aiagents4pharma 1.17.1__py3-none-any.whl → 1.18.0__py3-none-any.whl

aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -8,6 +8,7 @@ import logging
 from typing import Annotated
 import hydra
 from langchain_openai import ChatOpenAI
+from langchain_core.language_models.chat_models import BaseChatModel
 from langgraph.checkpoint.memory import MemorySaver
 from langgraph.graph import START, StateGraph
 from langgraph.prebuilt import create_react_agent, ToolNode, InjectedState
@@ -26,7 +27,8 @@ from ..states.state_talk2biomodels import Talk2Biomodels
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
-def get_app(uniq_id, llm_model='gpt-4o-mini'):
+def get_app(uniq_id,
+            llm_model: BaseChatModel = ChatOpenAI(model='gpt-4o-mini', temperature=0)):
     '''
     This function returns the langraph app.
     '''
@@ -51,8 +53,6 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
                     QueryArticle()
                 ])
 
-    # Define the model
-    llm = ChatOpenAI(model=llm_model, temperature=0)
     # Load hydra configuration
     logger.log(logging.INFO, "Load Hydra configuration for Talk2BioModels agent.")
     with hydra.initialize(version_base=None, config_path="../configs"):
@@ -62,7 +62,7 @@ def get_app(uniq_id, llm_model='gpt-4o-mini'):
     logger.log(logging.INFO, "state_modifier: %s", cfg.state_modifier)
     # Create the agent
     model = create_react_agent(
-                llm,
+                llm_model,
                 tools=tools,
                 state_schema=Talk2Biomodels,
                 state_modifier=cfg.state_modifier,

aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml

@@ -10,22 +10,14 @@ steady_state_prompt: >
 
   Here are some instructions to help you answer questions:
 
-  1. Before you answer any question, follow the plan and solve
-  technique. Start by understanding the question, then plan your
-  approach to solve the question, and finally solve the question
-  by following the plan. Always give a brief explanation of your
-  answer to the user.
+  1. If the user wants to know the time taken by the model to reach
+  steady state, you should look at the `steady_state_transition_time`
+  column of the data for the model species.
+  
+  2. The highest value in the column `steady_state_transition_time`
+  is the time taken by the model to reach steady state.
 
-  2. If the user wants to know the time taken by the model to reach
-  steady state, you should look at the steady_state_transition_time
-  column of the data for the model species. The highest value in
-  this column is the time taken by the model to reach steady state.
-
-  3. To get accurate results, trim the data to the relevant columns
-  before performing any calculations. This will help you avoid
-  errors in your calculations, and ignore irrelevant data.
-
-  4. Please use the units provided below to answer the questions.
+  3. Please use the units provided below to answer the questions.
 simulation_prompt: >
   Following is the information about the data frame:
   1. First column is the time column, and the rest of the columns

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -7,6 +7,8 @@ This is the state file for the Talk2BioModels agent.
 from typing import Annotated
 import operator
 from langgraph.prebuilt.chat_agent_executor import AgentState
+from langchain_core.language_models import BaseChatModel
+from langchain_core.embeddings import Embeddings
 
 def add_data(data1: dict, data2: dict) -> dict:
     """
@@ -26,7 +28,8 @@ class Talk2Biomodels(AgentState):
     """
     The state for the Talk2BioModels agent.
     """
-    llm_model: str
+    llm_model: BaseChatModel
+    text_embedding_model: Embeddings
     pdf_file_name: str
     # A StateGraph may receive a concurrent updates
     # which is not supported by the StateGraph. Hence,

aiagents4pharma/talk2biomodels/tests/test_ask_question.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
 def test_ask_question_tool():
@@ -10,7 +11,7 @@ def test_ask_question_tool():
     Test the ask_question tool without the simulation results.
     '''
     unique_id = 12345
-    app = get_app(unique_id, llm_model='gpt-4o-mini')
+    app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
 
