hughyau/academicforge

1

scientific-visualization Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, col…

hughyau/academicforge

81

2

planning-with-files Implements Manus-style file-based planning to organize and track progress on complex tasks. Creates task_plan.md, fin…

hughyau/academicforge

24

3

figure-style Publication-grade figure correctness and legibility rules. Load before drawing any plot and call `apply_figure_style(…

hughyau/academicforge

22

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literature-review Find, verify, and synthesize scientific literature — from "what's the seminal paper for X" through full multi-source …

hughyau/academicforge

20

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paper-narrative Judge and reshape the STORY a paper's figures tell. Input is the work itself — manuscript (or abstract) + figure deck…

hughyau/academicforge

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alphafold2 Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, g…

hughyau/academicforge

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figure-composer Compose one publication-grade multi-panel figure. Entry from a one-line claim + data files, OR from an existing figur…

hughyau/academicforge

19

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pdf-explore Use this skill when the user has attached a PDF, paper, report, or other document and the answer needs content from m…

hughyau/academicforge

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self-awareness Claude Science's own session database schema and SDK surface for introspection via host.query(). Load this when you n…

hughyau/academicforge

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algorithmic-art Creating algorithmic art using p5.js with seeded randomness and interactive parameter exploration. Use this when user…

hughyau/academicforge

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boltz Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. …

hughyau/academicforge

18

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borzoi Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when…

hughyau/academicforge

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chai1 Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai D…

hughyau/academicforge

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compute-env-setup Set up a compute environment on a remote provider so Claude Science jobs can run there. Covers direct SSH/conda hosts…

hughyau/academicforge

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customize Create, configure, and maintain custom agent profiles and author new skills via the `repl` tool. Use when the user wa…

hughyau/academicforge

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esmfold2 Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding (Candido et al. 2026, github.com/Biohub/esm). Single-sequence and…

hughyau/academicforge

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evo2 Score, embed, and generate DNA sequences with Evo 2, a long-context genomic foundation model. Use this skill when: (1…

hughyau/academicforge

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fair-esm2 Embed proteins with Meta AI's ESM-2 (`fair-esm` package). Use this skill when: (1) Extracting per-residue or per-sequ…

hughyau/academicforge

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ligandmpnn Inverse-fold a backbone with ligand, nucleic-acid, and metal context using LigandMPNN (Dauparas et al. 2023, github.c…

hughyau/academicforge

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managed-model-endpoints Register a model service in the managed family — a local model server container the daemon starts/stops on demand, or…

hughyau/academicforge

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openfold3 Structure prediction using OpenFold3, an open-weights PyTorch reproduction of AlphaFold3 from the AlQuraishi Lab. Use…

hughyau/academicforge

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product-self-knowledge Stop and consult this skill whenever your response would include specific facts about Anthropic's products. Covers: C…

hughyau/academicforge

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proteinmpnn Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, gith…

hughyau/academicforge

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remote-compute-ssh Submit→wait_for_notification→harvest workflow for the user's SSH/SLURM hosts. Load once you've decided to dispatch re…

hughyau/academicforge

18

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scgpt Embed and annotate single-cell expression data with scGPT, a foundation model for single-cell biology. Use this skill…

hughyau/academicforge

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solublempnn Inverse-fold a backbone with SolubleMPNN — ProteinMPNN retrained on a soluble-PDB subset (Dauparas et al. 2022) — for…

hughyau/academicforge

18

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using-model-endpoint Call a registered model endpoint over its native HTTP API from the endpoint's scoped inference kernel (BASE_URL prelo…

hughyau/academicforge

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diffdock Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind dif…

hughyau/academicforge

17

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indication-dossier Generate a therapeutic indication dossier. Covers the patient population, epidemiology, disease biology, standard of …

hughyau/academicforge

17

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remote-compute-modal Run GPU jobs on the user's own Modal account via host.compute.create('byoc:modal', ...). Covers the create→submit→wai…

hughyau/academicforge

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skill-creator Create new skills, modify and improve existing skills, and measure skill performance. Use when users want to create a…

hughyau/academicforge

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web-artifacts-builder Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologie…

hughyau/academicforge

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learn Use this skill when the user wants intellectual understanding — learning how or why something works, not getting a ta…

hughyau/academicforge

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scvi-tools Probabilistic single-cell RNA-seq with scvi-tools — scVI for a batch-corrected latent space, scANVI for semi-supervis…

hughyau/academicforge

16

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finishing-a-development-branch Use when implementation is complete, all tests pass, and you need to decide how to integrate the work - guides comple…

hughyau/academicforge

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receiving-code-review Use when receiving code review feedback, before implementing suggestions, especially if feedback seems unclear or tec…

hughyau/academicforge

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requesting-code-review Use when completing tasks, implementing major features, or before merging to verify work meets requirements

hughyau/academicforge

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verification-before-completion Use when about to claim work is complete, fixed, or passing, before committing or creating PRs - requires running ver…

hughyau/academicforge

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writing-plans Use when you have a spec or requirements for a multi-step task, before touching code

hughyau/academicforge

8

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writing-skills Use when creating new skills, editing existing skills, or verifying skills work before deployment

hughyau/academicforge

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brainstorming You MUST use this before any creative work - creating features, building components, adding functionality, or modifyi…

hughyau/academicforge

7

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dispatching-parallel-agents Use when facing 2+ independent tasks that can be worked on without shared state or sequential dependencies

hughyau/academicforge

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executing-plans Use when you have a written implementation plan to execute in a separate session with review checkpoints

hughyau/academicforge

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subagent-driven-development Use when executing implementation plans with independent tasks in the current session

hughyau/academicforge

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systematic-debugging Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes

hughyau/academicforge

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test-driven-development Use when implementing any feature or bugfix, before writing implementation code

hughyau/academicforge

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using-git-worktrees Use when starting feature work that needs isolation from current workspace or before executing implementation plans -…

hughyau/academicforge

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using-superpowers Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before A…

hughyau/academicforge

7