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Skillsalterlab-denario

alterlab-denario

Writing & research

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Updated 10-15 19:56

About this skill

Denario

Overview

Denario (by AstroPilot-AI) is a multiagent AI system designed to automate scientific research workflows from a described dataset through publication-ready manuscripts. It implements agents with AG2 and LangGraph, using cmbagent as the research-analysis backend, to handle hypothesis generation, methodology development, computational analysis, and paper writing.

Source: https://github.com/AstroPilot-AI/Denario | Docs: https://denario.readthedocs.io | Paper: arXiv:2510.26887 (v1.0, Nov 2025).

When to Use This Skill

Use this skill when:

  • Analyzing datasets to generate novel research hypotheses
  • Developing structured research methodologies
  • Executing computational experiments and generating visualizations
  • Conducting literature searches for research context
  • Writing journal-formatted LaTeX papers from research results
  • Automating the complete research pipeline from data to publication

Does NOT Trigger

Scenario Use Instead
A cited literature review or fact-check with no dataset to analyze alterlab-deep-research
Coordinating research → writing → review → revision for your own manuscript alterlab-research-pipeline
Drafting or revising a paper you are writing yourself (IMRaD, bilingual abstract) alterlab-paper-writer
LLM-driven hypothesis generation and testing on a tabular dataset (HypoGeniC) alterlab-hypogenic
Consulting-style market or industry report alterlab-market-research

Denario output is AI-generated end to end: treat its ideas, code, results, and citations as drafts that a researcher must verify, and disclose the AI assistance in any resulting manuscript.

Installation

Install with uv (recommended). Quote the extra so zsh does not glob [app]:

uv init
uv add "denario[app]"

The [app] extra pulls in the Streamlit GUI (DenarioApp); omit it for headless/library use. For Docker deployment or building from source, see references/installation.md.

LLM API Configuration

On init, Denario reads provider keys from the environment via its KeyManager (no config object). The relevant variables:

  • OPENAI_API_KEY — required (the analysis/results module needs it; OpenAI models are the cmbagent-mode defaults).
  • GOOGLE_API_KEY — optional, a Gemini API key, needed whenever a Gemini model is selected (the mode="fast", check_idea, and get_paper defaults are Gemini). Note this is a plain Gemini key, not a Vertex AI service-account JSON.
  • ANTHROPIC_API_KEY — optional (Claude).
  • PERPLEXITY_API_KEY — optional, only for citation search.

Set them in the shell or a .env in the working directory (KeyManager calls load_dotenv() itself). Google Vertex AI is also supported as a backend; see references/llm_configuration.md for that and .env/Docker details.

Model IDs: pass current ones explicitly

denario 1.0.1 (the current release; the GitHub master is unchanged as of 2026-09) hard-codes defaults that providers have since retired, so choose models per call instead of relying on them:

  • mode="fast" (get_idea/get_method) defaults to gemini-2.0-flash, which Google shut down on 2026-06-01 — the default path now fails. Pass llm= explicitly.
  • The cmbagent defaults (mode="cmbagent" and get_results) use o3-mini (OpenAI shutdown scheduled for 2026-10-23) alongside gpt-4o and gpt-4.1; override every o3-mini role: idea_hater_model, plan_reviewer_model, formatter_model, and (in get_results) researcher_model.
  • The registry entry "gpt-4.5" (gpt-4.5-preview) was retired on 2025-07-14; do not select it.

String model names must be keys of denario.models (e.g. "gpt-4.1", "gpt-5", "gpt-5-mini", "gemini-2.5-flash", "gemini-2.5-pro"); for any other provider model ID, pass an LLM object — routing is by substring (gemini → Google, gpt/o3 → OpenAI, claude → Anthropic):

from denario import Denario, LLM

den = Denario(project_dir="./my_research")
den.get_idea(mode="fast", llm="gpt-4.1")  # a registry key the provider still serves
den.get_method(mode="fast", llm=LLM(name="gemini-3.6-flash", max_output_tokens=8192, temperature=0.7))

gemini-3.6-flash is Google's listed replacement for gemini-2.0-flash; Google now limits the Gemini 2.5 models to existing users, so new Google accounts should use the LLM object route. Check the provider model lists before a long run — IDs keep rotating. See references/llm_configuration.md for per-stage parameters.

Core Research Workflow

Denario follows a structured four-stage research pipeline:

1. Data Description

Define the research context by specifying available data and tools:

from denario import Denario

den = Denario(project_dir="./my_research")
den.set_data_description("""
Available datasets: time-series data on X and Y
Tools: pandas, sklearn, matplotlib
Research domain: [specify domain]
""")

2. Idea Generation

Generate research hypotheses from the data description:

den.get_idea(llm="gpt-4.1")  # pass a live model; the built-in fast-mode default is retired

This produces a research question or hypothesis based on the described data. get_idea() and get_method() take a mode argument: mode="fast" (default; LangGraph backend, faster but less reliable) or mode="cmbagent" (cmbagent backend, slower but more reliable). Alternatively, provide a custom idea:

den.set_idea("Custom research hypothesis")

3. Methodology Development

Develop the research methodology:

den.get_method(llm="gpt-4.1")

This creates a structured approach for investigating the hypothesis. Can also accept markdown files with custom methodologies:

den.set_method("path/to/methodology.md")

4. Results Generation

Execute computational experiments and generate analysis:

den.get_results(researcher_model="gpt-4.1", plan_reviewer_model="gpt-4.1", formatter_model="gpt-4.1")

This runs the methodology, performs computations, creates visualizations, and produces findings. Can also provide pre-computed results:

den.set_results("path/to/results.md")

5. Paper Generation

Create a publication-ready LaTeX paper:

from denario import Journal

den.get_paper(journal=Journal.APS)

The generated paper includes proper formatting for the specified journal, integrated figures, and complete LaTeX source.

Available Journals

get_paper(journal=...) defaults to Journal.NONE (plain LaTeX, unsrt bibliography). The Journal enum (from denario import Journal) supports:

  • Journal.NONE — generic LaTeX, no journal preset
  • Journal.AAS — American Astronomical Society (e.g. ApJ)
  • Journal.APS — American Physical Society (Physical Review, PRL, PRA, ...)
  • Journal.ICML — International Conference on Machine Learning
  • Journal.JHEP — Journal of High Energy Physics (incl. JCAP)
  • Journal.NeurIPS — Conference on Neural Information Processing Systems
  • Journal.PASJ — Publications of the Astronomical Society of Japan

Launching the GUI

Run the graphical user interface:

denario run

This launches a web-based interface for interactive research workflow management.

Common Workflows

End-to-End Research Pipeline

from denario import Denario, Journal

# Initialize project
den = Denario(project_dir="./research_project")

# Define research context
den.set_data_description("""
Dataset: Time-series measurements of [phenomenon]
Available tools: pandas, sklearn, scipy
Research goal: Investigate [research question]
""")

# Generate research idea and methodology (explicit models; see "Model IDs" above)
den.get_idea(llm="gpt-4.1")
den.get_method(llm="gpt-4.1")

# Execute analysis (cmbagent agents); replace the o3-mini defaults before OpenAI retires them
den.get_results(researcher_model="gpt-4.1", plan_reviewer_model="gpt-4.1", formatter_model="gpt-4.1")

# Create publication (default writer LLM is gemini-2.5-flash; pass llm= to change it)
den.get_paper(journal=Journal.APS)

Hybrid Workflow (Custom + Automated)

# Provide custom research idea
den.set_idea("Investigate the correlation between X and Y using time-series analysis")

# Auto-generate methodology
den.get_method(llm="gpt-4.1")

# Auto-generate results
den.get_results(researcher_model="gpt-4.1", plan_reviewer_model="gpt-4.1", formatter_model="gpt-4.1")

# Generate paper
den.get_paper(journal=Journal.APS)

Literature / Novelty Check

Use den.check_idea(mode="semantic_scholar") (or mode="futurehouse") to test whether an idea is original against existing literature before committing to method/results. See references/examples.md.

Detailed References

For comprehensive documentation:

  • Installation options: references/installation.md
  • LLM configuration: references/llm_configuration.md
  • Complete API reference: references/research_pipeline.md
  • Example workflows: references/examples.md

Troubleshooting

Common issues and solutions:

  • API key errors: Ensure environment variables are set correctly (see references/llm_configuration.md)
  • LaTeX compilation: Install TeX distribution or use Docker image with pre-installed LaTeX
  • Package conflicts: Use virtual environments or Docker for isolation
  • Python version: denario 1.0.x requires Python 3.12 or 3.13 (>=3.12,<3.14)
  • KeyError: LLM '...' not available: the string is not a denario.models key; pass an LLM(...) object instead
  • Model not found / deprecated errors from the provider: a retired default is in use; pass a current model (see "Model IDs" above)

Part of the AlterLab Academic Skills suite.