ResearchPilot Workspace

ResearchPilot Workspace is a local workspace template for file-based PhD research management.

It is designed to pair with ResearchPilot-skills, giving those skills a stable place to write reports, plans, notes, project indexes, schedules, protocols, and cross-session handoff files.

中文简介

ResearchPilot Workspace 是一个面向博士科研工作的本地文件化工作区模板。

它的目标不是提供聊天提示词，而是提供一套长期可维护的目录结构、首页导航、模板文件和检索边界，让 ResearchPilot-skills 在真实科研场景中有稳定的落盘环境。

它特别适合：

• 想把日报、周报、月报、实验方案、会议纪要、protocol 和行动项长期保存在本地的人
• 想在 Obsidian 中把科研工作流真正结构化的人
• 想降低长对话依赖、减少跨会话幻觉的人

What this repository is

This repository is a workspace template, not a skill pack.

It provides:

• a consistent research directory structure
• root navigation pages for daily use
• project-bounded retrieval entry points
• reusable templates for project indexes, retrieval scopes, and handoff files
• a lightweight Obsidian-compatible vault structure

Best for

• molecular biology PhD workflows
• bioinformatics-heavy research workflows
• plant science and pomology research groups
• researchers who want durable local files instead of chat-only history

Core ideas

• formal outputs should be written to files
• missing information should be marked as 待确认
• project files should be retrieved before global scanning
• protocols, research memory, schedules, and experiment plans should stay separated
• the workspace should remain usable in plain Markdown and in Obsidian

Directory structure

• 00_Inbox/
  • raw notes and pending inputs
• 01_Daily_Logs/
  • daily logs
• 02_Weekly_Reports/
  • weekly reports
• 03_Monthly_Reports/
  • monthly reports
• 04_Projects/
  • project folders, PROJECT.md, and RETRIEVAL_SCOPE.md
• 05_Experiment_Plans/
  • formal experiment plans
• 06_Meeting_Notes/
  • meeting notes and decision capture
• 09_Templates/
  • reusable templates and context-control docs
• 11_Schedules/
  • experiment and non-experiment schedule files
• 12_Actions/
  • action tracking outputs
• 13_Research_Memory/
  • stable habits, constraints, and retrieval-control notes
• 14_Protocols/
  • protocol originals, normalized files, published files, and indexes
• 15_Handoffs/
  • cross-session handoff notes

Included root pages

• Home.md
• Dashboard.md
• Projects_Index.md
• Protocols_Index.md
• Reports_Index.md
• Schedules_Index.md
• Actions_Index.md
• Research_Memory_Index.md
• Handoffs_Index.md

Included templates

• 09_Templates/project-index-template.md
• 09_Templates/retrieval-scope-template.md
• 09_Templates/workflow-handoff-template.md
• 09_Templates/CONTEXT_CONTROL_STRATEGY.md
• 09_Templates/NEW_SESSION_STARTER.md
• 09_Templates/RESEARCHPILOT_SUBAGENT_POLICY.md

Recommended startup flow

1. Fill 13_Research_Memory/user-research-profile.md
2. Put protocol source files into 14_Protocols/_raw/
3. Create one folder per active project under 04_Projects/
4. Add PROJECT.md and RETRIEVAL_SCOPE.md for each active project
5. Start with:
   • @daily-log-to-report
   • @experiment-planner
   • @meeting-note-to-action

For a guided first-use sequence, see GETTING_STARTED.md.

Recommended companion repository

Use this template together with:

• ResearchPilot-skills

The cleanest public setup is:

• one repository for installable skills
• one repository for the workspace template

中文：workspace 名字可以改

可以改。

ResearchPilot-workspace 只是模板仓库名，不是强制的实际工作目录名。你或其他用户在本地使用时，可以把工作区命名为：

• MyPhD-Workspace
• Citrus-Research-Vault
• LuoLab-Research
• 任何自己喜欢的名字

真正重要的是保留内部标准目录结构和关键文件，例如：

• 04_Projects/
• 05_Experiment_Plans/
• 14_Protocols/
• 15_Handoffs/
• AGENTS.md
• Home.md
• Dashboard.md

建议：

• 可以改仓库名
• 可以改本地文件夹名
• 不要随意改内部标准目录名，除非你也准备同步修改相关 skill 约定

English: Can the workspace be renamed?

Yes.

ResearchPilot-workspace is just the template repository name. Users may rename the actual local workspace directory freely. What should remain stable is the internal directory structure and the key workspace entry files.

Obsidian compatibility

This repository can be opened directly as an Obsidian vault.

It is intentionally lightweight:

• Markdown
• YAML front matter
• wikilinks
• optional Dataview
• optional CSS snippets

The dashboard should still remain useful even if Dataview is not installed.

Public release status

This workspace template is suitable for public sharing after basic repo hygiene:

• remove machine-local junk files
• keep personal project data out of the template
• keep installation examples path-agnostic

Those checks have been applied in the current template repository.