aiagents4pharma 1.46.4__tar.gz → 1.47.0__tar.gz

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aiagents4pharma
-Version: 1.46.4
+Version: 1.47.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/aiagents4pharma/talk2aiagents4pharma/install.md

@@ -11,10 +11,6 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 _This agent is available on Docker Hub._
 
-**Prerequisites**
-
-- [Milvus](https://milvus.io) (for a vector database)
-
 ---
 
 #### 1. Download files
@@ -61,7 +57,7 @@ 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-1.46.4 → aiagents4pharma-1.47.0}/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-1.46.4 → aiagents4pharma-1.47.0}/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-1.47.0/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-1.46.4 → aiagents4pharma-1.47.0}/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-1.46.4 → aiagents4pharma-1.47.0}/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-1.47.0/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-1.46.4 → aiagents4pharma-1.47.0}/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-1.46.4 → aiagents4pharma-1.47.0}/aiagents4pharma/talk2knowledgegraphs/install.md

@@ -22,12 +22,6 @@ If your machine has NVIDIA GPU(s), please install the following this:
 
 _This agent is available on Docker Hub._
 
-**Prerequisites**
-
-- If your machine has NVIDIA GPU(s), please install [nvidia-container-toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/1.17.8/install-guide.html) (required for GPU support with Docker; enables containers to access NVIDIA GPUs for accelerated computing). After installing `nvidia-container-toolkit`, please restart Docker to ensure GPU support is enabled.
-
-- [Milvus](https://milvus.io) (for a vector database)
-
 ---
 
 #### 1. Download files
@@ -74,7 +68,7 @@ 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-1.46.4 → aiagents4pharma-1.47.0}/app/frontend/streamlit_app_talk2aiagents4pharma.py

@@ -213,7 +213,7 @@ with main_col1:
 
         # Help text
         st.button(
-            "Know more ↗",
+            "How to use this application ↗",
             #   icon="ℹ️",
             on_click=streamlit_utils.help_button,
             use_container_width=False,

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/app/frontend/streamlit_app_talk2biomodels.py

@@ -70,10 +70,7 @@ if needs("NVIDIA/"):
 
 missing = [var for var in needed_env if var not in os.environ]
 if missing:
-    st.warning(
-        "Missing environment settings for the selected provider(s): "
-        + ", ".join(missing)
-    )
+    st.warning("Missing environment settings for the selected provider(s): " + ", ".join(missing))
 
