Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
A skill your agent uses for PaddleHelix protein sequence pretraining, prediction, protein function workflows, tokenizer/model guidance, and safe protein input validation.
Install Protein Sequence Function
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-function --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .claude/skills/protein-sequence-function && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .claude/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-functionType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-function --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .agents/skills/protein-sequence-function && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .agents/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-function --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .cursor/skills/protein-sequence-function && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .cursor/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/VectorSpaceLab/AREX-Skill.git --path skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-function --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .gemini/skills/protein-sequence-function && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .gemini/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-functionInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .github/skills/protein-sequence-function && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .github/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill protein-sequence-function --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function .opencode/skills/protein-sequence-function && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "protein-sequence-function" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function into .opencode/skills/protein-sequence-function/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "protein-sequence-function", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
protein-sequence-function- GitHub stars
- 328
- Token cost
- ~921 tokens
- SKILL.md length
- 335 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 157
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
A skill your agent uses for PaddleHelix protein sequence pretraining, prediction, protein function workflows, tokenizer/model guidance, and safe protein input validation.
- Works in 4 steps: Classify the request as TAPE sequence… → Validate sequences and model config… → Check that all user-provided data,… → …
- PaddleHelix protein sequence pretraining
- SKILL.md covers Route First, Safe First Steps, Bundled Helper and Reference Map, plus 1 more section
- Runs Python scripts from its folder; calls python
What it does
Protein Sequence Function is an agent skill from VectorSpaceLab/AREX-Skill. Use for PaddleHelix protein sequence pretraining, prediction, protein function workflows, tokenizer/model guidance, and safe protein input validation.
Its SKILL.md is about 920 tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `references/api-reference.md`, `references/data-formats.md` and `references/troubleshooting.md`).
It sits in Research & Science. The repository describes itself as: A Skill Library for Automated Machine Learning.
When your agent uses it
- PaddleHelix protein sequence pretraining
- Protein function workflows
- Tokenizer/model guidance
- Safe protein input validation
Example prompts
- “/protein-sequence-function”
Requirements
- Python 3
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Classify the request as TAPE sequence modeling, graph-based function prediction, PPI, or HelixProtX multimodal protein routing.
- Validate sequences and model config before constructing a training/eval/predict command.
- Check that all user-provided data, checkpoint, graph, and label paths are explicit; do not assume app defaults are valid.
- Confirm before starting downloads, training, GPU/distributed jobs, graph preprocessing over PDB, or HelixProtX demos.
What it can do on your machine
Read from SKILL.md and the folder at commit ac3fe1a. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Protein Sequence Function loads about 921 tokens when it runs, and up to ~7.7k if it reads all its reference files. Until then it costs about 44 tokens; SKILL.md has 335 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 335 words (~921 tokens).
“Use this sub-skill when the task asks about PaddleHelix TAPE-style protein sequence models, protein property prediction, protein function prediction apps, protein sequence tokenization, FASTA/plain sequence validation, PPI routing, or HelixProtX high-level protein modality routing.”
- name
- protein-sequence-function
- disable-model-invocation
- true
- metadata.disco-role
- operating
- license
- NOASSERTION
Files
SKILL.md and 5 other files (scripts, references) in skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function of VectorSpaceLab/AREX-Skill.
- SKILL.md
- references/api-reference.md
- references/data-formats.md
- references/troubleshooting.md
- references/workflows.md
- scripts/validate_protein_inputs.py
Open the folder on GitHubat commit ac3fe1a
Compare with similar skills
Protein Sequence Function next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Protein Sequence Function this skillVectorSpaceLab/AREX-Skill | 328 | — | ~921 | Automated safety check: Pass | Custom licence | |
| Hypothesis Generationspacering-net/codeg | 3.8k | 15 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 83k | 5 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 46k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Read arXiv Paperkarpathy/nanochat | 58k | 2 repos | ~494 | Automated safety check: Pass | MIT | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT |
Similar skills
GitHub Deep Research
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Read arXiv Paper
karpathy/nanochat
Fetches the TeX source of an arXiv paper from its URL, reads it and writes a markdown summary tied to the nanochat project.
Content Research Writer
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
Peer Review
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
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Related
Categories
Questions about Protein Sequence Function
What does Protein Sequence Function do?
A skill your agent uses for PaddleHelix protein sequence pretraining, prediction, protein function workflows, tokenizer/model guidance, and safe protein input validation. Protein Sequence Function is an agent skill from VectorSpaceLab/AREX-Skill. Use for PaddleHelix protein sequence pretraining, prediction, protein function workflows, tokenizer/model guidance, and safe protein input validation.
When should I use Protein Sequence Function?
Protein Sequence Function fits situations like: paddleHelix protein sequence pretraining; protein function workflows; tokenizer/model guidance; safe protein input validation.
How do I install Protein Sequence Function in Claude Code?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a claude-code`. Or copy the skill folder (skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function in VectorSpaceLab/AREX-Skill) into .claude/skills/protein-sequence-function in your project. Claude Code loads it when a task matches its description.
How do I install Protein Sequence Function in Codex?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a codex`. Or copy the skill folder (skills/repositories/repo-skills/paddlehelix/sub-skills/protein-sequence-function in VectorSpaceLab/AREX-Skill) into .agents/skills/protein-sequence-function in your project. Codex loads it when a task matches its description.
Can I use Protein Sequence Function in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add VectorSpaceLab/AREX-Skill --skill protein-sequence-function -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/protein-sequence-function, .gemini/skills/protein-sequence-function, .github/skills/protein-sequence-function and .opencode/skills/protein-sequence-function in your project.
What does Protein Sequence Function need to run?
Going by SKILL.md and its folder, Protein Sequence Function needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Protein Sequence Function access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Protein Sequence Function safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Protein Sequence Function use?
Protein Sequence Function has a licence file (declared in SKILL.md) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Protein Sequence Function use?
About 921 tokens (SKILL.md is roughly 3.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 6.8k tokens, read only when the agent opens those files.
What are the alternatives to Protein Sequence Function?
Skills that share tags, products or a category with Protein Sequence Function: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Protein Sequence Function?
VectorSpaceLab (a GitHub organization) maintains it in VectorSpaceLab/AREX-Skill, which has 328 GitHub stars. The repository holds 157 skills in this directory. The repository was last updated on September 3, 2026.
Source: VectorSpaceLab/AREX-Skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.