open-science

In the author's own words, from each skill's SKILL.md.

• alphafold2

  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…

  resources/skills/alphafold2/SKILL.md on GitHub (opens in a new tab)

• boltz

  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.

  resources/skills/boltz/SKILL.md on GitHub (opens in a new tab)

• borzoi

  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.

  resources/skills/borzoi/SKILL.md on GitHub (opens in a new tab)

• chai1

  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.

  resources/skills/chai1/SKILL.md on GitHub (opens in a new tab)

• compute-env-setup

  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.

  resources/skills/compute-env-setup/SKILL.md on GitHub (opens in a new tab)

• customize

  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.

  resources/skills/customize/SKILL.md on GitHub (opens in a new tab)

• diffdock

  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 startin…

  resources/skills/diffdock/SKILL.md on GitHub (opens in a new tab)

• env-management

  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 for…

  resources/skills/env-management/SKILL.md on GitHub (opens in a new tab)

• esmfold2

  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 SA…

  resources/skills/esmfold2/SKILL.md on GitHub (opens in a new tab)

• evo2

  Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1) Computing per-nucleotide or per-sequence likelihoods for variant effect scoring, (2) Embedding genomic windows for downstream classification, (3) Generating DNA conditioned on a prefix, (4) Scoring regulatory or coding regions across species.

  resources/skills/evo2/SKILL.md on GitHub (opens in a new tab)

• fair-esm2

  Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequence embeddings for downstream ML, (2) Masked-LM likelihood / mutation effect scoring, (3) Contact prediction from a sequence.

  resources/skills/fair-esm2/SKILL.md on GitHub (opens in a new tab)

• figure-composer

  Compose one publication-grade multi-panel figure. Start from a one-line claim plus immutable data Artifact Version references, or inspect an existing figure and draft its outline directly. Plan a 12-column panel outline, delegate one worker per panel, compose and inspect the result, then run at most three adversarial review rounds while regenerating only affected panels. For a standalone plot use…

  resources/skills/figure-composer/SKILL.md on GitHub (opens in a new tab)

• figure-style

  Publication-grade correctness and legibility rules for final-deliverable scientific figures, not exploratory plots. Use for a figure that will ship in a report, paper, export, or kept artifact. Covers data fidelity, label economy, color threading, chart choice, layout, and render-then-verify QA without imposing a visual house style. For multi-panel composition use `figure-composer`; for whole-pap…

  resources/skills/figure-style/SKILL.md on GitHub (opens in a new tab)

• indication-dossier

  Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.

  resources/skills/indication-dossier/SKILL.md on GitHub (opens in a new tab)

• ligandmpnn

  Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.com/dauparas/LigandMPNN). Reach for this skill to redesign the residues lining a binding pocket around a bound small molecule or cofactor, to design metal-coordinating sites where the geometry must be respected, or to get threaded designed-sequence PDBs out of any MPNN run.

  resources/skills/ligandmpnn/SKILL.md on GitHub (opens in a new tab)

• literature-review

  Find, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source reviews. Covers grounding claims in real retrieved sources, avoiding fabricated citations, handling retractions, and calibrating confidence to evidence strength.

  resources/skills/literature-review/SKILL.md on GitHub (opens in a new tab)

• openfold3

  Structure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use this skill when predicting protein/nucleic-acid/ligand complex structures with an Apache-2.0-licensed AF3 reimplementation.

  resources/skills/openfold3/SKILL.md on GitHub (opens in a new tab)

• paper-narrative

  Judge and reshape the story told by an entire paper figure deck. Use when writing or revising a paper to derive a grounded brief from the manuscript and captions, review the full deck as a handling editor, and hand an ordered figure arc to `figure-composer`.

  resources/skills/paper-narrative/SKILL.md on GitHub (opens in a new tab)

• proteinmpnn

  Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

  resources/skills/proteinmpnn/SKILL.md on GitHub (opens in a new tab)

• remote-compute-ssh

  Evaluate and use SSH Remote Compute before choosing where to run GPU, high-memory, parallel, batch, model-inference, bioinformatics, or other long-running scientific work; supports short remote commands and asynchronous jobs with automatic harvest and analysis.

  resources/skills/remote-compute-ssh/SKILL.md on GitHub (opens in a new tab)

• scgpt

  Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill when: (1) Producing cell embeddings from an AnnData for clustering/integration, (2) Zero-shot or fine-tuned cell-type annotation, (3) Gene-level representation for perturbation/GRN tasks. For probabilistic single-cell models (scVI etc.), use the scvi-tools library.

  resources/skills/scgpt/SKILL.md on GitHub (opens in a new tab)

• scvi-tools

  Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervised label transfer, and Bayesian differential expression. Reach for this skill to integrate scRNA-seq batches, embed cells for clustering, transfer annotations from a reference onto a query, or score differentially expressed genes per cluster. For spatial deconvolution / mapping use…

  resources/skills/scvi-tools/SKILL.md on GitHub (opens in a new tab)

• self-awareness

  Inspect Open-Science's JavaScript control REPL, discover managed Project files, Sessions, and Agent Frames, and safely feature-gate host.* calls with host.capabilities(). Use when an Agent needs to discover available host APIs, locate an Artifact or Upload Version, diagnose a Session, or read a Frame transcript in the current Project.

  resources/skills/self-awareness/SKILL.md on GitHub (opens in a new tab)

• skill-creator

  Create, revise, evaluate, publish, and improve Open-Science Skills through the native JavaScript host.skills composer. Use when the user wants a reusable workflow, an existing Skill changed, test cases or benchmarks for a Skill, or better Skill triggering.

  resources/skills/skill-creator/SKILL.md on GitHub (opens in a new tab)

• solublempnn

  Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for sequences biased toward cytosolic expression and reduced aggregation. Reach for this skill when designs from vanilla ProteinMPNN are aggregating or going to inclusion bodies, when redesigning a membrane-adjacent fold for soluble expression, or when an E. coli expression screen is…

  resources/skills/solublempnn/SKILL.md on GitHub (opens in a new tab)

No skill matches that filter.

Similar skills

• career-opsby career-ops-hq Open-source AI job search agent and job finder: scan job boards, score each job 1-5 against your CV before you apply, tailor an ATS-friendl… 75.1k stars · 6 skills
• cherry-studioby CherryHQ AI productivity studio with smart chat, autonomous agents, and 300+ assistants. Unified access to frontier LLMs 52.7k stars · 30 skills
• invisible_dotsby feder-cr Open-source, self-hosted alternative to OpenAI Dots, Grok Bot. Built to be undetectable by anti-bot systems. 32.1k stars · 1 skill
• cliby googleworkspace Google Workspace CLI — one command-line tool for Drive, Gmail, Calendar, Sheets, Docs, Chat, Admin, and more. Dynamically built from Google… 31.5k stars · 30 skills
• distillyby titanwings Distilly — Distill how they think into reusable Skills for any Agent or Bot. Formerly Colleague Skill（原同事 Skill）. 25.7k stars · 1 skill
• ego-liteby citrolabs The fastest browser for AI agents to run browser automation, built for sharing your logged-in browser state with your AI agents, like Codex… 17.5k stars · 2 skills