aiagents4pharma 1.46.5__py3-none-any.whl → 1.48.0__py3-none-any.whl

aiagents4pharma/talk2aiagents4pharma/Dockerfile

@@ -58,6 +58,7 @@ LABEL description="AI Agents for Pharma - Streamlit Application"
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
   ca-certificates \
   curl \
+  gnupg \
   libmagic1 \
   libopenblas0 \
   libomp5 \
@@ -66,6 +67,23 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
   && update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 1 \
   && update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1
 
+# Install CUDA runtime libraries required by cudf/cupy
+RUN curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub \
+    | gpg --dearmor -o /usr/share/keyrings/nvidia-cuda-keyring.gpg \
+  && echo "deb [signed-by=/usr/share/keyrings/nvidia-cuda-keyring.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/ /" \
+    > /etc/apt/sources.list.d/nvidia-cuda.list \
+  && apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+    cuda-cudart-12-6 \
+    cuda-cudart-dev-12-6 \
+    cuda-nvrtc-12-6 \
+    cuda-nvrtc-dev-12-6 \
+    libcublas-12-6 \
+    libcusparse-12-6 \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64
+
 # Copy UV virtual environment from build stage
 COPY --from=uv-install /opt/venv /opt/venv
 

aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2biomodels/agents/t2b_agent.py

@@ -20,6 +20,7 @@ from ..tools.get_annotation import GetAnnotationTool
 from ..tools.get_modelinfo import GetModelInfoTool
 from ..tools.parameter_scan import ParameterScanTool
 from ..tools.query_article import QueryArticle
+from ..tools.save_model import SaveModelTool
 from ..tools.search_models import SearchModelsTool
 from ..tools.simulate_model import SimulateModelTool
 from ..tools.steady_state import SteadyStateTool
@@ -54,6 +55,7 @@ def get_app(uniq_id, llm_model: BaseChatModel):
             ParameterScanTool(),
             GetAnnotationTool(),
             QueryArticle(),
+            SaveModelTool(),
         ]
     )
 

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -42,6 +42,7 @@ class Talk2Biomodels(AgentState):
     # 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]
+    model_as_string: Annotated[list, operator.add]
     dic_simulated_data: Annotated[list[dict], add_data]
     dic_scanned_data: Annotated[list[dict], add_data]
     dic_steady_state_data: Annotated[list[dict], add_data]

aiagents4pharma/talk2biomodels/tests/test_save_model.py

@@ -0,0 +1,47 @@
+"""
+Test cases for Talk2Biomodels.
+"""
+
+import tempfile
+
+from langchain_core.messages import HumanMessage
+from langchain_openai import ChatOpenAI
+
+from ..agents.t2b_agent import get_app
+
+LLM_MODEL = ChatOpenAI(model="gpt-4o-mini", temperature=0)
+
+
+def test_save_model_tool():
+    """
+    Test the save_model tool.
+    """
+    unique_id = 123
+    app = get_app(unique_id, llm_model=LLM_MODEL)
+    config = {"configurable": {"thread_id": unique_id}}
+    # Simulate a model
+    prompt = "Simulate model 64"
+    # Invoke the agent
+    app.invoke({"messages": [HumanMessage(content=prompt)]}, config=config)
+    current_state = app.get_state(config)
+    assert current_state.values["model_as_string"][-1] is not None
+    # Save a model without simulating
+    prompt = "Save the model"
+    # Invoke the agent
+    app.invoke({"messages": [HumanMessage(content=prompt)]}, config=config)
+    current_state = app.get_state(config)
+    assert current_state.values["model_as_string"][-1] is not None
+    # Create a temporary directory to save the model
+    with tempfile.TemporaryDirectory() as temp_dir:
+        # Save a model to the temporary directory
+        prompt = f"Simulate model 64 and save it model at {temp_dir}"
+        # Invoke the agent
+        app.invoke({"messages": [HumanMessage(content=prompt)]}, config=config)
+        current_state = app.get_state(config)
+        assert current_state.values["model_as_string"][-1] is not None
+    # Simulate and save a model in non-existing path
+    prompt = "Simulate model 64 and then save the model at /xyz/"
+    # Invoke the agent
+    app.invoke({"messages": [HumanMessage(content=prompt)]}, config=config)
+    current_state = app.get_state(config)
+    assert current_state.values["model_as_string"][-1] is not None

aiagents4pharma/talk2biomodels/tests/test_simulate_model.py

@@ -40,3 +40,5 @@ def test_simulate_model_tool():
     assert "1,3-bisphosphoglycerate" in dic_simulated_data[0]["data"]
     # Check if the data of the second model contains
     assert "mTORC2" in dic_simulated_data[1]["data"]
+    # Check if the model_as_string is not None
+    assert current_state.values["model_as_string"][-1] is not None

aiagents4pharma/talk2biomodels/tools/__init__.py

@@ -10,6 +10,7 @@ from . import (
     load_biomodel,
     parameter_scan,
     query_article,
+    save_model,
     search_models,
     simulate_model,
     steady_state,

aiagents4pharma/talk2biomodels/tools/save_model.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python3
+
+"""
+Tool for saving models.
+"""
+
+import logging
+import os
+from typing import Annotated
+
+from langchain_core.messages import ToolMessage
+from langchain_core.tools import BaseTool
+from langchain_core.tools.base import InjectedToolCallId
+from langgraph.prebuilt import InjectedState
+from langgraph.types import Command
+from pydantic import BaseModel, Field
+
+# Initialize logger
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class SaveModelInput(BaseModel):
+    """
+    Input schema for the save model tool.
+    """
+
+    path_to_folder: str = Field(
+        description="Path to folder to save the model. Keep it to . if not provided.", default="."
+    )
+    output_filename: str = Field(
+        description="Filename to save the model as. Default is 'saved_model.xml'.",
+        default="saved_model.xml",
+    )
+    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 SaveModelTool(BaseTool):
+    """
+    Tool for saving a model.
+    """
+
+    name: str = "save_model"
+    description: str = "A tool to save the current biomodel to a \
+                        user specified path with the default filename\
+                         'saved_model.xml'"
+    args_schema: type[BaseModel] = SaveModelInput
+    return_direct: bool = False
+
+    def _run(
+        self,
+        tool_call_id: Annotated[str, InjectedToolCallId],
+        state: Annotated[dict, InjectedState],
+        path_to_folder: str = ".",
+        output_filename: str = "saved_model.xml",
+    ) -> Command:
+        """
+        Run the tool.
+
+        Args:
+            path (str): The path to save the model.
+            tool_call_id (str): The tool call ID.
+
+        Returns:
+
+        """
+        logger.log(
+            logging.INFO,
+            "Saving model to path: %s with filename: %s",
+            path_to_folder,
+            output_filename,
+        )
+        # Check if path does not exist
+        if not os.path.exists(path_to_folder):
+            content = f"Error: Path {path_to_folder} does not exist."
+            logger.error(content)
+        else:
+            logger.info("Saving now")
+            # Save the model to the specified path
+            with open(os.path.join(path_to_folder, output_filename), "w", encoding="utf-8") as f:
+                f.write(state["model_as_string"][-1])
+            content = f"Model saved successfully to {path_to_folder}/{output_filename}."
+            logger.info(content)
+        # Return the updated state of the tool
+        return Command(
+            update={
+                # update the message history
+                "messages": [
+                    ToolMessage(
+                        content=content,
+                        tool_call_id=tool_call_id,
+                    )
+                ],
+            }
+        )

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -7,6 +7,7 @@ Tool for simulating a model.
 import logging
 from typing import Annotated
 
+import basico
 from langchain_core.messages import ToolMessage
 from langchain_core.tools import BaseTool
 from langchain_core.tools.base import InjectedToolCallId
@@ -116,6 +117,7 @@ class SimulateModelTool(BaseTool):
             "model_id": [sys_bio_model.biomodel_id],
             "sbml_file_path": [sbml_file_path],
             "dic_simulated_data": [dic_simulated_data],
+            "model_as_string": [basico.model_io.save_model_to_string()],
         }.items():
             if value:
                 dic_updated_state_for_model[key] = value

aiagents4pharma/talk2knowledgegraphs/Dockerfile

@@ -58,6 +58,7 @@ LABEL description="AI Agents for Pharma - Knowledge Graphs Application"
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
   ca-certificates \
   curl \
+  gnupg \
   libmagic1 \
   libopenblas0 \
   libomp5 \
@@ -66,6 +67,23 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-ins
   && update-alternatives --install /usr/bin/python3 python3 /usr/bin/python${PYTHON_VERSION} 1 \
   && update-alternatives --install /usr/bin/python python /usr/bin/python${PYTHON_VERSION} 1
 