 ########################################################################################
 # Streamlit app
@@ -209,12 +206,8 @@ with main_col2:
                                     validate=r"^http://.*$",  # Ensure the link is valid
                                     display_text=r"^http://identifiers\.org/(.*?)$",
                                 ),
-                                "Species Name": st.column_config.TextColumn(
-                                    "Species Name"
-                                ),
-                                "Description": st.column_config.TextColumn(
-                                    "Description"
-                                ),
+                                "Species Name": st.column_config.TextColumn("Species Name"),
+                                "Description": st.column_config.TextColumn("Description"),
                                 "Database": st.column_config.TextColumn("Database"),
                             },
                         )
@@ -234,9 +227,7 @@ with main_col2:
                                 ),
                                 "name": st.column_config.TextColumn("Name"),
                                 "format": st.column_config.TextColumn("Format"),
-                                "submissionDate": st.column_config.TextColumn(
-                                    "Submission Date"
-                                ),
+                                "submissionDate": st.column_config.TextColumn("Submission Date"),
                             },
                         )
                 else:
@@ -266,15 +257,19 @@ with main_col2:
                             ),
                         },
                     )
-                    intro_prompt = "Tell your name and about yourself. Always start with a greeting."
-                    intro_prompt += " and tell about the tools you can run to perform analysis with short description."
-                    intro_prompt += " We have provided starter questions (separately) outisde your response."
+                    intro_prompt = (
+                        "Tell your name and about yourself. Always start with a greeting."
+                    )
+                    intro_prompt += " and tell about every tools you can run to perform analysis with short description."
+                    intro_prompt += (
+                        " We have provided starter questions (separately) outisde your response."
+                    )
                     intro_prompt += " Do not provide any questions by yourself. Let the users know that they can"
                     intro_prompt += " simply click on the questions to execute them."
+                    intro_prompt += " Let them know that they can check out the use cases"
                     intro_prompt += (
-                        " Let them know that they can check out the use cases"
+                        " and FAQs described in the link below. Be friendly and helpful."
                     )
-                    intro_prompt += " and FAQs described in the link below. Be friendly and helpful."
                     intro_prompt += "\n"
                     intro_prompt += "Here is the link to the use cases: [Use Cases](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2biomodels/cases/Case_1/)"
                     intro_prompt += "\n"
@@ -290,15 +285,11 @@ with main_col2:
                     assistant_msg = ChatMessage(
                         current_state.values["messages"][-1].content, role="assistant"
                     )
-                    st.session_state.messages.append(
-                        {"type": "message", "content": assistant_msg}
-                    )
+                    st.session_state.messages.append({"type": "message", "content": assistant_msg})
                     st.empty()
         if len(st.session_state.messages) <= 1:
             for count, question in enumerate(streamlit_utils.sample_questions()):
-                if st.button(
-                    f"Q{count+1}. {question}", key=f"sample_question_{count+1}"
-                ):
+                if st.button(f"Q{count + 1}. {question}", key=f"sample_question_{count + 1}"):
                     # Trigger the question
                     prompt = question
                 # Add button click to chat history
@@ -306,8 +297,8 @@ with main_col2:
                     {
                         "type": "button",
                         "question": question,
-                        "content": f"Q{count+1}. {question}",
-                        "key": f"sample_question_{count+1}",
+                        "content": f"Q{count + 1}. {question}",
+                        "key": f"sample_question_{count + 1}",
                     }
                 )
 
@@ -315,9 +306,7 @@ with main_col2:
         if prompt:
             # Create a key 'uploaded_file' to read the uploaded file
             if uploaded_sbml_file:
-                st.session_state.sbml_file_path = uploaded_sbml_file.read().decode(
-                    "utf-8"
-                )
+                st.session_state.sbml_file_path = uploaded_sbml_file.read().decode("utf-8")
 
             # Display user prompt
             prompt_msg = ChatMessage(prompt, role="user")

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/app/frontend/utils/streamlit_utils.py

@@ -1513,78 +1513,20 @@ def update_t2kg_embedding_model():
     )
 
 
-@st.dialog("Get started with Talk2Biomodels 🚀")
+@st.dialog("How to use this application 🚀")
 def help_button():
     """
     Function to display the help dialog.
     """
     st.markdown(
-        """I am an AI agent designed to assist you with biological
-modeling and simulations. I can assist with tasks such as:
-1. Search specific models in the BioModels database.
+        """**FAQs**
+- Talk2KnowledgeGraphs: [click here](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2knowledgegraphs/faq/)
+- Talk2Biomodels: [click here](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2biomodels/faq/)
 
-```
-Search models on Crohns disease
-```
-
-2. Extract information about models, including species, parameters, units,
-name and descriptions.
-
-```
-Briefly describe model 537 and
-its parameters related to drug dosage
-```
-
-3. Simulate models:
-    - Run simulations of models to see how they behave over time.
-    - Set the duration and the interval.
-    - Specify which species/parameters you want to include and their starting concentrations/values.
-    - Include recurring events.
-
-```
-Simulate the model 537 for 2016 hours and
-intervals 300 with an initial value
-of `DoseQ2W` set to 300 and `Dose` set to 0.
-```
-
-4. Answer questions about simulation results.
-
-```
-What is the concentration of species IL6 in serum
-at the end of simulation?
-```
-
-5. Create custom plots to visualize the simulation results.
-
-```
-Plot the concentration of all
-the interleukins over time.
-```
-
-6. Bring a model to a steady state and determine the concentration of a species at the steady state.
-
-```
-Bring BioModel 27 to a steady state,
-and then determine the Mpp concentration
-at the steady state.
-```
-
-7. Perform parameter scans to determine the effect of changing parameters on the model behavior.
-
-```
-How does the value of Pyruvate change in
-model 64 if the concentration of Extracellular Glucose
-is changed from 10 to 100 with a step size of 10?
-The simulation should run for 5 time units with an
-interval of 10.
-```
-
-8. Check out the [Use Cases](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2biomodels/cases/Case_1/)
-for more examples, and the [FAQs](https://virtualpatientengine.github.io/AIAgents4Pharma/talk2biomodels/faq/)
-for common questions.
-
-9. Provide feedback to the developers by clicking on the feedback button.
+**Video**
+- [Watch the app overview](https://www.youtube.com/watch?v=3cU_OxY4HiE)
 
