Bioinformatics Research Management

Orchestrate hypothesis-driven bioinformatics research projects.

First Action

1. Read STEERING.md to get current Phase
2. Read notebook/tasks.md for detailed task progress
3. Determine next action based on Phase (see Phase Judgment below)

Phase Judgment

Check **Phase** in STEERING.md and determine next action:

| Phase | Condition | Next Action | |-------|-----------|-------------| | Project Setup | P01-P05 incomplete | Continue Project Setup flow | | Experiment Planning | No active experiment | Add New Experiment flow | | Experiment Execution | E01-E06 pending | Execute E01-E06 with subagents | | Experiment Execution | E07 pending | Execute E07 (run experiment) | | Analysis | E08-E10 pending | Execute E08-E10 with subagents | | Reporting | E11 pending | Execute E11 (create report) | | Completed | All tasks done | Ask user for next direction |

Phase Transitions

| From | To | Trigger | |------|----|---------| | Project Setup | Experiment Planning | P01-P05 all complete | | Experiment Planning | Experiment Execution | Experiment added, E01 started | | Experiment Execution | Analysis | E07 complete | | Analysis | Reporting | E10 complete | | Reporting | Experiment Planning | E11 complete (ready for next experiment) | | Reporting | Completed | User declares project complete |

When Phase does not match actual task status, update STEERING.md Phase first.

Role

Act as research strategist:

• Define project objectives and research questions
• Organize hypotheses into testable experiments
• Track progress across experiments
• Ensure scientific rigor (facts vs interpretation)

Delegate individual experiment tasks to subagents via Task tool.

Reference Documents

Load these as needed:

| Document | When to Load | Search Pattern | |----------|--------------|----------------| | references/tasks.md | Task ID/format lookup | grep "E0[0-9]" | | references/prompts.md | Subagent delegation | grep "Delegate" | | references/validation.md | Quality check | grep "Validation" |

Document Hierarchy

| Document | Role | Update Frequency | |----------|------|------------------| | README.md | Project overview (static) | Rarely | | STEERING.md | Current status, TODO, links (dynamic) | Frequently | | notebook/knowledge/ | Reusable procedures (reference) | As needed | | notebook/tasks.md | Experiment-level progress | Per experiment |

Project Structure

├── README.md             # Project overview
├── STEERING.md           # Current status & navigation
├── inbox/                # User input files (memos, meeting notes)
├── notebook/
│   ├── tasks.md          # Experiment progress
│   ├── knowledge/        # Reusable procedures
│   ├── labnote/Exp##_*.md
│   ├── report/Exp##_*.md
│   └── analysis/Exp##_*.ipynb
├── results/Exp##_*/      # Output data (gitignored)
└── data/raw/             # Input data (gitignored)

Lab Notebook Format

Lab notebooks (notebook/labnote/Exp##_*.md) follow a standardized structure.

Sub-experiment Numbering

When an experiment has multiple sub-experiments, use format: {Exp番号}-{n}

Example for Exp01c:

• 実験 1c-1: 初回導入
• 実験 1c-2: 比較実験
• 実験 1c-3: 再現性確認
• ...

Document Structure

# Exp##X: タイトル

Date: YYYY-MM-DD 〜 YYYY-MM-DD (ongoing)
Source: inbox/AI-XXXX-プロジェクト名/

## 概要

### 背景
(Why this experiment is needed)

### 全体仮説
1. 仮説 1
2. 仮説 2
3. 仮説 3

### 使用機器・試薬
- 機器 A
- 試薬 B

### データ
- Input: inbox/AI-XXXX-*/
- Output: results/Exp##X_*/

---

## 実験 {Exp番号}-{n}: サブ実験タイトル (YYYY-MM-DD)

実験者: 氏名

### 背景と仮説
（前回の結果を引用 → 考察 → 仮説形成 → 目的）

### 材料と方法
(How it was done - complete details without abbreviations)

### 結果
(Facts only, tables preferred)

### 考察
#### 仮説の検証
- 仮説が支持/否定されたかを結果とともに明記

#### 重要な発見 / 問題点
- 実験固有の重要ポイント

#### 次への示唆
- 次の実験で何を検討すべきか

---

## 運用データ
(Optional: Production/operational results)

---

## 総合考察

### 全体仮説の検証
| 仮説 | 検証実験 | 結果 |
|------|----------|------|

### 主要な知見
- Point 1
- Point 2

### 限界
- Limitation 1

---

## 結論
(Summary statement)

---

## 確定プロトコル vN (YYYY-MM-DD)
(Optional: Finalized protocol if established)

---

## Decision Log
| Date | Decision | Rationale |
|------|----------|-----------|

---

## Next Steps
1. Step 1
2. Step 2

Key Principles

1. Each sub-experiment has: 背景と仮説 → 材料と方法 → 結果 → 考察
2. Results section: Facts only (tables preferred)
3. 考察 section: Structured interpretation (see below)
4. Decision Log: Track all major decisions with rationale
5. 総合考察: Synthesize findings against overall hypotheses

Narrative Documentation Style

Sub-experiments connect through a logical flow: 前回の結果 → 考察 → 仮説形成 → 目的

背景と仮説セクションの構造

### 背景と仮説

（前回の実験結果を具体的な数値とともに引用）
実験 X-N で〜〜という結果が得られた。具体的には...

（考察：なぜその結果が得られたか、矛盾点・疑問点）
この結果から、**〜〜である**と考えられる。なぜなら...

（仮説形成：考察から導かれる論理的な推論）
**仮説**: 〜〜すれば、〜〜が改善する。

（目的：何を検証し、どのような判断を下すのか）
**目的**: 〜〜を検討し、〜〜を判定する。

考察セクションの構造

箇条書きを維持しつつ、結果を引用し、仮説検証・解釈・次への示唆を含める。

### 考察

#### 仮説の検証
- **仮説（〜〜）**: 支持/否定。結果の数値を引用して根拠を示す

#### 重要な発見 / 問題点
- 実験固有の重要ポイントを整理

#### 次への示唆
- 次の実験で何を検討すべきか

Lab Notebook Documentation Workflow

To produce high-quality lab notebooks, follow this interactive workflow.

Step 1: Create Documentation TODO List

Before editing any content, create a comprehensive TODO list for the documentation task.

For each sub-experiment to document, include:

| TODO Item | Description | |-----------|-------------| | 背景と仮説 | 前回の結果引用、考察、仮説形成、目的の4要素 | | 材料と方法 | 使用プラスミド、試薬、培養条件、手順 | | 結果 | 表形式でのデータ記録 | | 考察 | 仮説の検証、重要な発見、次への示唆 |

Example TODO list:

[ ] Exp01a-1 背景と仮説: 初回試行の背景、3つの仮説を明記
[ ] Exp01a-1 材料と方法: プラスミド、試薬調製、手順を記載
[ ] Exp01a-1 結果: NanoDrop測定、TF効率を表形式で記録
[ ] Exp01a-1 考察: 仮説検証、逆説的現象の発見、次への示唆
---
[ ] Exp01a-2 背景と仮説: 1a-1の結果を引用、Wash条件検討の理由
...

Step 2: Document One Sub-experiment

Complete one sub-experiment at a time:

1. Write 背景と仮説 section with narrative flow
2. Write 材料と方法 section with complete details
3. Write 結果 section with data tables
4. Write 考察 section with structured interpretation

Step 3: User Review (Required)

STOP after each sub-experiment and present to user for review.

Present format:

## Exp{番号}-{n} の記載が完了しました

### 背景と仮説
（記載内容のサマリー）

### 考察のポイント
- 仮説の検証結果: ...
- 重要な発見: ...
- 次への示唆: ...

---
この内容でよろしいですか？修正点があればお知らせください。

Wait for user approval before proceeding to next sub-experiment.

Step 4: Iterate

After user feedback:

1. Apply corrections to current sub-experiment
2. Mark TODO as complete
3. Proceed to next sub-experiment
4. Repeat Steps 2-4 until all TODOs complete

Step 5: Final Validation

After all sub-experiments documented:

1. Run textlint: textlint --fix -c ~/.local/share/textlint/.textlintrc.json {file}
2. Verify narrative flow across sub-experiments
3. Check 総合考察 reflects all findings

inbox/ の処理

ユーザーが inbox/ にファイルを置いた場合:

1. 内容を確認し、関連する情報を抽出
2. 適切な場所に統合（labnote, knowledge, README など）
3. 処理完了後、元ファイルの削除を提案

Workflow Overview

1. Project Setup

When Phase is "Project Setup":

1. Ask user: "研究について教えてください。どのようなデータがあり、何を明らかにしたいですか？"
2. Extract P01-P05 information from response
3. Fill gaps with follow-up questions
4. Update README.md, STEERING.md, notebook/tasks.md
5. Transition to "Experiment Planning"

2. Add New Experiment

When Phase is "Experiment Planning":

1. Ask user: "次の実験について教えてください。何を検証したいですか？"
2. Extract: Exp title, Observation, Hypothesis, Verification
3. Fill gaps with follow-up questions
4. Create experiment entry in tasks.md and STEERING.md
5. Transition to "Experiment Execution"
6. Execute E01-E06 (see below)

3. Execute E01-E06 (Experiment Setup)

Load references/prompts.md for detailed subagent prompts.

| Task | Action | User Input Required | |------|--------|---------------------| | E01 | Create labnote from template | No | | E02 | Fill Observation section | From Add New Experiment | | E03 | Fill Hypothesis section | From Add New Experiment | | E04 | Fill Verification section | From Add New Experiment | | E05 | Fill Tools & Data | Yes: ツールとデータパス | | E06 | Fill Methods | Yes: 実験手順 |

After E06 complete → Confirm with user before E07.

4. Execute E07 (Run Experiment)

Delegate experiment execution to subagent. → E07 complete → Transition to "Analysis"

5. Execute E08-E10 (Analysis)

| Task | Action | User Review | |------|--------|-------------| | E08 | Record results (facts only) | No | | E09 | Write interpretation | Yes | | E10 | Write conclusion | No |

→ E10 complete → Transition to "Reporting"

6. Execute E11 (Create Report)

Load references/prompts.md for report section mapping.

→ E11 complete → Update STEERING.md → Transition to "Experiment Planning"

7. Knowledge Management

When creating reusable procedures:

1. Save to notebook/knowledge/ with prefix (workflow_, protocol_, reference_)
2. Add link to STEERING.md Quick Links section