aiagents4pharma 1.10.0__tar.gz → 1.11.0__tar.gz

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.10.0
+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
@@ -74,6 +74,7 @@ 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)_
 
@@ -87,11 +88,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 ## 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
 

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/README.md

@@ -28,6 +28,7 @@ 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)_
 
@@ -41,11 +42,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 ## 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
 

{aiagents4pharma-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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-1.10.0 → 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

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tools/get_modelinfo.py

@@ -47,8 +47,10 @@ class GetModelInfoTool(BaseTool):
     """
     This tool ise used extract model information.
     """
-    name: str = "get_parameters"
-    description: str = "A tool for extracting model information."
+    name: str = "get_modelinfo"
+    description: str = """A tool for extracting name,
+                    description, species, parameters,
+                    compartments, and units from a model."""
     args_schema: Type[BaseModel] = GetModelInfoInput
 
     def _run(self,
@@ -81,7 +83,7 @@ class GetModelInfoTool(BaseTool):
         # Extract species from the model
         if requested_model_info.species:
             df_species = basico.model_info.get_species(model=model_obj.copasi_model)
-            dic_results['Species'] = df_species.index.tolist()
+            dic_results['Species'] = df_species['display_name'].tolist()
             dic_results['Species'] = ','.join(dic_results['Species'])
 
         # Extract parameters from the model

aiagents4pharma-1.11.0/aiagents4pharma/talk2biomodels/tools/parameter_scan.py

@@ -0,0 +1,292 @@
+#!/usr/bin/env python3
+
+"""
+Tool for parameter scan.
+"""
+
+import logging
+from dataclasses import dataclass
+from typing import Type, Union, List, Annotated
+import pandas as pd
+import basico
+from pydantic import BaseModel, Field
+from langgraph.types import Command
+from langgraph.prebuilt import InjectedState
+from langchain_core.tools import BaseTool
+from langchain_core.messages import ToolMessage
+from langchain_core.tools.base import InjectedToolCallId
+from .load_biomodel import ModelData, load_biomodel
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+@dataclass
+class TimeData:
+    """
+    Dataclass for storing the time data.
+    """
+    duration: Union[int, float] = 100
+    interval: Union[int, float] = 10
+
+@dataclass
+class SpeciesData:
+    """
+    Dataclass for storing the species data.
+    """
+    species_name: List[str] = Field(description="species name", default=[])
+    species_concentration: List[Union[int, float]] = Field(
+        description="initial species concentration",
+        default=[])
+
+@dataclass
+class TimeSpeciesNameConcentration:
+    """
+    Dataclass for storing the time, species name, and concentration data.
+    """
+    time: Union[int, float] = Field(description="time point where the event occurs")
+    species_name: str = Field(description="species name")
+    species_concentration: Union[int, float] = Field(
+        description="species concentration at the time point")
+
+@dataclass
+class ReocurringData:
+    """
+    Dataclass for species that reoccur. In other words, the concentration
+    of the species resets to a certain value after a certain time interval.
+    """
+    data: List[TimeSpeciesNameConcentration] = Field(
+        description="time, name, and concentration data of species that reoccur",
+        default=[])
+
+@dataclass
+class ParameterScanData(BaseModel):
+    """
+    Dataclass for storing the parameter scan data.
+    """
+    species_names: List[str] = Field(description="species names to scan",
+                              default=[])
+    parameter_name: str = Field(description="Parameter name to scan",
+                                 default_factory=None)
+    parameter_values: List[Union[int, float]] = Field(
+        description="Parameter values to scan",
+        default_factory=None)
+
+@dataclass
+class ArgumentData:
+    """
+    Dataclass for storing the argument data.
+    """
+    time_data: TimeData = Field(description="time data", default=None)
+    species_data: SpeciesData = Field(
+        description="species name and initial concentration data",
+        default=None)
+    reocurring_data: ReocurringData = Field(
+        description="""Concentration and time data of species that reoccur
+            For example, a species whose concentration resets to a certain value
+            after a certain time interval""")
+    parameter_scan_data: ParameterScanData = Field(
+        description="parameter scan data",
+        default=None)
+    scan_name: str = Field(
+        description="""An AI assigned `_` separated name of
+        the parameter scan experiment based on human query""")
+
+def add_rec_events(model_object, reocurring_data):
+    """
+    Add reocurring events to the model.
+    """
+    for row in reocurring_data.data:
+        tp, sn, sc = row.time, row.species_name, row.species_concentration
+        basico.add_event(f'{sn}_{tp}',
+                            f'Time > {tp}',
+                            [[sn, str(sc)]],
+                            model=model_object.copasi_model)
+
+def make_list_dic_scanned_data(dic_param_scan, arg_data, sys_bio_model, tool_call_id):
+    """
+    Prepare the list dictionary of scanned data
+    that will be passed to the state of the graph.
+
+    Args:
+        dic_param_scan: Dictionary of parameter scan results.
+        arg_data: The argument data.
+        sys_bio_model: The model data.
+        tool_call_id: The tool call ID.
+
+    Returns:
+        list: List of dictionary of scanned data.
+    """
+    list_dic_scanned_data = []
+    for species_name, df_param_scan in dic_param_scan.items():
+        logger.log(logging.INFO, "Parameter scan results for %s with shape %s",
+                    species_name,
+                    df_param_scan.shape)
+        # Prepare the list dictionary of scanned data
+        # that will be passed to the state of the graph
+        list_dic_scanned_data.append({
+            'name': arg_data.scan_name+':'+species_name,
+            'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
+            'tool_call_id': tool_call_id,
+            'data': df_param_scan.to_dict()
+        })
+    return list_dic_scanned_data
+def run_parameter_scan(model_object, arg_data, dic_species_data, duration, interval) -> dict:
+    """
+    Run parameter scan on the model.
+
+    Args:
+        model_object: The model object.
+        arg_data: The argument data.
+        dic_species_data: Dictionary of species data.
+        duration: Duration of the simulation.
+        interval: Interval between time points in the simulation.
+
+    Returns:
+        dict: Dictionary of parameter scan results. Each key is a species name
+        and each value is a DataFrame containing the results of the parameter scan.
+    """
+    # Extract all parameter names from the model and verify if the given parameter name is valid
+    df_all_parameters = basico.model_info.get_parameters(model=model_object.copasi_model)
+    all_parameters = df_all_parameters.index.tolist()
+    if arg_data.parameter_scan_data.parameter_name not in all_parameters:
+        logger.error(
+            "Invalid parameter name: %s", arg_data.parameter_scan_data.parameter_name)
+        raise ValueError(
+            f"Invalid parameter name: {arg_data.parameter_scan_data.parameter_name}")
+    # Extract all species name from the model and verify if the given species name is valid
+    df_all_species = basico.model_info.get_species(model=model_object.copasi_model)
+    all_species = df_all_species['display_name'].tolist()
+    # Dictionary to store the parameter scan results
+    dic_param_scan_results = {}
+    for species_name in arg_data.parameter_scan_data.species_names:
+        if species_name not in all_species:
+            logger.error("Invalid species name: %s", species_name)
+            raise ValueError(f"Invalid species name: {species_name}")
+        # Update the fixed model species and parameters
+        # These are the initial conditions of the model
+        # set by the user
+        model_object.update_parameters(dic_species_data)
+        # Initialize empty DataFrame to store results
+        # of the parameter scan
+        df_param_scan = pd.DataFrame()
+        for param_value in arg_data.parameter_scan_data.parameter_values:
+            # Update the parameter value in the model
+            model_object.update_parameters(
+                {arg_data.parameter_scan_data.parameter_name: param_value})
+            # Simulate the model
+            model_object.simulate(duration=duration, interval=interval)
+            # If the column name 'Time' is not present in the results DataFrame
+            if 'Time' not in df_param_scan.columns:
+                df_param_scan['Time'] = model_object.simulation_results['Time']
+            # Add the simulation results to the results DataFrame
+            col_name = f"{arg_data.parameter_scan_data.parameter_name}_{param_value}"
+            df_param_scan[col_name] = model_object.simulation_results[species_name]
+
+        logger.log(logging.INFO, "Parameter scan results with shape %s", df_param_scan.shape)
+        # Add the results of the parameter scan to the dictionary
+        dic_param_scan_results[species_name] = df_param_scan
+    # return df_param_scan
+    return dic_param_scan_results
+
+class ParameterScanInput(BaseModel):
+    """
+    Input schema for the ParameterScan tool.
+    """
+    sys_bio_model: ModelData = Field(description="model data",
+                                     default=None)
+    arg_data: ArgumentData = Field(description=
+                                   """time, species, and reocurring data
+                                   as well as the parameter scan name and
+                                   data""",
+                                   default=None)
+    tool_call_id: Annotated[str, InjectedToolCallId]
+    state: Annotated[dict, InjectedState]
+
+# Note: It's important that every field has type hints. BaseTool is a
+# Pydantic class and not having type hints can lead to unexpected behavior.
+class ParameterScanTool(BaseTool):
+    """
+    Tool for parameter scan.
+    """
+    name: str = "parameter_scan"
+    description: str = """A tool to perform parameter scan
+        of a list of parameter values for a given species."""
+    args_schema: Type[BaseModel] = ParameterScanInput
+
+    def _run(self,
+        tool_call_id: Annotated[str, InjectedToolCallId],
+        state: Annotated[dict, InjectedState],
+        sys_bio_model: ModelData = None,
+        arg_data: ArgumentData = None
+    ) -> Command:
+        """
+        Run the tool.
+
+        Args:
+            tool_call_id (str): The tool call ID. This is injected by the system.
+            state (dict): The state of the tool.
+            sys_bio_model (ModelData): The model data.
+            arg_data (ArgumentData): The argument data.
+
+        Returns:
+            Command: The updated state of the tool.
+        """
+        logger.log(logging.INFO, "Calling parameter_scan tool %s, %s",
+                   sys_bio_model, arg_data)
+        sbml_file_path = state['sbml_file_path'][-1] if len(state['sbml_file_path']) > 0 else None
+        model_object = load_biomodel(sys_bio_model,
+                                  sbml_file_path=sbml_file_path)
+        # Prepare the dictionary of species data
+        # that will be passed to the simulate method
+        # of the BasicoModel class
+        duration = 100.0
+        interval = 10
+        dic_species_data = {}
+        if arg_data:
+            # Prepare the dictionary of species data
+            if arg_data.species_data is not None:
+                dic_species_data = dict(zip(arg_data.species_data.species_name,
+                                            arg_data.species_data.species_concentration))
+            # Add reocurring events (if any) to the model
+            if arg_data.reocurring_data is not None:
+                add_rec_events(model_object, arg_data.reocurring_data)
+            # Set the duration and interval
+            if arg_data.time_data is not None:
+                duration = arg_data.time_data.duration
+                interval = arg_data.time_data.interval
+
+        # Run the parameter scan
+        dic_param_scan = run_parameter_scan(model_object,
+                                           arg_data,
+                                           dic_species_data,
+                                           duration,
+                                           interval)
+
+        logger.log(logging.INFO, "Parameter scan results ready")
+        # Prepare the list dictionary of scanned data
+        list_dic_scanned_data = make_list_dic_scanned_data(dic_param_scan,
+                                                           arg_data,
+                                                           sys_bio_model,
+                                                           tool_call_id)
+        # Prepare the dictionary of updated state for the model
+        dic_updated_state_for_model = {}
+        for key, value in {
+            "model_id": [sys_bio_model.biomodel_id],
+            "sbml_file_path": [sbml_file_path],
+            "dic_scanned_data": list_dic_scanned_data,
+            }.items():
+            if value:
+                dic_updated_state_for_model[key] = value
+        # Return the updated state
+        return Command(
+                update=dic_updated_state_for_model|{
+                # update the message history
+                "messages": [
+                    ToolMessage(
+                        content=f"Parameter scan results of {arg_data.scan_name}",
+                        tool_call_id=tool_call_id
+                        )
+                    ],
+                }
+            )

