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 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.
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…
Skill Claude CodeCodex
This tree defaults to review. Before executing any candidate rule, the host governance process must prove its lifecycle and private provenance from an authoritative record that binds the current complete tree hash. If an accepted or deployed record cannot be proven, uniquely locate the owning distillation, candidate…
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: