Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis.
Install Simbiology Simulate Model
$ npx skills add matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install matlab/matlab-agentic-toolkit simbiology-simulate-model --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/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .claude/skills/simbiology-simulate-model && 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 "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .claude/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-modelType 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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install matlab/matlab-agentic-toolkit simbiology-simulate-model --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .agents/skills/simbiology-simulate-model && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .agents/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install matlab/matlab-agentic-toolkit simbiology-simulate-model --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .cursor/skills/simbiology-simulate-model && 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 "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .cursor/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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/matlab/matlab-agentic-toolkit.git --path skills-catalog/computational-biology/simbiology-simulate-model--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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install matlab/matlab-agentic-toolkit simbiology-simulate-model --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .gemini/skills/simbiology-simulate-model && 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 "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .gemini/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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 matlab/matlab-agentic-toolkit simbiology-simulate-modelInstalls 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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .github/skills/simbiology-simulate-model && 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 "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .github/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install matlab/matlab-agentic-toolkit simbiology-simulate-model --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/matlab/matlab-agentic-toolkit.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills-catalog/computational-biology/simbiology-simulate-model .opencode/skills/simbiology-simulate-model && 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 "simbiology-simulate-model" agent skill from https://github.com/matlab/matlab-agentic-toolkit/tree/main/skills-catalog/computational-biology/simbiology-simulate-model into .opencode/skills/simbiology-simulate-model/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "simbiology-simulate-model", 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
simbiology-simulate-model- GitHub stars
- 1.1k
- Token cost
- ~3.8k tokens
- SKILL.md length
- 972 words
- Files
- 5 (incl. scripts, references)
- Skills in repo
- 144
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis.
- Works in 9 steps: Add helper scripts to the MATLAB path… → Element-wise operators in observables → StatesToLog for constant parameters → …
- Explore what-if
- SKILL.md covers When to Use, When NOT to Use, Must-Follow Rules and Decision Table, plus 6 more sections
- Identify influential parameters
What it does
Simbiology Simulate Model is an agent skill from matlab/matlab-agentic-toolkit. Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis. Use when asked to run, simulate, predict, explore what-if, or identify influential parameters.
Its SKILL.md is about 3.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `manifest.yaml`, `references/sensitivity-analysis-guidance.md` and `references/stochastic-simulation-guidance.md`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: The MATLAB Agentic Toolkit brings proven MATLAB capabilities to AI agents, making engineering and scientific workflows agent-ready.
When your agent uses it
- Explore what-if
- Identify influential parameters
Example prompts
- “/simbiology-simulate-model”
Workflow steps
9 steps, taken from the step headings in SKILL.md.
- Add helper scripts to the MATLAB path first
- Element-wise operators in observables
- StatesToLog for constant parameters
- All reactions must be MassAction for SSA
- Do NOT combine Scenarios with +
- Reset local sensitivity options after use
- Set MaximumWallClock to prevent hung simulations
- Unit conversion requires TimeUnits
- Scenario results are interleaved, not blocked
What it can do on your machine
Read from SKILL.md and the folder at commit 3303f05. 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/, which the agent can run.
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
Simbiology Simulate Model loads about 3.8k tokens when it runs, and up to ~5.8k if it reads all its reference files. Until then it costs about 52 tokens; SKILL.md has 972 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 972 words (~3,834 tokens).
“Run simulations of SimBiology models: deterministic ODE, stochastic SSA, scenario exploration, and sensitivity analysis.”
- name
- simbiology-simulate-model
- license
- https://www.mathworks.com/content/dam/mathworks/license/pmrl/license.md
- metadata.author
- MathWorks
- metadata.version
- 2.0
Files
SKILL.md and 4 other files (scripts, references) in skills-catalog/computational-biology/simbiology-simulate-model of matlab/matlab-agentic-toolkit.
- SKILL.md
- manifest.yaml
- references/sensitivity-analysis-guidance.md
- references/stochastic-simulation-guidance.md
- scripts/getModelByUUID.p
Open the folder on GitHubat commit 3303f05
Compare with similar skills
Simbiology Simulate Model 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 |
|---|---|---|---|---|---|---|
| Simbiology Simulate Model this skillmatlab/matlab-agentic-toolkit | 1.1k | — | ~3.8k | Automated safety check: Pass | Custom licence | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Dbsnp Database
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Related
Categories
Questions about Simbiology Simulate Model
What does Simbiology Simulate Model do?
Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis. Simbiology Simulate Model is an agent skill from matlab/matlab-agentic-toolkit. Simulate SimBiology models — ODE, stochastic (SSA), scenarios, and sensitivity analysis.
When should I use Simbiology Simulate Model?
Simbiology Simulate Model fits situations like: explore what-if; identify influential parameters.
How do I install Simbiology Simulate Model in Claude Code?
Run `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a claude-code`. Or copy the skill folder (skills-catalog/computational-biology/simbiology-simulate-model in matlab/matlab-agentic-toolkit) into .claude/skills/simbiology-simulate-model in your project. Claude Code loads it when a task matches its description.
How do I install Simbiology Simulate Model in Codex?
Run `npx skills add matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a codex`. Or copy the skill folder (skills-catalog/computational-biology/simbiology-simulate-model in matlab/matlab-agentic-toolkit) into .agents/skills/simbiology-simulate-model in your project. Codex loads it when a task matches its description.
Can I use Simbiology Simulate Model 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 matlab/matlab-agentic-toolkit --skill simbiology-simulate-model -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/simbiology-simulate-model, .gemini/skills/simbiology-simulate-model, .github/skills/simbiology-simulate-model and .opencode/skills/simbiology-simulate-model in your project.
What does Simbiology Simulate Model need to run?
SKILL.md names no scripts, command-line tools or credentials: Simbiology Simulate Model is instructions for the agent only.
Does Simbiology Simulate Model 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 Simbiology Simulate Model 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 Simbiology Simulate Model use?
Simbiology Simulate Model has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Simbiology Simulate Model use?
About 3.8k tokens (SKILL.md is roughly 15k 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 2k tokens, read only when the agent opens those files.
What are the alternatives to Simbiology Simulate Model?
Skills that share tags, products or a category with Simbiology Simulate Model: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Simbiology Simulate Model?
matlab (a GitHub organization) maintains it in matlab/matlab-agentic-toolkit, which has 1,134 GitHub stars. The repository holds 144 skills in this directory. The repository was last updated on September 30, 2026.
Source: matlab/matlab-agentic-toolkit on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.