+# Install CUDA runtime libraries required by cudf/cupy
+RUN curl -fsSL https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/3bf863cc.pub \
+  | gpg --dearmor -o /usr/share/keyrings/nvidia-cuda-keyring.gpg \
+  && echo "deb [signed-by=/usr/share/keyrings/nvidia-cuda-keyring.gpg] https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/ /" \
+  > /etc/apt/sources.list.d/nvidia-cuda.list \
+  && apt-get update \
+  && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
+  cuda-cudart-12-6 \
+  cuda-cudart-dev-12-6 \
+  cuda-nvrtc-12-6 \
+  cuda-nvrtc-dev-12-6 \
+  libcublas-12-6 \
+  libcusparse-12-6 \
+  && rm -rf /var/lib/apt/lists/*
+
+ENV LD_LIBRARY_PATH=/usr/local/cuda/lib64
+
 # Copy UV virtual environment from build stage
 COPY --from=uv-install /opt/venv /opt/venv
 

aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example

@@ -15,7 +15,7 @@ MILVUS_HOST=localhost
 MILVUS_PORT=19530
 MILVUS_USER=root
 MILVUS_PASSWORD=Milvus
-MILVUS_DATABASE=your_database_name_here
+MILVUS_DATABASE=t2kg_primekg
 
 # Specify the data directory for multimodal data to your own data directory
 # DATA_DIR=/your_absolute_path_to_your_data_dir/

aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py

@@ -150,6 +150,7 @@ class DynamicDataLoader:
         self.normalize_vectors = self.use_gpu  # Only normalize for GPU (original logic)
         self.vector_index_type = "GPU_CAGRA" if self.use_gpu else "HNSW"
         self.metric_type = "IP" if self.use_gpu else "COSINE"
+        self.vector_index_params = self._build_vector_index_params()
 
         logger.info("Loader Configuration:")
         logger.info("  Using GPU acceleration: %s", self.use_gpu)
@@ -284,6 +285,29 @@ class DynamicDataLoader:
             else:
                 return list(data)
 
+    def _build_vector_index_params(self) -> dict[str, Any]:
+        """Return index params tuned for the selected backend."""
+        base_params: dict[str, Any] = {
+            "index_type": self.vector_index_type,
+            "metric_type": self.metric_type,
+        }
+
+        if self.vector_index_type == "GPU_CAGRA":
+            base_params["params"] = {
+                "graph_degree": int(os.getenv("CAGRA_GRAPH_DEGREE", "32")),
+                "intermediate_graph_degree": int(
+                    os.getenv("CAGRA_INTERMEDIATE_GRAPH_DEGREE", "40")
+                ),
+                "search_width": int(os.getenv("CAGRA_SEARCH_WIDTH", "64")),
+            }
+        elif self.vector_index_type == "HNSW":
+            base_params["params"] = {
+                "M": int(os.getenv("HNSW_M", "16")),
+                "efConstruction": int(os.getenv("HNSW_EF_CONSTRUCTION", "200")),
+            }
+
+        return base_params
+
     def connect_to_milvus(self):
         """Connect to Milvus and setup database."""
         logger.info("Connecting to Milvus at %s:%s", self.milvus_host, self.milvus_port)
@@ -442,10 +466,7 @@ class DynamicDataLoader:
         )
         collection.create_index(
             field_name="desc_emb",
-            index_params={
-                "index_type": self.vector_index_type,
-                "metric_type": self.metric_type,
-            },
+            index_params=self.vector_index_params.copy(),
             index_name="desc_emb_index",
         )
 
@@ -569,18 +590,12 @@ class DynamicDataLoader:
             )
             collection.create_index(
                 field_name="desc_emb",
-                index_params={
-                    "index_type": self.vector_index_type,
-                    "metric_type": self.metric_type,
-                },
+                index_params=self.vector_index_params.copy(),
                 index_name="desc_emb_index",
             )
             collection.create_index(
                 field_name="feat_emb",
-                index_params={
-                    "index_type": self.vector_index_type,
-                    "metric_type": self.metric_type,
-                },
+                index_params=self.vector_index_params.copy(),
                 index_name="feat_emb_index",
             )
 
