Using AI Agents (Hermes) in Scientific
Workflows
Alexandre Strube
June 2026
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
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
“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
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)
Recommended but not required:
Basic Python familiarity
Git installed
Telegram account (for bot integration)
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
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
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
arxiv Skill: Literature Search
/skill arxiv
Now ask natural language questions: - “Search for papers on
reinforcement learning for scientific discovery” - “Find the top 5
papers on transformer architectures and generate BibTeX” - “Save the
BibTeX entries to ~/papers/rl_discovery.bib”
Key point: Skills change the context — you ask natural language, not
special commands.
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/