Skill Claude CodeCodex
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…
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Compose one publication-grade multi-panel figure. Entry from a one-line claim + data refs, OR from an existing figure via deriveoutline(png). Runs a per-figure loop: outline (12-col grid, per-panel ask + labelbudget) → fan-out one sub-agent per panel (each loads figure-style) → tile + stamp letters → adversarial…
Skill Claude CodeCodex
Publication-grade figure correctness and legibility rules. Load before drawing any plot and call applyfigurestyle() — sets a role-mapped font-size ladder, outward ticks, frameless legends, and 300-dpi output. The skill is a checklist, not a house look: data fidelity (claim-titles tested against every row, excluded…
Skill Claude CodeCodex
Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of care, regulatory precedent, and landmark clinical trials.
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Register a model service in the managed family — a local model server container the daemon starts/stops on demand, or a remote upstream model API (https). Read the runbook, allocate a port (local only), compose idempotent start/stop scripts (local only), register once. Load when the user wants a model service…
Skill Claude CodeCodex
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.
Skill Claude CodeCodex
Judge and reshape the STORY a paper's figures tell. Input is the work itself — manuscript (or abstract) + figure deck — no hand-written brief. derivepaperbrief(abstract, captions) extracts pitch/vision/per-figure-claims; a handling-editor reviewer on the full deck returns hookverdict (would Fig 1 make me send this for…
Skill Claude CodeCodex
Use this skill when the user has attached a PDF, paper, report, or other document and the answer needs content from more than one place in it: summarize the methods or any other section, compare sections, find where a topic is discussed, read a value or label off a figure or chart, or find/list/extract every instance…
Skill Claude CodeCodex
Stop and consult this skill whenever your response would include specific facts about Anthropic's products. Covers: Claude Code (how to install, Node.js requirements, platform/OS support, MCP server integration, configuration), Claude API (function calling/tool use, batch processing, SDK usage, rate limits, pricing…
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
Run GPU jobs on the user's own Modal account via host.compute.create('byoc:modal', ...). Covers the create→submit→waitfornotification flow, the computeprovider kernel for env setup, image/volume resolution, and the two approval cards. Load once you've decided to dispatch to Modal.
Skill Claude CodeCodex
Submit→waitfornotification→harvest workflow for the user's SSH/SLURM hosts. Load once you've decided to dispatch remote.
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
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…
Skill Claude CodeCodex
Claude Science's own session database schema and SDK surface for introspection via host.query(). Load this when you need to query your own conversation history, token usage, cost accounting, execution log, or artifact metadata beyond what host.frames()/host.artifacts() provide — e.g. "how many tokens has this session…
Skill Claude CodeCodex
Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a skill from scratch, edit, or optimize an existing skill, run evals to test a skill, benchmark skill performance with variance analysis, or optimize a skill's description for better triggering accuracy.
Agent
Analyze blind comparison results to understand WHY the winner won and generate improvement suggestions.
Agent
Compare two outputs WITHOUT knowing which skill produced them.
Agent
Evaluate expectations against an execution transcript and outputs.
Skill Claude CodeCodex
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…