docker
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
Skill by yejunbin
Install
Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.
npx agentmarket install skill/yejunbin-docker
Asks which of your tools to add it to (Claude Code, Codex, Cursor, VS Code, Windsurf, Gemini CLI, Claude Desktop) and shows the change first. See https://agentmart.dev/cli.
Get the weekly diff
The weekly diff: one email a week with new agent tools, notable updates and grade changes, plus security alerts for tools you follow. Double opt-in, one-click unsubscribe.
About
Use cases: devops, research
Reviews
Write a reviewNo reviews yet. Installed it? Reviews come from verified installers only. How reviews work
Permissions: not checked yet.
What's inside
- Skill name
docker- Description
- Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks. Use when the user selects Docker as the execution environment or asks to run code safely, in isolation, or in a sandbox.
- License
- MIT
- Allowed tools
- Bash(docker:*)
- Instructions
- 80 lines in SKILL.md · view on GitHub
Before installing
- Pre-approves some shell commands
Files (1)
- SKILL.md
SKILL.md (first lines)
# Docker Sandbox Run research code inside Docker containers while Darwin stays on the host. The container gets the project files, runs the commands, and results sync back. ## When to use - User selects "Docker Sandbox" as the execution environment in `/replicate` or `/autoresearch` - Running untrusted code from a paper's repository - Experiments that install packages or modify system state - Any time the user asks to run something "safely" or "isolated" ## How it works 1. Build or pull an appropriate base image for the research code 2. Mount the project directory into the container 3. Run experiment commands inside the container 4. Results write back to the mounted directory ## Running commands in a container For Python research code (most common): ```bash docker run --rm -v "$(pwd)":/workspace -w /workspace python:3.11 bash -c " pip install -r requirements.txt && python train.py " ``` For projects with a Dockerfile: ```bash docker build -t darwin-experiment . docker run --rm -v "$(pwd)/results":/workspace/results darwin-experiment ``` For GPU workloads: ```bash docker run --rm --gpus all -v "$(pwd)":/workspace -w /workspace pytorch/pytorch:latest bash -c " pip install -r requirements.txt && python train.py " ``` ## Choosing the base image | Research type | Base image | | --- | --- | | Python ML/DL | `pytorch/pytorch:latest` or `tensorflow/tensorflow:latest-gpu` | | Python general | `python:3.11` | | Node.js | `node:20` | | R / statistics | `rocker/r-ver:4` | | Julia | `julia:1.10` | | Multi-language | `ubuntu:24.04` with manual installs | ## Persistent containers For iterative experiments (like `/autoresearch`), create a named container instead of `--rm`. Choose a descriptive name based on the experiment: ```bash docker create --name <name> -v "$(pwd)":/workspace -w /workspace python:3.11 tail -f /dev/null docker start <name> docker exec <name> bash -c "pip install -r requirements.txt" docker exec <name> bash -c "python train.py" ``` This preserves installed packages across iterations. Clean up with: ```bash docker stop <name> && docker rm <name> ``` ## Notes - The mounted workspace syncs results back to the host automatically - Containers are network-enabled by default — add `--network none` for full isolation - For GPU access, Docker must be configured with the NVIDIA Container Toolkit
From yejunbin/darwin, MIT.
More from yejunbin/darwin
- 0.534score
bio-research
yejunbin
Search, read, and query research papers via the `alpha` CLI (bioRxiv-backed).
SkillCFreshness: C★ 7Claude Code +9 - 0.534score
modal-compute
yejunbin
Run GPU workloads on Modal's serverless infrastructure.
SkillCFreshness: C★ 7Claude Code +9 - 0.534score
contributing
yejunbin
Contribute changes to the Darwin repository itself.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
gene-lookup
yejunbin
Look up gene information from HGNC, OMIM, ClinVar, and UniProt.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
clinical-trial-check
yejunbin
Search and summarize clinical trials from ClinicalTrials.gov and EU CTR.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
biorxiv-monitor
yejunbin
Monitor bioRxiv and medRxiv preprints for a topic, author, or keyword.
SkillCFreshness: C★ 7Claude Code +9 - 0.529score
jobs
yejunbin
Inspect active background research work including running processes, scheduled follow-ups, and pending tasks.
SkillCFreshness: C★ 7Claude Code +9 - 0.529score
autoresearch
yejunbin
Autonomous experiment loop that tries ideas, measures results, keeps what works, and discards what doesn't.
SkillCFreshness: C★ 7Claude Code +9 - 0.528score
pathway-enrichment
yejunbin
Guide gene list enrichment analysis using over-representation and GSEA approaches.
SkillCFreshness: C★ 7Claude Code +9 - 0.528score
biomarker-roc
yejunbin
Evaluate biomarker performance with ROC analysis, AUC, sensitivity, and specificity.
SkillCFreshness: C★ 7Claude Code +9 - 0.528score
dosage-calc
yejunbin
Calculate drug dosages with renal and hepatic adjustments.
SkillCFreshness: C★ 7Claude Code +9 - 0.528score
geo-reanalysis
yejunbin
Guide reanalysis of GEO datasets with standard bioinformatics pipelines.
SkillCFreshness: C★ 7Claude Code +9
Signals
- Stars
- 7
- Forks
- 1
- Open issues
- 1
- Last commit (this folder)
- May 8, 2026 (5 months ago)
From GitHub (fetched Oct 24, 2026).
Details
- License
- MIT
- Repository
- github.com/yejunbin/darwin
- First seen
- Oct 24, 2026
- Last checked
- Oct 24, 2026
- Source
- GitHubgithub-graphql
Same skill elsewhere
Copies of this SKILL.md published by others; search shows only one of them.
- 0.854score
docker
Companion-Inc
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillAFreshness: A★ 10KClaude Code +9 - 0.358score
docker
TQuang122
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillAFreshness: A★ 2Claude Code +9 - 0.285score
docker
ParamJani21
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillCFreshness: CClaude Code +9 - 0.263score
docker
itsamirkhon
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillDFreshness: D★ 2Claude Code +9 - 0.256score
docker
maedoc
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillDFreshness: D★ 1Claude Code +9 - 0.246score
docker
WilmerGaspar
Execute research code inside isolated Docker containers for safe replication, experiments, and benchmarks.
SkillDFreshness: DClaude Code +9
More from yejunbin
- 0.534score
bio-research
yejunbin
Search, read, and query research papers via the `alpha` CLI (bioRxiv-backed).
SkillCFreshness: C★ 7Claude Code +9 - 0.534score
modal-compute
yejunbin
Run GPU workloads on Modal's serverless infrastructure.
SkillCFreshness: C★ 7Claude Code +9 - 0.534score
contributing
yejunbin
Contribute changes to the Darwin repository itself.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
clinical-trial-check
yejunbin
Search and summarize clinical trials from ClinicalTrials.gov and EU CTR.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
biorxiv-monitor
yejunbin
Monitor bioRxiv and medRxiv preprints for a topic, author, or keyword.
SkillCFreshness: C★ 7Claude Code +9 - 0.531score
gene-lookup
yejunbin
Look up gene information from HGNC, OMIM, ClinVar, and UniProt.
SkillCFreshness: C★ 7Claude Code +9
Cite this page
docker skill. Agent Mart. https://agentmart.dev/skills/yejunbin-docker (last updated 2026-10-24)