Using AI Agents (Hermes) in Scientific Workflows

Alexandre Strube

June 2026

Open this on your laptop

go.fzj.de/2026-hdc-rs

Resources:

Team:

Alexandre Strube

Who Is This For?

  • You’re a researcher who uses AI tools (ChatGPT, Claude, etc.) but want more power
  • You’re tired of copy-pasting between tools and want automation
  • You need privacy — your data can’t leave your machine or Helmholtz infrastructure

You don’t need:

  • Prior experience with AI agents
  • Deep technical knowledge (terminal familiarity helps)
  • A powerful machine (local models optional — Blablador API works on any laptop)

Good to know:

  • WHAT YOU ARE DOING
  • You’re giving a powerful AI agent access to your tools and data
  • It can read/write files, execute code, browse the web, and more
  • With great power comes great responsibility — be mindful of what you ask it to do

AI Agent?

  • A program that uses an LLM to plan and execute tasks using tools
  • Benefits for researchers: automation, reproducibility, speed

Why Hermes Specifically?

Hermes vs. ChatGPT in a browser

Feature ChatGPT Web Hermes Agent
Tool access Limited Terminal, files, browser, APIs
Automation Manual Cron jobs, background tasks
Memory Session-only Persistent, structured
Privacy Data to OpenAI Local or Helmholtz-only
Integration None Skills, webhooks, gateways

Hermes

  • Remembers across sessions
  • Writes its own reusable skills
  • Prunes them in the background
  • And validates them offline through an evolutionary engine called GEPA
  • Open-source, multi-model, tool-calling, privacy-first
  • Runs locally on your machine — your data stays with you
  • Connects to Blablador
  • Also supports: OpenRouter, Claude, ChatGPT, Gemini and local models

Hermes vs. other agent frameworks:

  • Simpler setup — curl | bash vs. Docker + config hell
  • Built-in skills — 50+ reusable workflows out of the box
  • Privacy-first — runs locally by default, Blablador integration
  • Research-focused — arxiv, llm-wiki, citation tools bundled

Why Blablador?

“So hoping that in 1 year one can use JUPITER or JARVIS to run something on the level of Claude of now is entirely unrealistic.    Like, fairy tale unrealistic.”

  • From a colleague last week.
  • I hope he is wrong.

Life can be hard even if you are Microsoft

https://nitter.net/hedgiemarkets/status/2057531661785628841?s=58

Remember

  • When you stop paying the provider, the tokens stop
  • Your work stops.

Why Blablador?

  • Blablador API: state-of-the-art open models, 35 GPUs 24/7, Helmholtz authentication
  • More coming
  • Explosion in token numbers

It’s all about the right tool for the job

Why NOT Blablador?

  • User asked me yesterday (11.06.2026):
    • Why is your infrastructure not as good as Claude or ChatGPT?
    • Chatgpt: 600 billion dollars in infra plus people.
    • Claude: 30 billion dollars in infra plus secret accords.
    • Blablador: 1 person, 50 GPUs, 0 dollars in infra costs (all donated)

🤌

🖕

Current OUTDATED

(11.06.2026) state-of-the-art models

Closed vs Open Source, result of 10 benchmarks

Prerequisites

  • Terminal access (macOS, Linux, or WSL on Windows)
  • Telegram (if desired)

Outline

  • Installation & setup: 20 min
  • Configuration & model selection: 10 min
  • Telegram bot: 10 min
  • Skills (arxiv, llm-wiki): 30 min
  • Custom skill creation: 10 min

Configuration

Blablador Token:

  • Log in to codebase.helmholtz.cloud
  • Edit Profile → Access → Personal Access Tokens → Add New Token
  • Check date, add scope “Read user”
  • Copy the token - you won’t see it again.

Installing Hermes

curl -fsSL https://hermes-agent.nousresearch.com/install.sh | bash
  • hermes setup — Full setup
  • Custom endpoint (enter URL manually)

Connecting to Blablador

  • API endpoint: https://api.helmholtz-blablador.fz-juelich.de/v1/
  • Still have your token?
  • Api mode: 1 - Auto-detect
  • Default model: alias-fast (Gpt-OSS-120b)

Connecting to Blablador

  • Terminal Backend: local
  • Most other options depend on what you want to do — We can change them later

Connecting to Blablador

  • Verify: hermes doctor

Memory

https://x.com/akshay_pachaar/status/2054564519280804028

🍆

Size matters

  • (Context size, that is)
  • Bigger context windows → more memory, less forgetting
  • One should balance model size, context window, and latency for the task at hand

Creating the searxng-search Skill

Prompt to create it:

"Add a custom search backend to Hermes. I have a self-hosted SearXNG instance at https://search.blablador.fz-juelich.de. Remember to use it for ANY web search."

Quick Test

Verify everything works:

hermes chat -q "What is the capital of France?"

Blablador Model Aliases

Alias Model Use case Context
alias-fast Gpt-OSS-120b High throughput 128K
alias-code Qwen3-Coder-Next-FP8 Code 98K
alias-large Qwen3.5-122B-A10B-FP8 Best accuracy/speed and multi-modal 256K

Blablador Model Aliases

Alias Model Use case Context
alias-huge Minimax 2.7 229B High quality 96k
alias-qwen-huge Qwen3.5-397B Experimental runs on Juwels Booster 256k
alias-trillion Kimi-K2.6 1.1T parameters Experimental runs on Juwels Booster 256k
alias-embeddings Qwen3-Embedding-8B Text embeddings 4K

Blablador Model Aliases

  • Aliases are stable — the actual model can change without breaking your code
  • All models free for Helmholtz researchers
  • Important: Context windows are finite (8K-256K). Rate limits apply. Monitor usage via hermes logs --follow

Practical: making it more than a chatbot

Creating a Telegram Bot

Register a bot: message BotFather on Telegram, then add to ~/.hermes/.env:

TELEGRAM_BOT_TOKEN=YOUR_TOKEN
TELEGRAM_CHAT_ID=<your_chat_id>

Run: hermes gateway run and send /status in your Telegram chat.

Bots

Why not whatsapp or matrix?

  • Telegram: Bot API is well-documented and supported by Hermes out of the box.
  • Matrix: integration is possible but requires more setup and you need multiple accounts or platform bot support (fz doesn’t).
  • Whatsapp: no bot API — so it’s not a good idea to run on your own account

Voice & TTS

hermes tools enable tts
hermes config set tts.provider NeuTTS
  • Generate speech: /voice or /speak "Hello class"
  • Fallback: hermes config set tts.provider edge

Core Hermes Commands

Command Description
/reset Start a fresh session
/skill <name> Load a skill (e.g. arxiv)
/model Change model/provider on the fly
/stop Kill background processes

Core Hermes Commands

Command Description
/cron create "SCHEDULE" "PROMPT" Schedule recurring jobs (e.g., daily digests)
/voice on Enable TTS for voice output
/background <prompt> Run long tasks without blocking the chat
/queue <prompt> Don’t interrupt the chat

Hermes Profiles

  • Each profile has its own model/provider, config, memory, and tool approvals
  • hermes profile list
  • A profile becomes a new tool:
    • hermes profile create researcher --description "Reads source code and external docs, writes findings."
  • researcher help

Goals

  • /goal: a standing objective that survives across turns.
  • After every turn a lightweight judge model checks whether the goal is satisfied by the assistant. Default: 20 turns
  • Ralph Loop
  • Example: /goal Create four files /tmp/note_{1..4}.txt, one per turn, each containing its number as text

Samba picks the right skill

Key Skills for Research

Skills are reusable, documented workflows — load with /skill <name>, then ask natural language questions.

  • hermes-agent — Full setup guide, CLI reference, troubleshooting
  • arxiv — Search papers, fetch abstracts, generate BibTeX entries
  • llm-wiki — Build a personal, inter-linked markdown knowledge base
  • plan / test-driven-development — Development workflows

Skills

/skill hermes-agent
/skill arxiv
/skill llm-wiki
  • Full list: hermes skills list or hermes skills browse

Custom Skills: Creating Them

hermes-tech-digest — daily tech news digest to Telegram:

"Add a skill for generating a daily tech news digest and sending it
to Telegram via the gateway. Remember to use it whenever someone wants a daily news roundup."

Write your own: /skill hermes-agent-skill-authoring

hermes-tech-digest: Configure & Run

Tell Hermes your interests:

"Customize the hermes-tech-digest skill. Set my topics to:
AI, machine learning, open source, Apple Silicon"

Run once to test: load the skill, then ask Hermes to run it.

Schedule daily delivery:

"Scheduled hermes-tech-digest to run every day at 8 AM"

Practical Workflows

  • Literature search with arxiv skill
  • Basic scripting and data analysis
  • Telegram bot setup
  • Code & Development: Scripting, debugging, deploying services
  • Experiment Management: Cron jobs, background tasks, parameter sweeps

Practical: Data Analysis & Scripting

"write a script that fits a Gaussian to column 3 of my_data.csv"
  • Always use uv for package management — never pip:

    uv pip install pandas matplotlib scipy
  • Debug with Hermes: “Explain the error in my script”

  • Reproducible: “Create a requirements.txt for this project”

Practical: Experiment Management

hermes cron create "0 2 * * *" "run_training.py --nightly"

Monitor running jobs:

hermes logs --follow

Stop a job:

/stop

or

hermes cron pause <job_id>

Important: /background runs in the current session. hermes cron creates persistent scheduled jobs.

Practical: Writing & Publishing

Convert notes to LaTeX:

"convert my notes in research_notes.md to LaTeX"

Check citations: “Verify all BibTeX entries are correct”

Send to Telegram: “Send the PDF to my class Telegram channel”

Practical: Voice Announcements

  • Generate lecture audio with VibeVoice:

    /voice on
    "explain attention mechanism" --voice
  • Great for accessibility, language support, and review

  • Example: “Create a 2-minute summary of today’s lecture”

Common Issues & Troubleshooting

  • Model won’t load:
  • Blablador: Check API key in ~/.hermes/config.yaml
  • Local MLX: Ensure enough RAM (8GB+ for 7B models)
  • Try different alias: /model alias-large --provider blablador

Common Issues & Troubleshooting

  • Tool permissions denied:
  • Check Hermes config for approvals
  • Set to smart for auto-approval of low-risk actions
  • Review ~/.hermes/config.yaml for tool restrictions

Common Issues & Troubleshooting

  • SearXNG skill not working:
  • Test endpoint: curl https://search.blablador.fz-juelich.de/api?q=test
  • Re-create skill with correct URL

Common Issues & Troubleshooting

  • Telegram bot offline:
  • Check token: hermes config show
  • Restart gateway: hermes gateway run
  • Verify chat ID format (no leading zeros)

Common Issues & Troubleshooting

  • Tools not working after enabling:
  • Critical: Tools require /reset to take effect
  • Run /reset after hermes tools enable <name>
  • Tool changes do NOT apply mid-conversation (preserves prompt caching)

Common Issues & Troubleshooting

  • Skill loaded but nothing happens:
  • You must ask natural language questions after loading
  • Example: /skill arxiv then “search for papers on X”
  • Skills change context, they don’t add commands

Security & Best Practices

Security Configuration

hermes config set security.redact_secrets true
hermes config set approvals.mode smart
chmod 700 ~/.hermes && chmod 600 ~/.hermes/.env
  • Never share your .env or API keys
  • Review commands before approving destructive operations
  • Use smart mode - auto-approves low-risk, prompts on high-risk

Privacy & Data Protection

  • Built-in memory stores data locally in ~/.hermes/memories/
  • External providers (optional) - all self-hosted, open-source
  • Secret redaction - automatically hides API keys in tool output
  • No data exfiltration - private data stays private

Privacy & Data Protection

Verify your setup:

hermes config check
hermes memory status

What I hope you can do with Hermes

  • Automate literature reviews — search arxiv, extract summaries, build citations
  • Build personal knowledge bases — link concepts, track research evolution
  • Write & debug code faster — let agents handle boilerplate, you focus on logic
  • Schedule recurring tasks — daily digests, nightly training, automated reports
  • Communicate via Telegram — query your agent on-the-go, get voice responses
  • Create custom skills — encode your own workflows for reuse

Next Steps

  • Deepen your skills:
  • Explore hermes skills browse for 50+ native skills
  • Read /skill hermes-agent for full CLI reference
  • Join the Hermes Discord: https://discord.gg/NousResearch

Next Steps

Advanced topics: - Multi-agent orchestration with /delegate_task - Custom tool development (Python SDK) - Deploying Hermes as a service for your team

Samba and Potato have questions too

Questions?

  • Slides: https://strube1.pages.jsc.fz-juelich.de/hermes-course
  • Source: https://gitlab.jsc.fz-juelich.de/strube1/hermes-course
  • Hermes docs: https://hermes-agent.nousresearch.com/docs/