+[![Watch the app overview](https://img.youtube.com/vi/3cU_OxY4HiE/0.jpg)](https://www.youtube.com/watch?v=3cU_OxY4HiE)
 """
     )
 

aiagents4pharma-1.47.0/docs/talk2biomodels/tools/get_annotation.md

@@ -0,0 +1 @@
+::: aiagents4pharma.talk2biomodels.tools.get_annotation

aiagents4pharma-1.47.0/docs/talk2biomodels/tools/parameter_scan.md

@@ -0,0 +1 @@
+::: aiagents4pharma.talk2biomodels.tools.parameter_scan

aiagents4pharma-1.47.0/docs/talk2biomodels/tools/save_model.md

@@ -0,0 +1 @@
+::: aiagents4pharma.talk2biomodels.tools.save_model

aiagents4pharma-1.47.0/docs/talk2biomodels/tools/steady_state.md

@@ -0,0 +1 @@
+::: aiagents4pharma.talk2biomodels.tools.steady_state

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/mkdocs.yml

@@ -32,10 +32,14 @@ nav:
       - Tools:
           - Search models: talk2biomodels/tools/search_models.md
           - Model information: talk2biomodels/tools/get_modelinfo.md
+          - Model annotation: talk2biomodels/tools/get_annotation.md
           - Simulate model: talk2biomodels/tools/simulate_model.md
           - Ask questions: talk2biomodels/tools/ask_question.md
           - Custom plots: talk2biomodels/tools/custom_plotter.md
           - Load biomodel: talk2biomodels/tools/load_biomodel.md
+          - Save model: talk2biomodels/tools/save_model.md
+          - Parameter scan: talk2biomodels/tools/parameter_scan.md
+          - Steady state: talk2biomodels/tools/steady_state.md
 
   - Talk2Cells:
       - Introduction: talk2cells/intro.md

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/package-lock.json

@@ -10,7 +10,7 @@
 				"@semantic-release/github": "^11.0.1",
 				"semantic-release": "^24.0.0"
 			},
-			"version": "1.46.4"
+			"version": "1.47.0"
 		},
 		"node_modules/@babel/code-frame": {
 			"version": "7.26.2",
@@ -10955,5 +10955,5 @@
 			"dev": true
 		}
 	},
-	"version": "1.46.4"
+	"version": "1.47.0"
 }

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/package.json

@@ -26,5 +26,5 @@
 			]
 		]
 	},
-	"version": "1.46.4"
+	"version": "1.47.0"
 }

{aiagents4pharma-1.46.4 → aiagents4pharma-1.47.0}/pyproject.toml

@@ -85,7 +85,7 @@ dependencies = [
   "cloudscraper==1.2.71",
   "azure-identity==1.24.0",
 ]
-version = "1.46.4"
+version = "1.47.0"
 
 [project.optional-dependencies]
 dev = [
@@ -133,7 +133,7 @@ extension-pkg-allow-list = ["pcst_fast"]
 disable = ["R0801", "R0902", "W0221", "W0122"]
 
 [tool.ruff]
-target-version = "1.46.4"
+target-version = "1.47.0"
 line-length = 100
 
 [tool.ruff.lint]
@@ -155,7 +155,7 @@ ignore = [
 "__init__.py" = ["F401"]
 
 [tool.mypy]
-python_version = "1.46.4"
+python_version = "1.47.0"
 warn_return_any = true
 warn_unused_configs = true
 disallow_untyped_defs = true