@@ -706,10 +721,7 @@ class DynamicDataLoader:
         )
         collection.create_index(
             field_name="feat_emb",
-            index_params={
-                "index_type": self.vector_index_type,
-                "metric_type": self.metric_type,
-            },
+            index_params=self.vector_index_params.copy(),
             index_name="feat_emb_index",
         )
 
@@ -796,8 +808,7 @@ class DynamicDataLoader:
                 logger.info("  %s: %d entities", coll, collection.num_entities)
 
         except Exception:
-            logger.error("Error occurred during data loading")
-            logger.debug("Detailed error information available in debug mode")
+            logger.exception("Error occurred during data loading")
             raise
 
 
@@ -867,8 +878,7 @@ def main():
         logger.info("Data loading interrupted by user")
         sys.exit(1)
     except Exception:
-        logger.error("Fatal error occurred during data loading")
-        logger.debug("Detailed error information available in debug mode")
+        logger.exception("Fatal error occurred during data loading")
         sys.exit(1)
 
 

{aiagents4pharma-1.46.5.dist-info → aiagents4pharma-1.48.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.46.5
+Version: 1.48.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.46.5.dist-info → aiagents4pharma-1.48.0.dist-info}/RECORD

@@ -1,6 +1,6 @@
 aiagents4pharma/__init__.py,sha256=B-tLRCbWgti-jlCnW_qknNKrG4j1t9nhBb-gXaz0Wtg,187
 aiagents4pharma/talk2aiagents4pharma/.dockerignore,sha256=-hAM7RzkGbjDeU411-kXOmYzNfl3Z9OlLWvN9zMDAXE,89
-aiagents4pharma/talk2aiagents4pharma/Dockerfile,sha256=J2QvwifcCxtz9EzPaq99zhSygHV9ADsB5ZQ_cmiwATI,3533
+aiagents4pharma/talk2aiagents4pharma/Dockerfile,sha256=DScrZujkLc5OY79XP5KSAfxiniQlZ5MWHkbtw534JY4,4295
 aiagents4pharma/talk2aiagents4pharma/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3pqLslG7suaCk,74
 aiagents4pharma/talk2aiagents4pharma/__init__.py,sha256=gjVTAhBHKPEFBbv_2T-MWuDdwHhAKfWIo-lQSrcsLNE,97
 aiagents4pharma/talk2aiagents4pharma/install.md,sha256=5oyy9P8fd03x3f_jOFZTGg2G1AzxMIOrH2vVd8ZS4Iw,4201
@@ -13,9 +13,9 @@ aiagents4pharma/talk2aiagents4pharma/configs/agents/main_agent/default.yaml,sha2
 aiagents4pharma/talk2aiagents4pharma/configs/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 aiagents4pharma/talk2aiagents4pharma/configs/app/frontend/default.yaml,sha256=BpDv_Bau0F7xDPzMHVYxedKpZQAPdo0rAsRnfH32-U8,3470
-aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2aiagents4pharma/docker-compose/cpu/docker-compose.yml,sha256=2I8jyzaFXSGsBMMFOZ4Hz7hAH3A-ELpoYCphkpT_8rA,2631
-aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2aiagents4pharma/docker-compose/gpu/docker-compose.yml,sha256=bZwpaLynxyY6YOj2Sdz3MEVKgBY-FFXTC_K_KmZrMuM,3001
 aiagents4pharma/talk2aiagents4pharma/states/__init__.py,sha256=VuVAFmoH8p2erE-mYiaa0uoqTuFynBcXia5Y8lmjI34,109
