Skill rating

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

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

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

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 pa

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-c

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 ed

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 di

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 case

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

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-crea

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 scori

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) G

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 scori

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 th

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

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,

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 in

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 comman

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 RFdiff

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

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 bin

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 sear

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

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 cit

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 binder