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DeepScientist is a local research studio that manages the cycle from baseline experiments through research findings and paper-ready outputs. Researchers use it to organize autonomous scientific investigations, review progress, and take control when needed. The catalogue add-ons provide workflows and agent integrations for running research projects with it.
This repository also configures its own agents. See what DeepScientist tells them →
Skill Codex
Install, repair, and validate DeepScientist on Windows with WSL2 until the Windows browser can open the DeepScientist Web UI. Use when an agent needs to set up or fix DeepScientist on a Windows machine, including WSL distro creation, Linux-side Node/Python prerequisites, Codex auth/relay configuration, WSL proxy…
Skill Claude CodeCodex
Look up any arxiv paper on alphaxiv.org to get a structured AI-generated overview. This is faster and more reliable than trying to read a raw PDF.
Skill Claude CodeCodex
Use when a quest needs one or more follow-up runs such as ablations, robustness checks, error analysis, or failure analysis after a main experiment.
Skill Claude CodeCodex
Use when a quest needs to attach, import, reproduce, repair, verify, compare, or publish a baseline and its metrics.
Skill Claude CodeCodex
Use when the quest needs an explicit go, stop, branch, reuse-baseline, write, finalize, reset, or user-decision transition with reasons and evidence.
Skill Claude CodeCodex
Use when a quest is ready for a concrete implementation pass or a main experiment run tied to a selected idea and an accepted baseline.
Skill Claude CodeCodex
Use when a quest needs a polished milestone chart, paper-facing figure, appendix figure, or a mandatory render-inspect-revise pass before treating a figure as final.
Skill Claude CodeCodex
Use when the quest is ready to consolidate final claims, limitations, recommendations, summary state, and graph exports before stopping or archiving.
Skill Claude CodeCodex
Use when a quest needs concrete hypotheses, limitation analysis, candidate directions, or a selected idea relative to the active baseline.
Skill Claude CodeCodex
Use when a quest does not start from a blank state and the agent must first audit, trust-rank, and reconcile existing baselines, results, drafts, or review materials before choosing the next anchor.
Skill Codex
Prepare, audit, or revise Nature-ready Data Availability statements, data repository plans, dataset citations, and FAIR metadata checklists for manuscripts. Use when the user asks about Nature data availability, research data sharing, repository selection, accession numbers, restricted or sensitive data, source data…
Skill Codex
Submission-grade Nature/high-impact journal figure workflow for Python or R. Use whenever the user asks to create, revise, audit, or polish manuscript figures, multi-panel scientific plots, or journal-ready SVG/PDF/TIFF outputs, especially for Nature-family or other high-impact journals. Before plotting, define the…
Skill Codex
Build a complete but efficient Nature-style Chinese PPTX presentation from a scientific paper, preprint, PDF, article text, abstract, figure legends, or reading notes. Use this skill whenever the user asks to make slides/PPT/PPTX for journal club, group meeting, paper sharing, thesis seminar, lab meeting, department…
Skill Codex
Polish, restructure, or translate academic prose into Nature-leaning English using the paper-architecture and writing-strategy principles from Scientific English Writing & Communication, with phrase-level support from Academic Phrasebank. Use whenever the user asks to polish a manuscript paragraph, abstract…
Skill Claude CodeCodex
Use when an algorithm-first quest should manage candidate briefs, optimization frontier, branch promotion, or fusion-aware search instead of the paper-oriented default loop.
Skill Claude CodeCodex
Use when creating, revising, validating, or repairing a research-paper outline before writing; turns experiment evidence into a clear paper idea, scoped claims, method abstraction, evaluation plan, analysis plan, and evidence boundaries without copying run logs into the manuscript.
Skill Codex
Use when structured numeric data, arrays, or CSV-like measurements should be turned into a publication-quality figure by adapting a bundled paper-style plotting template instead of improvising a new chart from scratch.
Skill Claude CodeCodex
Use when a quest already has a paper, draft, or review package and the task is to map reviewer feedback into experiments, manuscript deltas, and a durable rebuttal / revision response.
Skill Claude CodeCodex
Use when a draft, paper, or paper-like report is substantial enough for an independent skeptical audit before finalization, rebuttal, or revision routing.
Skill Claude CodeCodex
Use for natural-science or engineering tasks, scientific software routing, simulation, dataset analysis, model fitting, package checks, HPC-through-shell work, validation, and evidence-backed scientific claims using DeepScientist's artifact.science(...) Science Evidence Graph. Includes a progressive-disclosure catalog…
Skill Claude CodeCodex
Use when a quest needs problem framing, literature scouting, dataset or metric clarification, or baseline discovery before deeper work.
Skill Claude CodeCodex
Use when a quest has enough evidence to draft or refine a paper, report, or research summary without inventing missing support.
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: