Instructions file CodexOpenCode
Instructions for ResearAI/DeepScientist, covering deepscientist repository guide, mission, read first, scope boundary for coding agents and non-negotiable contracts.
Instructions file
Instructions for ResearAI/DeepScientist, covering claude.md, project overview, quick start commands, installation and setup and install from repository.
Agent
Specialist for isolated follow-up analyses inside an analysis campaign.
Agent
Core operating contract shared by all DeepScientist quest turns.
Agent
Lead orchestrator for the DeepScientist research graph.
Agent
Baseline specialist for attach/import/reproduce/repair work.
Agent
Shared execution contract for specialized DeepScientist workers.
Agent
Evidence-bound writer for papers, reports, and summaries.
Skill Claude CodeCodex
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 Claude CodeCodex
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 Claude CodeCodex
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 Claude CodeCodex
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 Claude CodeCodex
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.