research▌

### Primekg - name: "primekg" - description: "Query the Precision Medicine Knowledge Graph (PrimeKG) for multiscale biological data including genes, drugs, diseases, phenotypes, and more."

### Pathml - name: "pathml" - description: "Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model tra..."

### Scholar Evaluation - name: "scholar-evaluation" - description: "Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and wri..."

### Opentrons Integration - name: "opentrons-integration" - description: "Official Opentrons Protocol API for OT-2 and Flex robots. Use when writing protocols specifically for Opentrons hardware with full access to Protocol API v2 features. Best for production Opentrons pro..."

### Scientific Brainstorming - name: "scientific-brainstorming" - description: "Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-st..."

### Qutip - name: "qutip" - description: "Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics, decoherence, quantum optics, or cavity QED. Best for physics research, open system d..."

### Scanpy - name: "scanpy" - description: "Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA..."

### Rowan - name: "rowan" - description: "Rowan is a cloud-native molecular modeling and medicinal-chemistry workflow platform with a Python API. Use for pKa and macropKa prediction, conformer and tautomer ensembles, docking and analogue dock..."

### Qiskit - name: "qiskit" - description: "IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production workloads, or needing IBM optimization tools. Best for IBM hardware execution, quan..."

### Research Lookup - name: "research-lookup" - description: "Look up current research information using parallel-cli search (primary, fast web search), the Parallel Chat API (deep research), or Perplexity sonar-pro-search (academic paper searches). Automaticall..." - allowed-tools: "Read Write Edit Bash"