Ten Practices for Refactoring Scientific Pipelines to nf-core DSL2 on Shared Slurm HPC
Ten Practices for Refactoring Scientific Pipelines to nf-core DSL2 on Shared Slurm HPC. US-RSE (2026). Long paper.
CV
Education
- M.S. in Computer Science (Biomedical Informatics), Arizona State University, 2023
- B.S. in Computer Science, Arizona State University, 2022
- B.S. in Biology, Wuhan University, 2017
Work experience
- Jan 2024 – Present: HPC Systems Administrator
- Research Computing, Research Technology Office, Arizona State University — Tempe, AZ
- Port bioinformatics LLMs and scientific software to Intel Gaudi2 accelerators and generate accompanying benchmark data
- Develop benchmarking and post-maintenance testing software for heterogeneous HPC clusters
- Tune workflow-management system performance and scheduling on Slurm-based HPC
- Refactor genomic sequencing software to modern nf-core standards, contributing to the Earth BioGenome Project
- Develop a large-scale Nextflow-based virus detection and discovery pipeline with the NASA OSDR Microbiome Analysis Working Group
- Integrate the HPC account management system with the university registration database for automated account provisioning
- Customize the Open OnDemand web portal to support scientific applications and agentic AI functionality
- Manage HPC software stacks and databases; provide real-time troubleshooting for job, software, and hardware issues
- Jan 2022 – Dec 2023: Graduate Research Assistant
- ASU Biodesign Institute, Efrem Lim Lab — Tempe, AZ
- Developed an explainable neural network pipeline for microbiome-based classification of COVID-19 patient samples (400 features), using a multilayer perceptron (mean AUC 0.75) with SHAP for feature importance analysis
- Designed a DBSCAN-based clustering workflow to establish the true-positive threshold for KrakenUniq classification output
- Contributed to an open-source Python package for model-agnostic feature reduction methods
- Served on the Arizona Department of Health Services COVID-19 Sequencing Project team; built an ETL pipeline managing sequencing data for over one-third of the Arizona patient population, reporting results to government agencies and hospitals
- Built a generalizable genomic workflow that identified two novel bat coronaviruses from 250 raw samples on ASU supercomputing resources
- Jun 2021 – Jan 2022: Research Assistant
- ASU School of Sustainable Engineering and the Built Environment — Tempe, AZ
- Connected twelve analog and digital environmental sensors to Arduino Uno and Raspberry Pi platforms to build IoT sensor enclosures for mobile weather stations
- Built a real-time Adafruit data dashboard integrating MQTT, Google Drive, and SQLite for data logging and visualization
- Sep 2020 – Jun 2021: Research Assistant
- ASU School of Mathematical and Statistical Sciences — Tempe, AZ
- Designed an undergraduate machine learning curriculum (MAT 400-level) that has been taught at ASU since Fall 2021
- Processed 50,000 rows of U.S. population mobility data using the spectral clustering algorithm to model COVID-19 transmission patterns
- May 2020 – Aug 2020: Software Development and Testing Intern
- Autowise.ai & Boschung — Chandler, AZ & Chicago, IL
- Designed and executed software and hardware tests for a self-driving robotic street sweeper, resolving issues identified during virtual and real-world road trials
- Reviewed and managed testing data, providing feedback and recommendations to the R&D and Business teams
- Led relocation of the full test set from Chandler to Chicago, including establishing a new test environment, producing new LiDAR maps, and training personnel for ongoing operations
- Sep 2019 – Jan 2020: Volunteer Research Assistant
- ASU Biodesign Institute — Tempe, AZ
- Applied natural language processing and machine learning algorithms to find associations among genes across more than 1,700 biomedical papers, using Python and Excel
- Extracted and cleaned protein sequences from over 3,500 records in the NCBI database, using Biopython, Pandas, and NumPy
- Adapted multiple-sequence alignment, motif searching, and text-mining algorithms to cluster and identify universal features among antibody protein sequences
- Sep 2019 – Dec 2019: Research Assistant — ZooPhy Data Expansion Project
- ASU Biodesign Center for Environmental Health Engineering (with Dr. Matthew Scotch) — Tempe, AZ
- Developed the Geoname Climate Data Integration System (GCIS) for ZooPhy, supporting the reconstruction of virus spread through phylogeography
- Integrated NOAA GHCN temperature and precipitation data — cleaned and parsed into a PostgreSQL relational database — to enhance ZooPhy’s epidemiological and phylogeographic capabilities
- Built a command-line interface to manage the databases
- Sep 2018 – Apr 2019: Research Affiliate
- Mayo Clinic — Phoenix, AZ
- Conducted field observations across Mayo Clinic ambulatory and ancillary care settings to analyze clinical-environment issues and observe provider–EHR interaction during migration to the Epic system, reporting findings in TOYOTA A3 problem-solving format
