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agents.py

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+from crewai import Agent
+import google.generativeai as genai
+from tools import pmc_search, google_scholar_search, today_tool
+import os
+
+def get_gemini_llm():
+    genai.configure(api_key=os.getenv('GEMINI_API_KEY'))
+    model = genai.GenerativeModel('gemini-pro')
+    return model
+
+def get_researcher_agent(verbose):
+    return Agent(
+        role="Research Scientist",
+        goal="Research and collect scientific articles on the given topic from PMC and Google Scholar.",
+        backstory="""You are an expert research scientist specializing in comprehensive literature review. 
+                  Your task is to collect at least 20 relevant scientific articles using PMC and Google Scholar.
+                  You should ensure the articles are recent and relevant to the topic.""",
+        llm=get_gemini_llm(),
+        tools=[pmc_search, google_scholar_search],
+        allow_delegation=False,
+        verbose=verbose
+    )
+
+def get_writer_agent(verbose):
+    return Agent(
+        role="Scientific Writer",
+        goal="Write a comprehensive scientific paper based on the collected research.",
+        backstory="""You are an experienced scientific writer with expertise in academic publishing.
+                  Your task is to write a well-structured scientific paper following the standard format:
+                  Introduction, Materials and Methods, Results, Discussion, Conclusion, and References.
+                  Results and Discussion sections should be at least one page long.
+                  Use proper APA citation format for all references.""",
+        llm=get_gemini_llm(),
+        tools=[today_tool],
+        allow_delegation=False,
+        verbose=verbose
+    )

app.py

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+import gradio as gr
+import os
+from dotenv import load_dotenv
+from crew import get_crew
+import threading
+
+# Load environment variables
+load_dotenv()
+
+# Global lock for thread safety
+lock = threading.Lock()
+
+VERBOSE = False
+
+def invoke(topic):
+    """Generate scientific paper based on the topic"""
+    if not topic:
+        raise gr.Error("Topic is required.")
+    
+    with lock:
+        # Generate the paper
+        paper = str(get_crew(VERBOSE).kickoff(inputs={"topic": topic}))
+        return paper
+
+# Create the Gradio interface
+css = """
+.gradio-container {
+    font-family: 'Arial', sans-serif;
+}
+.paper-output {
+    font-size: 16px;
+    line-height: 1.6;
+    padding: 20px;
+    background: #f9f9f9;
+    border-radius: 10px;
+    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
+}
+"""
+
+demo = gr.Interface(
+    fn=invoke,
+    inputs=[
+        gr.Textbox(
+            label="Research Topic",
+            placeholder="Enter your research topic...",
+            lines=2
+        )
+    ],
+    outputs=[
+        gr.Markdown(
+            label="Generated Scientific Paper",
+            elem_classes="paper-output"
+        )
+    ],
+    title="AI Scientific Paper Generator",
+    description="""This application uses AI agents to generate comprehensive scientific papers. 
+                   The first agent researches your topic using PubMed Central and Google Scholar, 
+                   collecting at least 20 relevant articles. The second agent then synthesizes this 
+                   research into a well-structured scientific paper with proper citations.
+                   
+                   Created by Dr. Fernando Ly""",
+    article="""### How it works
+               1. Enter your research topic
+               2. The Research Agent will collect relevant scientific articles
+               3. The Writing Agent will generate a structured paper with:
+                  - Introduction
+                  - Materials and Methods
+                  - Results
+                  - Discussion
+                  - Conclusion
+                  - References (APA format)
+               
+               The paper will include proper citations and be based on real scientific literature.""",
+    css=css,
+    theme=gr.themes.Soft(
+        primary_hue="blue",
+        secondary_hue="gray"
+    )
+)
+
+# Launch the app
+if __name__ == "__main__":
+    demo.launch()