     ##########################################
@@ -20,7 +21,8 @@ def test_ask_question_tool():
     # case, the tool should return an error
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config,
+            {"llm_model": ChatOpenAI(model='gpt-4o-mini', temperature=0)})
     # Define the prompt
     prompt = "Call the ask_question tool to answer the "
     prompt += "question: What is the concentration of CRP "

aiagents4pharma/talk2biomodels/tests/test_get_annotation.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels get_annotation tool.
 import random
 import pytest
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 from ..tools.get_annotation import prepare_content_msg
 
@@ -16,7 +17,9 @@ def make_graph_fixture():
     unique_id = random.randint(1000, 9999)
     graph = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    graph.update_state(config, {"llm_model": "gpt-4o-mini"})
+    graph.update_state(config, {"llm_model": ChatOpenAI(model='gpt-4o-mini',
+                                    temperature=0)
+                                })
     return graph, config
 
 def test_no_model_provided(make_graph):
@@ -85,7 +88,6 @@ def test_invalid_species_provided(make_graph):
                 # (likely due to an invalid species).
                 test_condition = True
                 break
-    # assert test_condition
     assert test_condition
 
 def test_invalid_and_valid_species_provided(make_graph):

aiagents4pharma/talk2biomodels/tests/test_integration.py

@@ -4,8 +4,11 @@ Test cases for Talk2Biomodels.
 
 import pandas as pd
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_integration():
     '''
     Test the integration of the tools.
@@ -13,7 +16,7 @@ def test_integration():
     unique_id = 1234567
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     # ##########################################
     # ## Test simulate_model tool
     # ##########################################
@@ -34,7 +37,7 @@ def test_integration():
     # results are available
     ##########################################
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     prompt = """What is the concentration of CRP in serum after 100 hours?
     Round off the value to 2 decimal places."""
     # Test the tool get_modelinfo
@@ -49,12 +52,15 @@ def test_integration():
 
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available
+    # simulation results are available but
+    # the species is not available
     ##########################################
-    prompt = "Plot only CRP related species."
-
+    prompt = """Call the custom_plotter tool to make a plot
+        showing only species `TP53` and `Pyruvate`. Let me
+        know if these species were not found. Do not
+        invoke any other tool."""
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -66,11 +72,8 @@ def test_integration():
     # Get the messages from the current state
     # and reverse the order
     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 += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_header += ['CRP{liver}']
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -80,24 +83,17 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Convert the artifact into a pandas dataframe
-    # for easy comparison
-    df = pd.DataFrame(predicted_artifact)
-    # Extract the headers from the dataframe
-    predicted_header = df.columns.tolist()
-    # Check if the header is in the expected_header
-    # assert expected_header in predicted_artifact
-    assert set(expected_header).issubset(set(predicted_header))
+    # Check if the the predicted artifact is `None`
+    assert predicted_artifact is None
+
     ##########################################
     # Test custom_plotter tool when the
-    # simulation results are available but
-    # the species is not available
+    # simulation results are available
     ##########################################
-    prompt = """Make a custom plot showing the
-        concentration of the species `TP53` over
-        time. Do not show any other species."""
+    prompt = "Plot only CRP related species."
+
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"}
+    app.update_state(config, {"llm_model": LLM_MODEL}
                     )
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -105,13 +101,15 @@ def test_integration():
                         config=config
                     )
     assistant_msg = response["messages"][-1].content
-    # print (response["messages"])
     current_state = app.get_state(config)
     # Get the messages from the current state
     # and reverse the order
     reversed_messages = current_state.values["messages"][::-1]
-    # Loop through the reversed messages until a
-    # ToolMessage is found.
+    # Loop through the reversed messages
+    # until a ToolMessage is found.
+    expected_header = ['Time', 'CRP{serum}', 'CRPExtracellular']
+    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
+    expected_header += ['CRP{liver}']
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -121,5 +119,11 @@ def test_integration():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Check if the the predicted artifact is `None`
-    assert predicted_artifact is None
+    # Convert the artifact into a pandas dataframe
+    # for easy comparison
+    df = pd.DataFrame(predicted_artifact)
+    # Extract the headers from the dataframe
+    predicted_header = df.columns.tolist()
+    # Check if the header is in the expected_header
+    # assert expected_header in predicted_artifact
+    assert set(expected_header).issubset(set(predicted_header))

