Skill: heterogeneous source integration and multi-hop reasoning

[Case 2]

• Initial Environment: An empty notebook is provided together with several biological data files and a preconfigured analysis environment. The answer depends on comparing differential-expression results across multiple strains.
• Real Question: How many genes are uniquely differentially expressed in strain 98 but not in either of strains 97 or 99?
• Real Trajectory: List the workspace; load the differential-expression outputs for all three strains; extract the gene sets that satisfy the relevant significance criteria; compute the set difference for strain 98 against strains 97 and 99; count the remaining genes; submit the final answer.
• Why this demonstrates the capability: No file directly stores the requested count. The agent must integrate results from several related analyses, maintain consistent selection criteria, and perform set-based reasoning. This is a classic multi-hop analytical trajectory over heterogeneous scientific outputs.

Pipeline Execution Instructions

To synthesize data for this capability, you must strictly follow a 3-phase pipeline. Do not hallucinate steps. Read the corresponding reference file for each phase sequentially:

1. Phase 1: Environment Exploration Read the exploration guidelines to discover raw knowledge seeds: references/EXPLORATION.md

2. Phase 2: Trajectory Selection Once Phase 1 is complete, read the selection criteria to evaluate the trajectory: references/SELECTION.md

3. Phase 3: Data Synthesis Once a trajectory passes Phase 2, read the synthesis instructions to generate the final data: references/SYNTHESIS.md