Setup

Community

BioTender-max

setup

First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.

Overview

Publisher	BioTender-max
Repository	`awesome-bio-agent-skills`
Skill name	`setup`
Stars	204
Forks	36
Bundled files	Instructions only
License	MIT
Links	Skill source Repository Homepage

Markdown instructions
A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.
Works with any LLM
AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.
Self-contained
Everything the model needs lives in the instructions — no extra files to sync.
Open source
Published by BioTender-max on GitHub. Read the source before you install it.

Installation

Install the Setup AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

Open the app and go to Plugins → Skills.
Choose "Install from GitHub".
Paste the skill folder URL below and confirm.
https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup
Enable the skill in any chat where you want it available.

Store

Installed

Skills

Add skills

Import one or more skills from a public GitHub folder or a local .skill or .zip archive, or SKILL.md file.

From GitHub URLFrom .skill, .zip, or SKILL.md

GitHub repo or folder

https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup

Points to a single skill folder, or any folder that contains multiple skills. Public repos only.

CancelContinue

Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills

git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git /tmp/awesome-bio-agent-skills
mkdir -p .claude/skills
cp -r /tmp/awesome-bio-agent-skills/skills/adaptyv/setup .claude/skills/setup

Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Setup in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Setup on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Setup is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

Loaded only when it is needed
The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.
Switch models mid-chat
Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

Setup Guide

Help users get their environment ready to run protein design tools.

Quick checklist

Run through this checklist when a user encounters setup issues:

Step	Check	Fix
1. Modal CLI	`modal --version`	`pip install modal`
2. Modal auth	`modal token show`	`modal setup`
3. biomodals	`ls biomodals/modal_*.py`	`git clone https://github.com/hgbrian/biomodals`
4. Test	`cd biomodals && modal run modal_boltzgen.py --help`	See troubleshooting

Diagnosing issues

Error: "modal: command not found"

Cause: Modal CLI not installed.

Fix:

bash
pip install modal

Then restart the terminal or run hash -r.

Error: "Permission denied" or "Unauthorized"

Cause: Modal not authenticated.

Fix:

bash
modal setup

This opens a browser. Click "Authorize" to complete authentication.

Error: "No such file or directory: modal_boltzgen.py"

Cause: biomodals repository not cloned or not in correct directory.

Fix:

bash
git clone https://github.com/hgbrian/biomodals
cd biomodals

Error: "uvx: command not found"

Cause: uvx is an optional wrapper from the uv package. It's not required.

Fix: Run modal directly (recommended):

bash
modal run modal_boltzgen.py --help

Or install uv if you prefer using uvx:

bash
pip install uv

Full setup steps

Step 1: Install Modal CLI

bash
pip install modal

Verify: modal --version

Step 2: Authenticate Modal

bash
modal setup

This opens a browser. Click "Authorize".

Verify: modal token show

Step 3: Clone biomodals

bash
git clone https://github.com/hgbrian/biomodals
cd biomodals

Verify: ls modal_*.py should show files like modal_boltzgen.py

Step 4: Test the Setup

bash
cd biomodals
modal run modal_boltzgen.py --help

Expected: Usage instructions appear showing --input-yaml, --protocol, --num-designs options.

Common workflows after setup

Once setup is complete, users can:

bash
cd biomodals

# Design binders with BoltzGen (requires YAML config)
modal run modal_boltzgen.py --input-yaml binder.yaml --protocol protein-anything --num-designs 50

# Generate backbones with RFdiffusion
modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-150/0 70-100" --num-designs 100

# Validate with Chai
modal run modal_chai1.py --input-faa designs.fasta

GPU selection

Set GPU with environment variable:

bash
GPU=A10G modal run modal_rfdiffusion.py --pdb target.pdb --contigs "A1-100/0 50-80" --num-designs 10
GPU=L40S modal run modal_boltzgen.py --input-yaml config.yaml --num-designs 50
GPU=A100 modal run modal_chai1.py --input-faa complex.fasta

GPU	VRAM	Best For
T4	16GB	ProteinMPNN, ESM
A10G	24GB	RFdiffusion, Chai
L40S	48GB	BoltzGen, BindCraft
A100	40-80GB	Large complexes

Modal free tier

Modal offers $30/month in free credits - enough for:

~500 BoltzGen designs
~2000 RFdiffusion backbones
~1000 Chai predictions

Full documentation: See Installation Guide

Frequently asked questions

What does the Setup AI skill do?

Why use Setup on TypingMind?

Because you install it once and use it with any model. Setup is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Setup in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/setup. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Setup?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Setup?

As many as you like. As long as a model supports skills, you can use Setup with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Setup AI skill free?

Yes. It is published on GitHub by BioTender-max under the MIT license. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

Setup Guide

Quick checklist

Diagnosing issues

Error: "modal: command not found"

Error: "Permission denied" or "Unauthorized"

Error: "No such file or directory: modal_boltzgen.py"

Error: "uvx: command not found"

Full setup steps

Step 1: Install Modal CLI

Step 2: Authenticate Modal

Step 3: Clone biomodals

Step 4: Test the Setup

Common workflows after setup

GPU selection

Modal free tier

Frequently asked questions

Related AI Skills

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