aiagents4pharma/talk2biomodels/tests/test_query_article.py

@@ -5,6 +5,7 @@ Test cases for Talk2Biomodels query_article tool.
 from pydantic import BaseModel, Field
 from langchain_core.messages import HumanMessage, ToolMessage
 from langchain_openai import ChatOpenAI
+from langchain_nvidia_ai_endpoints import NVIDIAEmbeddings
 from ..agents.t2b_agent import get_app
 
 class Article(BaseModel):
@@ -21,8 +22,10 @@ def test_query_article_with_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state by providing the pdf file name
+    # and the text embedding model
     app.update_state(config,
-      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf"})
+      {"pdf_file_name": "aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf",
+       "text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     prompt = "What is the title of the article?"
     # Test the tool query_article
     response = app.invoke(
@@ -55,6 +58,9 @@ def test_query_article_without_an_article():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     prompt = "What is the title of the uploaded article?"
+    # Update state by providing the text embedding model
+    app.update_state(config,
+      {"text_embedding_model": NVIDIAEmbeddings(model='nvidia/llama-3.2-nv-embedqa-1b-v2')})
     # Test the tool query_article
     app.invoke(
             {"messages": [HumanMessage(content=prompt)]},

aiagents4pharma/talk2biomodels/tests/test_search_models.py

@@ -3,6 +3,7 @@ Test cases for Talk2Biomodels search models tool.
 '''
 
 from langchain_core.messages import HumanMessage
+from langchain_nvidia_ai_endpoints import ChatNVIDIA
 from ..agents.t2b_agent import get_app
 
 def test_search_models_tool():
@@ -13,7 +14,8 @@ def test_search_models_tool():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config,
+            {"llm_model": ChatNVIDIA(model="meta/llama-3.3-70b-instruct")})
     prompt = "Search for models on Crohn's disease."
     # Test the tool get_modelinfo
     response = app.invoke(

aiagents4pharma/talk2biomodels/tests/test_steady_state.py

@@ -3,8 +3,11 @@ Test cases for Talk2Biomodels steady state tool.
 '''
 
 from langchain_core.messages import HumanMessage, ToolMessage
+from langchain_openai import ChatOpenAI
 from ..agents.t2b_agent import get_app
 
+LLM_MODEL = ChatOpenAI(model='gpt-4o-mini', temperature=0)
+
 def test_steady_state_tool():
     '''
     Test the steady_state tool.
@@ -12,7 +15,7 @@ def test_steady_state_tool():
     unique_id = 123
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
-    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    app.update_state(config, {"llm_model": LLM_MODEL})
     #########################################################
     # In this case, we will test if the tool returns an error
     # when the model does not achieve a steady state. The tool
@@ -37,8 +40,8 @@ def test_steady_state_tool():
     #########################################################
     # In this case, we will test if the tool is indeed invoked
     # successfully
-    prompt = """Run a steady state analysis of model 64.
-    Set the initial concentration of `Pyruvate` to 0.2. The
+    prompt = """Bring model 64 to a steady state. Set the
+    initial concentration of `Pyruvate` to 0.2. The
     concentration of `NAD` resets to 100 every 2 time units."""
     # Invoke the agent
     app.invoke(

aiagents4pharma/talk2biomodels/tools/ask_question.py

@@ -12,7 +12,6 @@ import pandas as pd
 from pydantic import BaseModel, Field
 from langchain_core.tools.base import BaseTool
 from langchain_experimental.agents import create_pandas_dataframe_agent
-from langchain_openai import ChatOpenAI
 from langgraph.prebuilt import InjectedState
 
 # Initialize logger
@@ -101,7 +100,7 @@ class AskQuestionTool(BaseTool):
         prompt_content += f"{basico.model_info.get_model_units()}\n\n"
         # Create a pandas dataframe agent
         df_agent = create_pandas_dataframe_agent(
-                        ChatOpenAI(model=state['llm_model']),
+                        state['llm_model'],
                         allow_dangerous_code=True,
                         agent_type='tool-calling',
                         df=df,

aiagents4pharma/talk2biomodels/tools/custom_plotter.py

@@ -5,10 +5,9 @@ Tool for plotting a custom figure.
 """
 
 import logging
-from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
+from typing import Type, Annotated, List, Tuple, Union, Literal
 from pydantic import BaseModel, Field
 import pandas as pd
-from langchain_openai import ChatOpenAI
 from langchain_core.tools import BaseTool
 from langgraph.prebuilt import InjectedState
 