- Proposed a Clinical Decision Support System (CDSS) based on Prescription Drug Monitoring Programs (PDMPs) for patient pain management; presented as a poster speaker at the 5th Annual Mayo Clinic–ASU BMI/BMD Student Poster and Employer Networking Event (April 2019)
- Completed a two-month intensive introduction to medical terminology, human anatomy, and physiology
- Apr 2014 – Jan 2018: Research Assistant
- Chinese Academy of Sciences — Wuhan, Hubei, China
- Designed and conducted cell-biology and BSL-2 animal experiments, including the handling of infectious materials; co-authored a paper published in the Journal of Biological Chemistry (2017)
- Project 1 — GPI anchor system genes regulate the formation of PrP in AsPC-1 cells
- Project 2 — PrP responds to the TNFα-triggered NF-κB signaling pathway by preventing the deubiquitinase activity of CYLD on RIP1 and TRAF2 (published)
- Project 3 — PrP expression influences the establishment of Herpes Simplex Virus Type 1 latency
- Techniques: fluorescence microscopy, UV-Vis spectrophotometry, RT-PCR/qPCR/PCR, CRISPR/Cas9 gene editing, molecular cloning; SDS-PAGE, Native PAGE, Western blot, Co-IP, IP, and ELISA
- Jan 2014 – Sep 2015: Team Leader / Slides & Poster Speaker
- iGEM Competition, Team WHU-China — Wuhan, China
- Led a synthetic-biology project constructing a DNA criticality-detector circuit in E. coli as an automatic medicine-dosage threshold for addressing human dental caries
- Awarded a Silver Medal at the iGEM 2015 Jamboree
Skills
- High-Performance Computing (HPC), Slurm, Linux cluster administration
- Research software engineering: Nextflow, nf-core, workflow optimization, benchmarking
- Bioinformatics and genomics pipelines
- Machine learning: neural networks (MLP), CatBoost, SHAP, DBSCAN, spectral clustering
- Python, ETL and data pipelines, relational and NoSQL databases
- Languages: English (full professional), Chinese (native/bilingual)
Publications
Provisioning a Large-Scale AI Platform Composed of Intel Gaudi2 Accelerators at Arizona State University
Provisioning a Large-Scale AI Platform Composed of Intel Gaudi2 Accelerators at Arizona State University. PEARC (2026). Long paper.
Optimizing Nextflow-based Software on Shared HPC Resources: A Case Study with make_lastz_chains
Optimizing Nextflow-based Software on Shared HPC Resources: A Case Study with make_lastz_chains. US-RSE (2025). Long paper.
Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children
Longitudinal dynamics of the nasopharyngeal microbiome in response to SARS-CoV-2 Omicron variant and HIV infection in Kenyan women and their children. mSystems, American Society for Microbiology (May 2025).
Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA
Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA. mBio, American Society for Microbiology (Feb 2023).
Prion protein is required for tumor necrosis factor alpha (TNFα)-triggered nuclear factor kappa B (NF-κB) signaling and cytokine production
Prion protein is required for tumor necrosis factor alpha (TNFα)-triggered nuclear factor kappa B (NF-κB) signaling and cytokine production. Journal of Biological Chemistry (Sep 2017). JBC Recommended Reads, Oct 2017.
Talks
Tuning Workflow Management Systems for Shared HPC Resources
Presentation at RMACC HPC Symposium, Boulder, CO, USA
HPL (Linpack) and Other Popular Benchmarks on Heterogeneous HPC Clusters
Presentation at RMACC HPC Symposium, Boulder, CO, USA
A Clinical Decision Support System Based on Prescription Drug Monitoring Programs for Patient Pain Management
Poster at 5th Annual Mayo Clinic–ASU BMI/BMD Student Poster and Employer Networking Event, Phoenix, AZ, USA
A DNA Criticality-Detector Circuit in E. coli for Automatic Medicine-Dosage Thresholds
Poster & Slides at International Genetically Engineered Machine (iGEM) 2015 Jamboree, Boston, MA, USA
Teaching
Grants and fellowships
- USRSE Travel Grant — US-RSE ‘25 (Awarded)
- RMACC Scholarship — RMACC HPC Symposium 2026 (Awarded)
- CCMNet Travel Grant, Cyberinfrastructure Community-wide Mentorship Network — PEARC ‘26 (Awarded)
- Better Scientific Software (BSSw) Fellowship Program — 2027 cycle (Application in preparation)
Service and leadership
- Committee Member, Scientific Subcommittee on IT and Informatics, Earth BioGenome Project
- Planning Committee Member, Operational Data Analytics (ODA) Birds-of-a-Feather session, SC26
- ASU Cluster Representative, Energy Efficient HPC Working Group (EE HPC WG)
- Mentor, “Tuning Workflow Management Systems on HPC,” Cyberinfrastructure Community-wide Mentorship Network (CCMNet), 2026
- Cyberinfrastructure Facilitator, CIREN project, 2026
- Certified Instructor, The Carpentries, 2024 – present
Certifications and professional development
- NSF-WildWEST Project Summer Field Camp — field engineering training, 2026
- CyberAmbassadors program (Engineering Futures) certificate, 2025
- Linux Cluster Institute entry- and intermediate-level certificates, 2024
Honors and awards
- Mathematical Contest in Modeling (MCM) 2021 — Successful Participant
- International Genetically Engineered Machine (iGEM) Competition 2015 — Silver Medal (Team WHU-China; Team Leader)