QingFeng Li

Build and run genomics analyses on DNAnexus, a cloud platform for biomedical data. Covers analysis apps, file organization, multi-step workflows, job monitoring, and automation with the dxpy Python library.

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• Build a genomics analysis app
• Upload and organize sequencing data
• Run analyses across multiple samples

Organize Word comments alongside the passages they refer to, draft individual responses, and add threaded replies to a new document. Produces context reports and reply templates, then checks the resulting document structure.

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• Responding to comments on a research paper
• Preparing replies to contract review comments
• Addressing comments on patent documents

Guide multi-step research with source checks, comparisons across sources, and recovery from tool errors. The skill tracks retrieved evidence and unresolved gaps so reports show what supports their claims and what remains unverified.

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• Check evidence across multiple sources
• Recover from failed searches or page retrievals
• Track retrieved sources and supporting claims

Investigates existing code before feature work, bug fixes, or refactoring. Finds similar implementations, reusable helpers, naming rules, and data handling patterns so proposed changes follow the project's established conventions.

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• Investigating similar features before implementation
• Checking existing conventions before fixing bugs
• Finding reusable helpers before refactoring

Create charts from existing CSV files, tables, or query results to show trends, distributions, comparisons, and relationships. The skill guides chart selection and axis choices for everyday analysis, presentation slides, and simple dashboards.

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• Charting monthly conversion rates
• Exploring latency and throughput relationships
• Turning CSV summaries into simple dashboards

Find official documentation for a library, framework, or API and match it to the version in use. Get source-backed answers and focused code examples, with any details that could not be verified clearly identified.

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• Checking API usage for a specific version
• Finding examples that match project dependencies
• Confirming answers against official documentation

Retrieve stock prices, exchange rates, cryptocurrency prices, company financial statements, and economic indicators through the Alpha Vantage API. It also covers historical data, news sentiment, and technical indicators, which summarize price and trading patterns.

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• Retrieve historical stock prices and trading volumes
• Collect company financial statements and earnings data
• Check foreign exchange and cryptocurrency prices

Design and implement data visualizations that explain patterns through clear charts, purposeful color, and a narrative. Choose suitable scales, check data sources, and add interactions that let viewers explore details.

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• Turn raw numbers into a visualization with a clear story
• Review chart scales and colors for misleading choices
• Build interactive charts for exploring details

Work with DNA, RNA, and protein sequences in Python. Read and convert biological files, compare sequences, search for similar sequences with BLAST, retrieve NCBI records, analyze protein structures, and build or visualize evolutionary trees.

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• Convert GenBank files to FASTA
• Calculate sequence length and GC content
• Search with BLAST and retrieve matching sequences

Look up how genetic differences affect medication response using ClinPGx. Retrieve gene–drug relationships, clinical guidelines, genetic variant functions, and drug labels to gather evidence for research and reviews of genotype-based dosing recommendations.

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• Investigate gene–drug relationships
• Review guidelines for genotype-based dosing
• Compare genetic variant frequencies across populations

Creates LaTeX/PDF reports for pharmaceutical and clinical research. Compares patient groups by biomarkers, measurable biological indicators, and prepares treatment recommendation documents with evidence ratings, statistical results, and decision flowcharts.

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• Comparing outcomes across biomarker-defined patient groups
• Preparing treatment recommendations with evidence ratings
• Creating flowcharts for biomarker-guided treatment selection

Manage complex agent tasks through agreed requirements, plans, execution, verification, and cleanup. The workflow sets approval boundaries, assigns skills to defined work units, records evidence, and reports verified deliverables alongside any remaining blockers.

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• Agree on requirements and completion criteria for complex tasks
• Assign skills and dependencies to individual work units
• Review requirements and plans at explicit approval boundaries

Draft case reports, diagnostic reports, clinical trial reports, and patient records using document-specific structures and templates. The skill guides completeness checks, patient de-identification, and documentation aligned with named clinical reporting guidelines and regulatory frameworks.

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• Drafting case reports for journal submission
• Organizing radiology, pathology, and laboratory reports
• Preparing clinical trial and serious adverse event reports

Build automated data checks with Great Expectations and dbt to detect missing values, duplicates, invalid ranges, and stale records. Define data contracts, shared agreements on data structure and quality, and summarize validation results across tables.

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• Add missing-value and duplicate checks to order data
• Build dbt tests for relationships between tables
• Define shared data requirements between teams

Investigate unusual transactions, sensor spikes, rare failures, and other suspicious records. The skill helps compare anomaly detection methods and thresholds, prepare records for human review, and plan checks for false alarms and missed anomalies.

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• Reviewing unusual transactions and possible fraud
• Investigating sensor spikes and rare failures
• Comparing anomaly detection methods and thresholds

Process datasets that exceed available memory and run Python computations across multiple cores or machines. The skill guides large table and array operations, multi-file cleaning and aggregation, custom task dependencies, and execution settings for parallel workflows.

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• Aggregate multiple CSV or Parquet files
• Process numeric arrays larger than available memory
• Clean JSON records and logs for analysis

Support experimental validation of designed proteins through a cloud laboratory. Prepare and optimize sequences, submit tests for binding, expression, thermal stability, or enzyme activity, track experiment progress, and retrieve results through the API.

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• Submit designed proteins for binding tests
• Request expression, thermal stability, or enzyme activity tests
• Optimize sequences for solubility before experiments

Carry a software project from requirements and design through implementation, testing, debugging, and deployment. Tracks progress in files, works through features incrementally, and resumes interrupted development, supporting new projects and broad refactoring efforts.

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• Building a new project from a specification
• Resuming an interrupted development project
• Developing features across multiple implementation steps