 aiagents4pharma/talk2aiagents4pharma/states/state_talk2aiagents4pharma.py,sha256=ahquXi8hg6Bk1ttskl9QaYdHq4rDWa_bK7hu81E75M4,468
@@ -27,7 +27,7 @@ aiagents4pharma/talk2biomodels/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3p
 aiagents4pharma/talk2biomodels/__init__.py,sha256=DxARZJu91m4WHW4PBSZvlMb1MCbjvkZg1YUnYJXMBSA,117
 aiagents4pharma/talk2biomodels/install.md,sha256=9YAEeW_vG5hv7WiMnNEzgKQIgVyHnpk1IIWXg_jhLxE,1520
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=4wPy6hWRJksX6z8qX1cVjFctZLpsja8JMngKHqn49N4,129
-aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=b_9pjnY3VGPRrzy-LCFrbJCkP1PT3M30NiQq6gbavaA,3267
+aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=hf-JTzcaOQIMG97qJb7EKe-jehghGiyXbbd9qSHFVIk,3341
 aiagents4pharma/talk2biomodels/api/__init__.py,sha256=KGok9mCa6RT8whDj3jT3kcpFO1yHxk5vVD8IExsI5Bc,92
 aiagents4pharma/talk2biomodels/api/ols.py,sha256=QSvbsD0V07-w0OU-wPQ4EypXi9bn_xl0NyliZQxRvCU,2173
 aiagents4pharma/talk2biomodels/api/uniprot.py,sha256=jXoyd7BhIQA9JNaGMVPzORpQ5k1Ix9iYYduMv6YG7hw,1147
@@ -50,7 +50,7 @@ aiagents4pharma/talk2biomodels/models/__init__.py,sha256=ykurWrvOAkx4ooknggsu6Ri
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=M9KVnLDNAWfM0MAxSDpAJKIq1R8ezjDW1C3C9oLsRNU,4998
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=dwoBK_g7aXVv7B97CqILTvsxGEbNH_iPLWQ1SoPg4cg,1928
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=Rxe64WLgcNKnKaEIPv3rXmwBUUrl1SP-B6F4Unf723w,140
-aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=kKtVBfSK92hjnG2zn9UVpSeeD4XnD59rusmHk98XBDI,1511
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=NLbkXS9857KqKdjZeZA_RMeulRhL4PG-nSjVOIzYD8c,1562
 aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml,sha256=RkWbstfLrT1mAfOtZf7JsBz6poyWg6-5G7H_IdVXEXg,72630
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=U3PsTiUZaUBD1IZanFGkDIOdFieDVJtGKQ5-woYUo8c,45
 aiagents4pharma/talk2biomodels/tests/article_on_model_537.pdf,sha256=rfBnG9XSGRZodq-NQsouQQ3dvm4JKcrAqEkoAQJmuDc,470738
@@ -63,11 +63,12 @@ aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=t8jR45pX7hKBGOjX
 aiagents4pharma/talk2biomodels/tests/test_load_biomodel.py,sha256=8nVSDa8_z85dyvxa8aYGQR0YGZDtpzLF5HhBmifCk6w,895
 aiagents4pharma/talk2biomodels/tests/test_param_scan.py,sha256=OFUeGlnEFAcSR3JODH0Yl2MVUBjiPqUNltcH-ICfSsE,2655
 aiagents4pharma/talk2biomodels/tests/test_query_article.py,sha256=IZ0oDRPmVxD-g6vQ-uGSiYaJ1hf_rTcnda5u_J3rE2Y,6929
+aiagents4pharma/talk2biomodels/tests/test_save_model.py,sha256=XgKYTNFbWQmKgF5mseTg5HrJhmN-Hg20v0hxkmwWh9U,1764
 aiagents4pharma/talk2biomodels/tests/test_search_models.py,sha256=JuNvBz2i3a82c1SVwxKBlEIm98p91zzbnpnjMmWOg9g,1201
-aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=NEP6hKoq_xzNxdHZ1xDQCGQV6ReVzfoRAFa4ST4CBPI,1544
+aiagents4pharma/talk2biomodels/tests/test_simulate_model.py,sha256=JmE28fBdl4I37AX6x8lK8PK3rNdvj5ohJn7u95gG11M,1658
 aiagents4pharma/talk2biomodels/tests/test_steady_state.py,sha256=5G3ug0mZDxQR8gCl3Xv6z3P1hfzUtXmyigYcVG9BfXE,3512
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=poMxOsKhg8USnptHPUjr6DptsO_HBZgV0G0C0lqF57s,2093
-aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=j6wTW09BOwFMzHERfJbsajctDsNxJDtWJHUE3FmTu-A,279
+aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=viqx475FR5-gP10lmVg7u8wAWUZSHXe3bbQzF5N9oMk,295
 aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=IbolM6zbYKHd_UCfLMa8bawt9fJH59cCUtkLB_wtxKI,4495
 aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=dk5HUmPwSTIRp2sbd8Q8__fwSE8m13UseonvcpyDs00,6636
 aiagents4pharma/talk2biomodels/tools/get_annotation.py,sha256=oHERHdY4KinQFg9udufEgJP3tE3x0gtoWWy4Kna9H78,12854
@@ -76,8 +77,9 @@ aiagents4pharma/talk2biomodels/tools/load_arguments.py,sha256=LZQNkAikXhG0AKRnfL
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=025-E5qo2uiJVvHIhyeDh1tfmXTeIguSgS0KIY0LiyY,1208
 aiagents4pharma/talk2biomodels/tools/parameter_scan.py,sha256=Hvq4igK0XBQ45YxhZpVNkVHWmaum7V3HGtIaaW8P_S0,11962
 aiagents4pharma/talk2biomodels/tools/query_article.py,sha256=f2KMhKuWXqs8MidZO367JEsXHIK8NsOm_YUszH6qwpM,2152
+aiagents4pharma/talk2biomodels/tools/save_model.py,sha256=2TEnzbt5z98qjL9eRZnXbS05iGuC7QylM-51HMfrjNE,2994
 aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=DWC4bHDnOiKBp534MNMN_AJ1rc21dXt768SvMRL6mrU,3133
-aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=bIA-4VDD-CJMqCNJ-dsquCQATob_9a-UGO5EhK2InJk,5098
+aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=4QU03Xp-AU_va0QXGQZN7btn_Dh-ALrZA3K1JqDXH_4,5185
 aiagents4pharma/talk2biomodels/tools/steady_state.py,sha256=zNbSDOITw9oomEqGSRqI224jZGsMw8LBka-2rG3moxs,7033
 aiagents4pharma/talk2biomodels/tools/utils.py,sha256=bpVtS-5_oDGdgjbsLeIVcOo1BJvS_pyg8PDg9z2dG5Q,521
 aiagents4pharma/talk2cells/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3pqLslG7suaCk,74
@@ -92,12 +94,12 @@ aiagents4pharma/talk2cells/tools/scp_agent/__init__.py,sha256=DAJp26kugSdVHfFyVR
 aiagents4pharma/talk2cells/tools/scp_agent/display_studies.py,sha256=nQltO147j1cFWUJ9mxg3JlWBLsqFivhJ93g1G7gWZko,602
 aiagents4pharma/talk2cells/tools/scp_agent/search_studies.py,sha256=xjsgYJ8Bn8RIzIu_bgn8D_2I8wzLOJeu9evT_vF15mM,2647
 aiagents4pharma/talk2knowledgegraphs/.dockerignore,sha256=-hAM7RzkGbjDeU411-kXOmYzNfl3Z9OlLWvN9zMDAXE,89
-aiagents4pharma/talk2knowledgegraphs/Dockerfile,sha256=qGy6I4oBvQonpDEANQaCW-5JMtHPdd2HKc-JJgoCyYQ,3384
+aiagents4pharma/talk2knowledgegraphs/Dockerfile,sha256=0Do2gcsbEeh07xnPNuApTV77bfEbhAYSdMEwE3U0CKU,4130
 aiagents4pharma/talk2knowledgegraphs/README.md,sha256=0eGxj7jxi_LrCvX-4I4KrQv-7T2ivo3pqLslG7suaCk,74
 aiagents4pharma/talk2knowledgegraphs/__init__.py,sha256=ZztaRzRlovSXtVX3i9Rvf84ivIjPn8RMPiYRkbkEJ0E,114
 aiagents4pharma/talk2knowledgegraphs/entrypoint.sh,sha256=EK_jGau1VuW1uTmFWZcKhLMK9VanC5l3q9axF4ZYgmI,5758