@@ -71,30 +70,44 @@ class CustomPlotterTool(BaseTool):
         species_names = df.columns.tolist()
         # Exclude the time column
         species_names.remove('Time')
+        logging.log(logging.INFO, "Species names: %s", species_names)
         # In the following code, we extract the species
         # from the user question. We use Literal to restrict
         # the species names to the ones available in the
         # simulation results.
-        class CustomHeader(TypedDict):
+        class CustomHeader(BaseModel):
             """
             A list of species based on user question.
+
+            This is a Pydantic model that restricts the species
+            names to the ones available in the simulation results.
+            
+            If no species is relevant, set the attribute
+            `relevant_species` to None.
             """
             relevant_species: Union[None, List[Literal[*species_names]]] = Field(
-                    description="""List of species based on user question.
-                    If no relevant species are found, it will be None.""")
+                    description="This is a list of species based on the user question."
+                    "It is restricted to the species available in the simulation results."
+                    "If no species is relevant, set this attribute to None."
+                    "If the user asks for very specific species (for example, using the"
+                    "keyword `only` in the question), set this attribute to correspond "
+                    "to the species available in the simulation results, otherwise set it to None."
+                    )
         # Create an instance of the LLM model
-        llm = ChatOpenAI(model=state['llm_model'], temperature=0)
+        logging.log(logging.INFO, "LLM model: %s", state['llm_model'])
+        llm = state['llm_model']
         llm_with_structured_output = llm.with_structured_output(CustomHeader)
         results = llm_with_structured_output.invoke(question)
+        if results.relevant_species is None:
+            raise ValueError("No species found in the simulation results \
+                             that matches the user prompt.")
         extracted_species = []
         # Extract the species from the results
         # that are available in the simulation results
-        for species in results['relevant_species']:
+        for species in results.relevant_species:
             if species in species_names:
                 extracted_species.append(species)
-        logger.info("Extracted species: %s", extracted_species)
-        if len(extracted_species) == 0:
-            return "No species found in the simulation results that matches the user prompt.", None
+        logging.info("Extracted species: %s", extracted_species)
         # Include the time column
         extracted_species.insert(0, 'Time')
         return f"Custom plot {simulation_name}", df[extracted_species].to_dict(orient='records')

aiagents4pharma/talk2biomodels/tools/get_annotation.py

@@ -5,7 +5,7 @@ This module contains the `GetAnnotationTool` for fetching species annotations
 based on the provided model and species names.
 """
 import math
-from typing import List, Annotated, Type, TypedDict, Union, Literal
+from typing import List, Annotated, Type, Union, Literal
 import logging
 from dataclasses import dataclass
 import hydra
@@ -17,7 +17,7 @@ from langgraph.prebuilt import InjectedState
 from langchain_core.tools.base import BaseTool
 from langchain_core.tools.base import InjectedToolCallId
 from langchain_core.messages import ToolMessage
-from langchain_openai import ChatOpenAI
+# from langchain_openai import ChatOpenAI
 from .load_biomodel import ModelData, load_biomodel
 from ..api.uniprot import search_uniprot_labels
 from ..api.ols import search_ols_labels
@@ -49,7 +49,7 @@ def extract_relevant_species_names(model_object, arg_data, state):
     all_species_names = df_species.index.tolist()
 
     # Define a structured output for the LLM model
-    class CustomHeader(TypedDict):
+    class CustomHeader(BaseModel):
         """
         A list of species based on user question.
         """
@@ -58,17 +58,21 @@ def extract_relevant_species_names(model_object, arg_data, state):
                 If no relevant species are found, it must be None.""")
 
