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mcp/skillhub

Agent Skill

Env Management skill

env-managementaipoch/open-scienceresources/skills/env-management/SKILL.md

Use when a notebook run fails on a missing package (ImportError, ModuleNotFoundError, "there is no package called"), when you need to inspect an installed package version, or when you need to install, add, or manage Python or R packages for the notebook runtime. Covers inspect_packages, routing Python vs R through manage_packages, why in-cell %pip/!pip/install.packages() and OS installers are forbidden, restarting the kernel after an install, and when to stop and ask the user.

5.3kApache-2.0

always on

105 tokname + description

once used

1,362 tokSKILL.md body

bundled files

0

repo stars

5.3kGitHub

Install the Env Management skill

Skills CLI (Claude Code, Codex, Cursor and others)

npx skills add https://github.com/aipoch/open-science --skill env-management

Claude Code, by hand (all projects)

git clone --depth 1 https://github.com/aipoch/open-science.git /tmp/open-science
mkdir -p ~/.claude/skills
cp -R /tmp/open-science/resources/skills/env-management ~/.claude/skills/env-management

For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.

What it costs your context

Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.

WhenWhat loadsCost
Every sessionName and description105 tok
When the agent uses itThe SKILL.md instructions1,362 tok
Only if openedNo bundled files—

Until it is used, env-management costs about 13× less than the median MCP server we measured (1,362 tokens on every turn). Installing all 25 skills from aipoch/open-science would load 2,130 tokens of descriptions. Skills vs MCP study

Checks

  • Tells the agent to pipe a download into a shell (curl … | sh). That runs whatever the URL serves at that moment, with your permissions.

Checked 2026-10-22 · method

What's inside

The headings of its SKILL.md. Read the full file on GitHub.

  • Environment and package management
  • When a package is missing
  • Check an installed version
  • Route by language
  • Restart the kernel after an install when told to
  • Never install any other way
  • When to stop and tell the user

More skills from aipoch/open-science

All skills in this repo
  1. alphafold2aipoch/open-science

    Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency pLDDT, ipTM, and RMSD, or to run a quick MSA-backed prediction using the public MMseqs2 server.

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  2. boltzaipoch/open-science

    Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.

    5.3k88 tok idle · 1,169 in use
  3. borzoiaipoch/open-science

    Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.

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  4. chai1aipoch/open-science

    Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab). Reach for this skill to predict an antibody-antigen or protein-ligand complex from a single FASTA, to re-fold designed binders as an AlphaFold-multimer alternative, or to drive co-folding from Python for batched campaigns on a GPU.

    5.3k98 tok idle · 942 in use
  5. compute-env-setupaipoch/open-science

    Prepare reproducible setup instructions and validate a user-managed named software environment on an Open-Science SSH Compute Host, including direct SSH and Slurm hosts. Use when a remote job needs packages, modules, cache variables, or a repeatable activation that the host does not already provide.

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  6. customizeaipoch/open-science

    Use when the user wants to create or manage a Specialist agent or create, revise, publish, or delete a Skill through the conversational `/Customize` entry. Routes Skill work to the internal skill-creator and handles Specialist work through the JavaScript host.agents SDK.

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  7. diffdockaipoch/open-science

    Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

    5.3k111 tok idle · 938 in use
  8. esmfold2aipoch/open-science

    Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and MSA modes; protein, DNA, RNA, ligand (CCD/SMILES), modified residues. FoldBench Ab-Ag 50-55%, PPI 70-77% DockQ-pass. Also covers the ESMC-{300M,600M,6B} protein language models from the same release: masked-LM logits, hidden states, mutation scoring, contact prediction, and the SAE interpretability head. MIT-licensed weights on HuggingFace org `biohub`. Use this skill when: (1) Predicting complex structures with single-sequence input, (2) Validating designed binders with ESMFold2-Fast, (3) Running ESMFold2 with MSA input, (4) Getting ESMC embeddings or per-residue mutation scores, (5) Choosing kernel backend and sampling-step settings for paper-faithful throughput.

    5.3k223 tok idle · 2,741 in use