HughYau/AcademicForge

HughYau/AcademicForge

Skill Claude CodeCodex

Submit→waitfornotification→harvest workflow for the user's SSH/SLURM hosts. Load once you've decided to dispatch remote.

HughYau/AcademicForge

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…

HughYau/AcademicForge

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…

HughYau/AcademicForge

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…

HughYau/AcademicForge

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.

HughYau/AcademicForge

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…

HughYau/AcademicForge

Skill Claude CodeCodex

Call a registered model endpoint over its native HTTP API from the endpoint's scoped inference kernel (BASEURL preloaded). Load once a task needs predictions from a registered model endpoint.

HughYau/AcademicForge

Skill Claude CodeCodex

Suite of tools for creating elaborate, multi-component claude.ai HTML artifacts using modern frontend web technologies (React, Tailwind CSS, shadcn/ui). Use for complex artifacts requiring state management, routing, or shadcn/ui components - not for simple single-file HTML/JSX artifacts.

HughYau/AcademicForge

Skill Claude CodeCodex

Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.