     # Create an instance of the LLM model
-    llm = ChatOpenAI(model=state['llm_model'], temperature=0)
+    llm = state['llm_model']
     # Get the structured output from the LLM model
     llm_with_structured_output = llm.with_structured_output(CustomHeader)
     # Define the question for the LLM model using the prompt
     question = cfg.prompt
     question += f'Here is the user question: {arg_data.user_question}'
     # Invoke the LLM model with the user question
-    dic = llm_with_structured_output.invoke(question)
+    results = llm_with_structured_output.invoke(question)
+    logging.info("Results from the LLM model: %s", results)
+    # Check if the returned species names are empty
+    if not results.relevant_species:
+        raise ValueError("Model does not contain the requested species.")
     extracted_species = []
     # Extract all the species names from the model
-    for species in dic['relevant_species']:
+    for species in results.relevant_species:
         if species in all_species_names:
             extracted_species.append(species)
     logger.info("Extracted species: %s", extracted_species)
@@ -136,10 +140,7 @@ class GetAnnotationTool(BaseTool):
 
         # Extract relevant species names based on the user question
         list_species_names = extract_relevant_species_names(model_object, arg_data, state)
-
-        # Check if the returned species names are empty
-        if not list_species_names:
-            raise ValueError("Model does not contain the requested species.")
+        print (list_species_names)
 
         (annotations_df,
          species_without_description) = self._fetch_annotations(list_species_names)

aiagents4pharma/talk2biomodels/tools/query_article.py

@@ -9,7 +9,6 @@ from typing import Type, Annotated
 from pydantic import BaseModel, Field
 from langchain_core.tools import BaseTool
 from langchain_core.vectorstores import InMemoryVectorStore
-from langchain_openai.embeddings import OpenAIEmbeddings
 from langchain_community.document_loaders import PyPDFLoader
 from langgraph.prebuilt import InjectedState
 
@@ -51,8 +50,13 @@ class QueryArticle(BaseTool):
         pages = []
         for page in loader.lazy_load():
             pages.append(page)
+        # Set up text embedding model
+        text_embedding_model = state['text_embedding_model']
+        logging.info("Loaded text embedding model %s", text_embedding_model)
         # Create a vector store from the pages
-        vector_store = InMemoryVectorStore.from_documents(pages, OpenAIEmbeddings())
+        vector_store = InMemoryVectorStore.from_documents(
+                                            pages,
+                                            text_embedding_model)
         # Search the article with the question
         docs = vector_store.similarity_search(question)
         # Return the content of the pages

aiagents4pharma/talk2biomodels/tools/search_models.py

@@ -5,14 +5,18 @@ Tool for searching models based on search query.
 """
 
 from typing import Type, Annotated
+import logging
 from pydantic import BaseModel, Field
 from basico import biomodels
 from langchain_core.tools import BaseTool
 from langchain_core.output_parsers import StrOutputParser
 from langchain_core.prompts import ChatPromptTemplate
-from langchain_openai import ChatOpenAI
 from langgraph.prebuilt import InjectedState
 
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 class SearchModelsInput(BaseModel):
     """
     Input schema for the search models tool.
@@ -43,8 +47,10 @@ class SearchModelsTool(BaseTool):
         Returns:
             dict: The answer to the question in the form of a dictionary.
         """
+        logger.log(logging.INFO, "Searching models with the query and model: %s, %s",
+                   query, state['llm_model'])
         search_results = biomodels.search_for_model(query)
-        llm = ChatOpenAI(model=state['llm_model'])
+        llm = state['llm_model']
         # Check if run_manager's metadata has the key 'prompt_content'
         prompt_content = f'''
                         Convert the input into a table.

