Open-source, local-first desktop AI research workbench for scientific computing with Python/R, MCP bioinformatics tools, SSH/WSL/GPU runtimes, and OpenAI/Anthropic models.
xuzhougeng/wisp-science is a local-first desktop workbench for scientific research that combines AI assistants with Python and R computing, literature search, scientific databases, and remote runtimes. Researchers use it to run analyses, manage project artifacts, and preserve evidence and decisions on their own machines. Its catalogue skills and instruction extend the workbench’s reusable agent workflows.
This repository also configures its own agents. See what wisp-science tells them →
Skill Claude CodeCodex
Use the InfiniSynapse CLI (agentinfini) for multi-turn AI data-analysis tasks, database/RAG context, and task workspace files. Use when the user mentions InfiniSynapse, agentinfini, database or RAG analysis, or asks to delegate analysis through InfiniSynapse.
Skill Claude CodeCodex
Organize multi-step scientific analyses into reproducible, self-contained modules. Use for workflows such as QC→PCA→DEG→GSEA that produce scripts, inputs, figures, tables, and methods. Creates a stable module layout, records exact inputs/parameters/package and database versions in each module README, keeps large data…
Skill Claude CodeCodex
A reviewer for life-science and biomedical papers, PDFs, figures, captions, and screenshots. It examines the scientific question, experiments, evidence, causality, and limitations.
Skill Claude CodeCodex
Use this skill to drive Wisp Browser Runtime sessions (shared daily Chrome or workspace Chrome) — open pages, read them, click, fill and submit forms, navigate, switch tabs, or scrape content that needs the user's existing cookies and login state. Triggers when the user asks to do something in their browser, log into…
Skill Claude CodeCodex
Author a Wisp custom theme CSS file that uses documented tokens and import constraints. Use when the user wants a custom look, hide the paragraph lead bar, restyle chat Markdown, override colors, or import a stylesheet under Settings → Appearance.
Skill Claude CodeCodex
Create a Wisp specialist or author a project-local skill using the tools Wisp actually exposes. Use when the user wants a custom Agent persona, a restricted specialist loadout, a new skill, or changes to an existing project-local skill.
Skill Codex
A workflow for turning books about concepts, theories, or analysis methods into reusable task instructions. It scans document images, links claims to evidence, and checks the result through human review.
Skill Claude CodeCodex
Compose or improve a publication-grade multi-panel scientific figure from a claim, concrete data paths, or an existing image. Use for figure outlining, parallel panel rendering, exact-grid composition, visual inspection, and adversarial figure review. Use figure-style for one standalone plot and paper-narrative for…
Skill Claude CodeCodex
Correctness and legibility checklist for publication figures, plus a matplotlib sidecar. Load before plotting anything and call applyfigurestyle() (role-mapped font ladder, outward ticks, frameless legends, 300-dpi saves, CJK-safe fonts). Covers data fidelity, label budgets, axis/colour/type rules, chart choice by…
Skill Claude CodeCodex
Build a sourced research dossier for one therapeutic indication — patient population, epidemiology, disease biology, standard of care, regulatory path, and landmark trials. Use when the user asks for an indication overview, disease landscape, or trial-design background.
Skill Claude CodeCodex
Instructions for turning a scientific paper PDF into a journal-club presentation or literature report. They require reconstructing the paper's scientific logic before creating the slides.
Skill Claude CodeCodex
Retrieve, verify, and synthesize scientific literature. Use for seminal-paper lookups, evidence summaries, method comparisons, and gap analyses. Every citation must come from a live lookup, never from memory; retractions are checked; the deliverable is argued prose with resolvable DOI links.
Skill Claude CodeCodex
A skill for setting up the local runtime for wisp-science projects, including Python, Node.js, and bioinformatics environments.
Skill Claude CodeCodex
Judge and reshape the story told by a manuscript and its figure deck. Use when revising paper structure, testing whether Figure 1 is a hook, ordering figures, moving panels, identifying missing analyses, or defining the claim passed to figure-composer.
Skill Claude CodeCodex
Use this skill when the user has attached a PDF, paper, report, or other document and the answer needs its content: summarize a section, compare sections, read specific pages, check the table of contents, or read a value off a figure. The read tool cannot parse PDF binary — python is the extraction path. Provides…
Skill Claude CodeCodex
Use when creating, migrating, or debugging pixi environments, especially for scientific Python, bioinformatics, single-cell analysis, CUDA/PyTorch, Jupyter/VS Code kernels, conda-to-pixi migration, or conda + PyPI mixed dependency issues.
Skill Codex
Inspect a registered execution server before compute planning and interpret its persisted capability profile. Use when a server is added, when the user clicks Probe, before enabling an unfamiliar SSH/WSL resource, or when deciding whether GPU, sudo/root, a scheduler, Python, R, conda, mamba, or environment modules are…
Skill Claude CodeCodex
Plan, validate, and document public-bioinformatics data acquisition for GEO/GSE/GSM/GPL/GDS, SRA/ENA, TCGA/GDC, GTEx, and DepMap. Covers expression matrices, raw reads, download manifests, caches, and optional geokit SOFT/Series Matrix acquisition for R workflows.
Skill Claude CodeCodex
Submit recoverable SSH-direct research Runs with live progress cards and model-free monitoring, including Slurm, PBS, LSF, and Grid Engine batch jobs from a cluster login node.
Skill Claude CodeCodex
Wisp-science's actual agent tool surface and runtime boundaries. Load this when deciding which Wisp tool can perform a task, checking whether Python can reach agent or desktop capabilities, choosing between interactive analysis and persisted Runs, or answering questions about delegation, images, skills, memory…
Skill Claude CodeCodex
Use when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach. Trigger for scRNA QC metrics, per-sample diagnosis, threshold discussion, mitochondrial/ambient/doublet assessment, MAD vs fixed cutoffs, or refactoring automated merge-first QC. The…
Skill Claude CodeCodex
Create, update, validate, and evaluate Wisp skills. Use when authoring a project-local or installable skill, refining its trigger description, adding deterministic scripts or Python/R runtime sidecars, or testing whether another Agent can follow the workflow.
Skill Claude CodeCodex
Social-media writing guidance that turns scientific discussions, paper findings, or figure explanations into text ready to share. It covers platforms such as Xiaohongshu, WeChat, and Twitter/X.
Skill Claude CodeCodex
Build, audit, authorize, recover, or finalize dynamic Zotero citations and bibliographies in Microsoft Word DOCX files with a protected-source, digest-bound workflow. Use for Word–Zotero citation conversion, static OOXML citation audits, mocked/offline validation, Refresh authorization/report review, UI-evidence…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: