Invoke after experiment-runner completes an investigation's query bundle. Evaluates all claims in current_investigation.json and produces an investigation-level adjudication. Writes claim_scores.json.
Invoke after investigation-decomposition. Runs all queries in an investigation bundle using shared data preparation. Writes code and results.
Invoke after main agent writes L2 assessment. Reads epistemic state (L1/L2), patterns, and investigations to recommend next action. Writes strategy_recommendation.json.
Gene set enrichment analysis (GSEA, Enrichr, over-representation). Invoke when query mentions enrichment, pathway analysis, GO analysis, GSEA, or gene set.
Invoke before running experiments for an investigation. Reads current_investigation.json and task_packet.json, writes current_investigation_requirements.json with shared data preparation and per-query requirements.
Gene ID conversion and annotation. Invoke when you need to map between any gene identifier formats.
Phylogenetic analysis: multiple sequence alignment (MAFFT), tree building (IQ-TREE, FastTree), tree metrics (treeness, branch lengths, patristic distances). Invoke when query involves phylogenetic trees, evolutionary analysis, sequence alignment, treeness, or…
Differential expression analysis for RNA-seq count data. Invoke when query mentions DESeq2, differential expression, DE genes, or RNA-seq comparison.