| name | bio-task-system |
| description | Step 2 of the bio-manuscript pipeline: design the task system. Use when identifying the dominant task taxonomy in a field and organizing it into a staged Level 1-4 difficulty ladder to prepare for downstream dataset and metric design. |
bio-task-system
Step 2: Task system design (任务体系构建)
Identify the main task categories in the field and organize them into a staged difficulty ladder.
Purpose
- Find the dominant task taxonomy in the target field
- Define Level 1-4 task tiers
- Ensure the task ladder increases in difficulty
- Prepare the task system for downstream dataset and metric design
Input Format
topic: [research topic]
paper_count: [number of related papers from Step 1]
Workflow
Step 2.1: Task taxonomy search
If there is substantial prior work, extract tasks from existing papers.
If there is not enough prior work, borrow the taxonomy from a parent domain and adapt it.
Typical adaptation logic:
- single-cell multi-omics -> spatial multi-omics
- modality alignment -> spatial-cell alignment
- batch integration -> cross-sample integration
Step 2.2: Task tier design
Define four levels:
- Level 1: basic validation task
- Level 2: intermediate application task
- Level 3: challenge task
- Level 4: flagship innovation task
Increase across three dimensions:
- Data complexity
- Technical difficulty
- Biological value
Step 2.3: Standardize task descriptions
For each task, write:
- definition
- difficulty level
- data requirements
- technical focus
- biological value
- representative methods
- mapped figure
Output Format
# Task System Design
## Task Sources
- Extracted from related papers:
- Borrowed from parent domain:
## Tier Overview
| Level | Task type | Difficulty | Figure |
|-------|-----------|------------|--------|
| 1 | ... | low | Figure 2 |
| 2 | ... | medium | Figure 3 |
| 3 | ... | high | Figure 4 |
| 4 | ... | highest | Figure 5 |
## Detailed Task Descriptions
### Task 1: [task name]
- Definition:
- Difficulty:
- Data requirements:
- Technical focus:
- Biological value:
- Representative methods:
- Mapped figure:
### Task 2: ...
## Progression Rationale
1. Data complexity rises across tasks
2. Technical difficulty rises across tasks
3. Biological value rises across tasks
## Next Step
- Use the task system to search for datasets in Step 3
Example Ladder
- Level 1: vertical integration
- Level 2: horizontal / cross-slice integration
- Level 3: mosaic integration with missing modalities
- Level 4: diagonal integration across platform / resolution / cohort
Usage
/bio-task-system "spatial multi-omics integration | paper_count: 5"
Notes
- Keep the ladder interpretable to reviewers.
- Avoid adding too many tasks; four well-designed tiers are usually enough.
- Make sure each task can later be tied to datasets, metrics, and figures.