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -138,7 +138,7 @@ class SimulateModelTool(BaseTool):
         # of the BasicoModel class
         duration = 100.0
         interval = 10
-        dic_species_data = None
+        dic_species_data = {}
         if arg_data:
             # Prepare the dictionary of species data
             if arg_data.species_data is not None:
@@ -151,22 +151,21 @@ class SimulateModelTool(BaseTool):
             if arg_data.time_data is not None:
                 duration = arg_data.time_data.duration
                 interval = arg_data.time_data.interval
-
+        # Update the model parameters
+        model_object.update_parameters(dic_species_data)
+        logger.log(logging.INFO,
+                   "Following species/parameters updated in the model %s",
+                   dic_species_data)
         # Simulate the model
-        df = model_object.simulate(
-            parameters=dic_species_data,
-            duration=duration,
-            interval=interval
-            )
-
+        df = model_object.simulate(duration=duration, interval=interval)
+        logger.log(logging.INFO, "Simulation results ready with shape %s", df.shape)
         dic_simulated_data = {
             'name': arg_data.simulation_name,
             'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
             'tool_call_id': tool_call_id,
             'data': df.to_dict()
         }
-
-        # Prepare the dictionary of updated state for the model
+        # Prepare the dictionary of updated state
         dic_updated_state_for_model = {}
         for key, value in {
             "model_id": [sys_bio_model.biomodel_id],
@@ -175,7 +174,6 @@ class SimulateModelTool(BaseTool):
             }.items():
             if value:
                 dic_updated_state_for_model[key] = value
-
         # Return the updated state of the tool
         return Command(
                 update=dic_updated_state_for_model|{

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.10.0
+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
@@ -74,6 +74,7 @@ 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)_
 
@@ -87,11 +88,7 @@ Our toolkit currently consists of three intelligent agents, each designed to sim
 
 ## 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
 

{aiagents4pharma-1.10.0 → aiagents4pharma-1.11.0}/aiagents4pharma.egg-info/SOURCES.txt

@@ -31,6 +31,7 @@ aiagents4pharma/talk2biomodels/tools/ask_question.py
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py
+aiagents4pharma/talk2biomodels/tools/parameter_scan.py
 aiagents4pharma/talk2biomodels/tools/search_models.py
 aiagents4pharma/talk2biomodels/tools/simulate_model.py
 aiagents4pharma/talk2cells/__init__.py

aiagents4pharma-1.11.0/release_version.txt

@@ -0,0 +1 @@
+v1.11.0

aiagents4pharma-1.10.0/release_version.txt

@@ -1 +0,0 @@
-v1.10.0