crew.py

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+from crewai import Crew, Process
+from agents import get_researcher_agent, get_writer_agent
+from tasks import get_research_task, get_writing_task
+
+def get_crew(verbose=False):
+    # Create Agents
+    researcher = get_researcher_agent(verbose)
+    writer = get_writer_agent(verbose)
+    
+    # Create Tasks
+    research_task = get_research_task(researcher)
+    writing_task = get_writing_task(writer)
+    
+    # Create Crew
+    crew = Crew(
+        agents=[researcher, writer],
+        tasks=[research_task, writing_task],
+        verbose=verbose,
+        process=Process.sequential
+    )
+    
+    return crew

requirements.txt

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+crewai==0.11.0
+google-generativeai==0.3.2
+scholarly==1.7.11
+biopython==1.83
+beautifulsoup4==4.12.2
+python-dotenv==1.0.0
+gradio==4.8.0

tasks.py

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+from crewai import Task
+
+def get_research_task(agent):
+    return Task(
+        description="""Research the given topic extensively using PMC and Google Scholar.
+                      1. Search for at least 20 relevant scientific articles
+                      2. For each article collect:
+                         - Title
+                         - Authors
+                         - Abstract
+                         - Key findings
+                         - Publication year
+                      3. Ensure articles are recent and from reputable sources
+                      4. Organize the information in a structured format
+                      5. Provide a brief summary of the collective findings""",
+        agent=agent
+    )
+
+def get_writing_task(agent):
+    return Task(
+        description="""Write a comprehensive scientific paper based on the research provided.
+                      The paper must follow this structure:
+                      1. Introduction:
+                         - Background of the topic
+                         - Research gap
+                         - Objectives
+                      2. Materials and Methods:
+                         - Research methodology
+                         - Data collection process
+                         - Analysis methods
+                      3. Results (at least one page):
+                         - Key findings from the literature
+                         - Data synthesis
+                         - Statistical analysis if applicable
+                      4. Discussion (at least one page):
+                         - Interpretation of results
+                         - Comparison with existing literature
+                         - Implications
+                         - Limitations
+                      5. Conclusion:
+                         - Summary of findings
+                         - Future research directions
+                      6. References:
+                         - All citations in APA format
+                         - Minimum 20 references
+                      
+                      Important:
+                      - Use proper academic writing style
+                      - Include in-text citations
+                      - Maintain logical flow between sections
+                      - Support claims with evidence from the literature""",
+        agent=agent
+    )

tools.py

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+from langchain.tools import tool
+from scholarly import scholarly
+from Bio import Entrez
+from bs4 import BeautifulSoup
+import requests
+import datetime
+
+@tool
+def pmc_search(query: str) -> str:
+    """Search PubMed Central (PMC) for articles"""
+    Entrez.email = "[email protected]"
+    handle = Entrez.esearch(db="pmc", term=query, retmax=10)
+    record = Entrez.read(handle)
+    handle.close()
+    
+    articles = []
+    for id in record["IdList"]:
+        handle = Entrez.efetch(db="pmc", id=id, rettype="full", retmode="xml")
+        article = BeautifulSoup(handle.read(), 'xml')
+        handle.close()
+        
+        title = article.find("article-title")
+        title = title.text if title else "No title"
+        
+        abstract = article.find("abstract")
+        abstract = abstract.text if abstract else "No abstract"
+        
+        articles.append({
+            "id": id,
+            "title": title,
+            "abstract": abstract
+        })
+    
+    return str(articles)
+
+@tool
+def google_scholar_search(query: str) -> str:
+    """Search Google Scholar for articles"""
+    search_query = scholarly.search_pubs(query)
+    results = []
+    count = 0
+    
+    for result in search_query:
+        if count >= 10:
+            break
+        pub = {
+            "title": result.bib.get('title', 'No title'),
+            "author": result.bib.get('author', 'No author'),
+            "year": result.bib.get('year', 'No year'),
+            "abstract": result.bib.get('abstract', 'No abstract')
+        }
+        results.append(pub)
+        count += 1
+    
+    return str(results)
+
+@tool
+def today_tool() -> str:
+    """Get today's date"""
+    return str(datetime.date.today())