{aiagents4pharma-1.17.1.dist-info → aiagents4pharma-1.18.0.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.17.1
-Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
+Version: 1.18.0
+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
@@ -19,6 +19,7 @@ Requires-Dist: langchain==0.3.7
 Requires-Dist: langchain-community==0.3.5
 Requires-Dist: langchain-core==0.3.31
 Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
 Requires-Dist: langchain-openai==0.2.5
 Requires-Dist: langchain_ollama==0.2.2
 Requires-Dist: langgraph==0.2.66
@@ -93,10 +94,16 @@ Check out the tutorials on each agent for detailed instrcutions.
    ```bash
    pip install .
    ```
-3. **Initialize OPENAI_API_KEY**
+3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY**
    ```bash
    export OPENAI_API_KEY=....
    ```
+   ```bash
+   export NVIDIA_API_KEY=....
+   ```
+_You can create a free account at NVIDIA and apply for their
+free credits [here](https://build.nvidia.com/explore/discover)._
+
 4. **[Optional] Initialize LANGSMITH_API_KEY**
    ```bash
    export LANGCHAIN_TRACING_V2=true

{aiagents4pharma-1.17.1.dist-info → aiagents4pharma-1.18.0.dist-info}/RECORD

@@ -1,7 +1,7 @@
 aiagents4pharma/__init__.py,sha256=Ua9fqYW5gV1SZ0nOyOMd4T3wTlBui1-mrlJzFUQLFgY,161
 aiagents4pharma/talk2biomodels/__init__.py,sha256=1cq1HX2xoi_a0nDPuXYoSTrnL26OHQBW3zXNwwwjFO0,181
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
-aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=CXlqDRqG_cxb1TUEL6960s2ActFiXblYPraagDDGQpo,3416
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=bbktkTinp5VHHmAZEs1yMPN3Bu7rnyxRq2Cb7xVe8Gw,3477
 aiagents4pharma/talk2biomodels/api/__init__.py,sha256=_GmDQqDLYpsUPUeE1nBNlT5AI9oTXIcqgOfNfvmonqA,123
 aiagents4pharma/talk2biomodels/api/kegg.py,sha256=QzYDAfJ16E7tbHGxP8ZNWRizMkMRS_HJuucueXEC1Gg,2943
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=qq0Qy-gJDxanQW-HfCChDsTQsY1M41ua8hMlTnfuzrA,2202
@@ -12,37 +12,37 @@ aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/__init__.py,sha256=-fAOR
 aiagents4pharma/talk2biomodels/configs/agents/t2b_agent/default.yaml,sha256=pSViMKwKyMQDm8LzbfIaGdxph73iHYaXMiv5YOuxM7k,536
 aiagents4pharma/talk2biomodels/configs/tools/__init__.py,sha256=B08KWjj7bpizuTETGnnngrEVK4nzdWGREdoCCSw1Sm4,102
 aiagents4pharma/talk2biomodels/configs/tools/ask_question/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=pMjs-peecRl8xtIucbEM1Z8Mm_8KGZj0JBrKKD3cMxU,1732
+aiagents4pharma/talk2biomodels/configs/tools/ask_question/default.yaml,sha256=7k49GkLbPy4v7w5-zfwkgBUPaH6R1IrRPCXvUiUiCKE,1300
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=PH25FTOuUjsmw_UUxoRb-4kptOYpicEn4GqS0phS3nk,4807
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
-aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=d_tDh93ip36hlUpMh-KOkYfBZ2SQwZlaY8p-1ZWKPhY,1355
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=S1UtXvocWR8Y9OVUp6pIDFnmaCcjbwmUbW8u79TuGcg,1508
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
-aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=yRkKK9HLB1bGGWm_WwOckwaUmmRfRAD9z2NFFGLIGTY,1560
+aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=rdForKfj2zj2IXl6ntK9_I0AbgsCv8MXOZ2khBnaPms,1620
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
-aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GqS3kCxxTTMTJFjTnJhilrxT6jbNb7Yi0fbaKkadU4E,8159
+aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GbobfjtCAOV0HddM4pb2o3c49Q05fKIM0Ubnf8BRxHM,8273
 aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=Y1sFhoMF4mbvlag7D-dEvv6ytjmAqzMLPvSvaVEI_Qk,2045
-aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=QHGOKrKyd0kBGy1tOMmkNSqN2Jc2oIXoUrAMpv-elBc,5058
+aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=XvQmnkIkAcgjmNwsW4FXiCwMMU7fpCpxfqhG2v2KyF4,5170
 aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=vRbnn4uVWFbfZbU4gVCjHi5WDCUrErut8ElzAPE5y84,2648
-aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=HhFgU5HzCipecEYlfbpPxN-SCIPKep22gpXCutWXRb8,2820
-aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=8ODFubLxWYD3I3KQWuUnJ2GZRzMjFpXInFBLxKxG_ME,929
+aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=lArISS111mQUZmjLY82PkRVPSTcN2h8KNF4gpTTvwL0,3185
+aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=ttOzN78b06ixYF_SbSyrhQSnmCgOMlSoeG9Q1FeRAis,1028
 aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=GjLE1DZpcKUAFSmoHD86vkfK0b5LJPM8a4WYyraazig,1487
-aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=zt15KQoQku6jyzvpJXwINGTyhEnQl8wX81ueHlxnUCA,3467
+aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=2bzxj74vekazgLG7hiMALRiqP_4sVmue9cN4zCZ42T8,3556
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=HSmBBViMi0jYf4gWX21IbppAfDzG0nr_S3KtKS9fZVQ,2165
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=6H2HWv5Q4NZYEmw-Ti5KZnJlEqhaC2HXSDZa6kiSl-U,350
-aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=ASkqT6VHUWcMdkVAlqqfbwq7_EBVAXdtmlkMFy7-XxI,4698
-aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
-aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=Cea0vid_KX1xjI6ZqDygREAcM7sC7wZXNLTkAN8Nk3Y,13387
+aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=NZwKT7DHc4TW9e8LOkHaRG_nqUs_lEandvi89DTXilQ,4640
+aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=DsnQIKebchy6tgzLZnY7VLVesu3Es-OdqLfW61kIn3A,4762
+aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=njxUmFuFwlzY3Doq-XlepGXJTMgnYfs88L4RkKSiptw,13438
 aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=57dkXrBeRpyiaW3dYkoWIfr6zSsFHcWRhvUVNyLcvUs,6363
 aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=bffNIlBDTCSFYiZprA73yi8Jbb8z3Oh2decVNh1UnZc,4162
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
 aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=aNh94LgBgVXBIczuNkbSsOZ9j54YVEdZWmZbZr7Nk8k,12465
-aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=1tpYiE69MYcqiNcRaBgNiYzkkNmuTnlxLuBL_FnRuBU,2058
-aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=b2OK-Z4ilddbEaJPSQlnZ6sHX3UAWXr_Hq-knoSbbAE,2654
+aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=6xfirRRMXN-wxqZxYYbKeEMXLMAHKl5IPShfpoOEBcc,2268
+aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=LdvfCNeiO8fU6lszd7UUzk4NXP6ETuMsCRb2SpXcztw,2841
 aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=qXs9lg9XgA7EaRiX3wBS8w_ug8tI-G3pzhcRg6dTRio,5060
 aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=j3ckuNlUtv7lT922MbN0JhT9H0JpWAdx2mLPwao6uu8,7123
 aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
@@ -112,8 +112,8 @@ aiagents4pharma/talk2scholars/tools/s2/display_results.py,sha256=B8JJGohi1Eyx8C3
 aiagents4pharma/talk2scholars/tools/s2/multi_paper_rec.py,sha256=0Y3q8TkF_Phng9L7g1kk9Fhyit9UNitWurp03H0GZv8,4455
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=CcgFN7YuuQ9Vl1DJcldnnvPrswABKjNxeauK1rABps8,4176
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=irS-igdG8BZbVb0Z4VlIjzsyBlUfREd0v0_RlUM-0_U,4994
-aiagents4pharma-1.17.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.17.1.dist-info/METADATA,sha256=6co2HtNzvTLVFczemaajMlZ-7RrM9lmbYwRD3zcfolw,6744
-aiagents4pharma-1.17.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.17.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.17.1.dist-info/RECORD,,
+aiagents4pharma-1.18.0.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.18.0.dist-info/METADATA,sha256=0DruGN7wacwsdocwdBJoIYnwqd6aGxii98DHkPkCu48,6991
+aiagents4pharma-1.18.0.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+aiagents4pharma-1.18.0.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.18.0.dist-info/RECORD,,