodel_id.
     """
     assert model.biomodel_id == 64
+    model.update_parameters(parameters={'Pyruvate': 0.5, 'KmPFKF6P': 1.5})
+    df_species = basico.model_info.get_species(model=model.copasi_model)
+    assert df_species.loc['Pyruvate', 'initial_concentration'] == 0.5
+    df_parameters = basico.model_info.get_parameters(model=model.copasi_model)
+    assert df_parameters.loc['KmPFKF6P', 'initial_value'] == 1.5
     # check if the simulation results are a pandas DataFrame object
-    assert isinstance(model.simulate(parameters={'Pyruvate': 0.5, 'KmPFKF6P': 1.5},
-                                     duration=2,
-                                     interval=2),
-                    pd.DataFrame)
-    assert isinstance(model.simulate(parameters={None: None}, duration=2, interval=2),
-                    pd.DataFrame)
+    assert isinstance(model.simulate(duration=2, interval=2), pd.DataFrame)
+    model.update_parameters(parameters={None: None})
     assert model.description == basico.biomodels.get_model_info(model.biomodel_id)["description"]
 
 def test_with_sbml_file():
@@ -35,8 +36,6 @@ def test_with_sbml_file():
     model_object = BasicoModel(sbml_file_path="./BIOMD0000000064_url.xml")
     assert model_object.sbml_file_path == "./BIOMD0000000064_url.xml"
     assert isinstance(model_object.simulate(duration=2, interval=2), pd.DataFrame)
-    assert isinstance(model_object.simulate(parameters={'NADH': 0.5}, duration=2, interval=2),
-                      pd.DataFrame)
 
 def test_check_biomodel_id_or_sbml_file_path():
     '''

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tests/test_langgraph.py

@@ -119,6 +119,68 @@ def test_simulate_model_tool():
     # Check if the data of the second model contains
     assert 'mTORC2' in dic_simulated_data[1]['data']
 
+def test_param_scan_tool():
+    '''
+    In this test, we will test the parameter_scan tool.
+    We will prompt it to scan the parameter `kIL6RBind`
+    from 1 to 100 in steps of 10, record the changes
+    in the concentration of the species `Ab{serum}` in
+    model 537.
+
+    We will pass the inaccuarate parameter (`KIL6Rbind`)
+    and species names (just `Ab`) to the tool to test
+    if it can deal with it.
+
+    We expect the agent to first invoke the parameter_scan
+    tool and raise an error. It will then invoke another
+    tool get_modelinfo to get the correct parameter
+    and species names. Finally, the agent will reinvoke
+    the parameter_scan tool with the correct parameter
+    and species names.
+
+    '''
+    unique_id = 123
+    app = get_app(unique_id)
+    config = {"configurable": {"thread_id": unique_id}}
+    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    prompt = """How will the value of Ab in model 537 change
+            if the param kIL6Rbind is varied from 1 to 100 in steps of 10?
+            Set the initial `DoseQ2W` concentration to 300.
+            Reset the IL6{serum} concentration to 100 every 500 hours.
+            Assume that the model is simulated for 2016 hours with
+            an interval of 2016."""
+    # Invoke the agent
+    app.invoke(
+        {"messages": [HumanMessage(content=prompt)]},
+        config=config
+    )
+    current_state = app.get_state(config)
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+    df = pd.DataFrame(columns=['name', 'status', 'content'])
+    names = []
+    statuses = []
+    contents = []
+    for msg in reversed_messages:
+        # Assert that the message is a ToolMessage
+        # and its status is "error"
+        if not isinstance(msg, ToolMessage):
+            continue
+        names.append(msg.name)
+        statuses.append(msg.status)
+        contents.append(msg.content)
+    df = pd.DataFrame({'name': names, 'status': statuses, 'content': contents})
+    # print (df)
+    assert any((df["status"] == "error") &
+               (df["name"] == "parameter_scan") &
+               (df["content"].str.startswith("Error: ValueError('Invalid parameter name:")))
+    assert any((df["status"] == "success") &
+               (df["name"] == "parameter_scan") &
+               (df["content"].str.startswith("Parameter scan results of")))
+    assert any((df["status"] == "success") &
+               (df["name"] == "get_modelinfo"))
+
 def test_integration():
     '''
     Test the integration of the tools.
@@ -184,9 +246,9 @@ def test_integration():
     reversed_messages = current_state.values["messages"][::-1]
     # Loop through the reversed messages
     # until a ToolMessage is found.
-    expected_header = ['Time', 'CRP[serum]', 'CRPExtracellular']
+    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
     expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_header += ['CRP[liver]']
+    expected_header += ['CRP{liver}']
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py

@@ -16,6 +16,8 @@ class TestBioModel(SysBioModel):
     sbml_file_path: Optional[str] = Field(None, description="Path to an SBML file")
     name: Optional[str] = Field(..., description="Name of the model")
     description: Optional[str] = Field("", description="Description of the model")
+    param1: Optional[float] = Field(0.0, description="Parameter 1")
+    param2: Optional[float] = Field(0.0, description="Parameter 2")
 
     def get_model_metadata(self) -> Dict[str, Union[str, int]]:
         '''
@@ -23,15 +25,18 @@ class TestBioModel(SysBioModel):
         '''
         return self.biomodel_id
 
-    def simulate(self,
-                 parameters: Dict[str, Union[float, int]],
-                 duration: Union[int, float]) -> List[float]:
+    def update_parameters(self, parameters):
+        '''
+        Update the model parameters.
+        '''
+        self.param1 = parameters.get('param1', 0.0)
+        self.param2 = parameters.get('param2', 0.0)
+
+    def simulate(self, duration: Union[int, float]) -> List[float]:
         '''
         Simulate the model.
         '''
-        param1 = parameters.get('param1', 0.0)
-        param2 = parameters.get('param2', 0.0)
-        return [param1 + param2 * t for t in range(int(duration))]
+        return [self.param1 + self.param2 * t for t in range(int(duration))]
 
 def test_get_model_metadata():
     '''
@@ -53,5 +58,6 @@ def test_simulate():
     Test the simulate method of the BioModel class.
     '''
     model = TestBioModel(biomodel_id=123, name="Test Model", description="A test model")
-    results = model.simulate(parameters={'param1': 1.0, 'param2': 2.0}, duration=4.0)
+    model.update_parameters({'param1': 1.0, 'param2': 2.0})
+    results = model.simulate(duration=4.0)
     assert results == [1.0, 3.0, 5.0, 7.0]

{aiagents4pharma-1.9.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tools/__init__.py

@@ -6,4 +6,5 @@ from . import simulate_model
 from . import ask_question
 from . import custom_plotter
 from . import get_modelinfo
+from . import parameter_scan
 from . import load_biomodel