 aiagents4pharma/talk2knowledgegraphs/install.md,sha256=1rCv2e6ywb-kZOxtqFJ25qpWHl2MCa9bW6nHYHfxJMI,5555
-aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=D5BB700QshEhY6paByXNLyMjOYyO4Csm4ODgbeeWfmc,35616
+aiagents4pharma/talk2knowledgegraphs/milvus_data_dump.py,sha256=RyPYjtF49DxL7MIWmVUprw0Wpu4HErHOAOQ2_wLUfVI,36095
 aiagents4pharma/talk2knowledgegraphs/agents/__init__.py,sha256=ugUvVYEdjbZ3y_dogfF5hpQ3lFPFrAvLSydlcpbkGo0,93
 aiagents4pharma/talk2knowledgegraphs/agents/t2kg_agent.py,sha256=GDeSjJNhAqQWagZOxAWUKqDhzUohHViSsu444W9SzRQ,3240
 aiagents4pharma/talk2knowledgegraphs/configs/__init__.py,sha256=H-yhTbJ_RXBLe3XSto5x6FmVrgbi7y1WKEfiwmKzLAk,87
@@ -127,9 +129,9 @@ aiagents4pharma/talk2knowledgegraphs/datasets/biobridge_primekg.py,sha256=M6NtpM
 aiagents4pharma/talk2knowledgegraphs/datasets/dataset.py,sha256=ls0e15uudIbb4zwHMHxjEovmH145RJ_hPeZni89KSnM,411
 aiagents4pharma/talk2knowledgegraphs/datasets/primekg.py,sha256=1WHlQCAyKjpBiX3JnIsSohUZe8Yi5pY-VDP4tCugxkg,7709
 aiagents4pharma/talk2knowledgegraphs/datasets/starkqa_primekg.py,sha256=JtP-jNIFDA3xQbzy5DkK2OHin5NnbWUGa_EJ_1OH6vE,7483
-aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2knowledgegraphs/docker-compose/cpu/docker-compose.yml,sha256=7BNUIkwP0cAUH1jznun5-RgsIAZisegLFGiiUZG9F1Y,2631
-aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example,sha256=twsuiEN-FczXfka40_bVoSQXaMDR_3J3ESKCqU4qSkg,585
+aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/.env.example,sha256=mfwCKG0bv6_IjEfIdQlEb6cnXsbaeAqC_U4kcIa03o0,574
 aiagents4pharma/talk2knowledgegraphs/docker-compose/gpu/docker-compose.yml,sha256=MVWmuxTmTTq3g4MFi9HtvHY0F4MegtprZ7FGIt-60Ms,3001
 aiagents4pharma/talk2knowledgegraphs/states/__init__.py,sha256=9X3zHxvtAJFQ0s0VLZ_-iBn4rMVfZWk5CQiWEKJkr0c,109
 aiagents4pharma/talk2knowledgegraphs/states/state_talk2knowledgegraphs.py,sha256=QECNXd8IWDh3WlMvePcd2T6G5XqjOI9EkZdWmICcCT0,1088
@@ -328,7 +330,7 @@ aiagents4pharma/talk2scholars/tools/zotero/utils/review_helper.py,sha256=-q-UuzP
 aiagents4pharma/talk2scholars/tools/zotero/utils/write_helper.py,sha256=K1EatPfC-riGyFmkOAS3ReNBaGPY-znne1KqOnFahkI,7339
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_path.py,sha256=sKkfJu3u4LKSZjfoQRfeqz26IESHRwBtcSDzLMLlJMo,6311
 aiagents4pharma/talk2scholars/tools/zotero/utils/zotero_pdf_downloader.py,sha256=DBrF5IiF7VRP58hUK8T9LST3lQWLFixLUfnpMSTccoQ,4614
-aiagents4pharma-1.46.5.dist-info/METADATA,sha256=Tnoq6TWzRepVimi-VimoYIP_hTsz24Z9jk328UuAfxw,17035
-aiagents4pharma-1.46.5.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-aiagents4pharma-1.46.5.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.46.5.dist-info/RECORD,,
+aiagents4pharma-1.48.0.dist-info/METADATA,sha256=LAfYILDy3HPzU2RdU1icFrP6s1N9pooLdFtRSaRzmfE,17035
+aiagents4pharma-1.48.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+aiagents4pharma-1.48.0.dist-info/licenses/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.48.0.dist-info/RECORD,,