Hello! I'm Justin Cheney, a Computer Science Honours student at the University of the Western Cape, Cape Town, South Africa. I'm actively engaged in multiple research and infrastructure roles spanning bioinformatics workflows, high-performance computing infrastructure, and nature-inspired AI research. My career goal is to advance High-Performance Computing (HPC) and computational biology by developing intelligent systems that optimize resource allocation, enable reproducible workflows, and democratize access to computational infrastructure across African institutions.
Currently, I'm working on:
- Bioinformatics Workflows & SOP Development at SANBI as part of the PHA4GE consortium, designing standardized bioinformatic workflows for epidemiologists
- HPC Infrastructure & GPU Configuration as a Research Assistant for the SI-NRF Centre of Excellence in Food Security
- Nature-Inspired AI Research with the Computational Intelligence Research Group (CIRG) across agri-food systems, smart healthcare, and resource optimization
- HPC Education & Documentation as Co-Lead Mentor at UWC for the CSIR CHPC Student Cluster Competition
My work focuses on the intersection of:
- 🖥️ High-Performance Computing (HPC): Optimizing cluster infrastructure, GPU configuration, and parallel computing for scientific research at scale
- 🧬 Bioinformatics & Workflows: Designing reproducible, standardized computational workflows for epidemiological research and pathogen analysis
- 🤖 Nature-Inspired AI & Deep Reinforcement Learning: Developing intelligent systems for resource optimization, job scheduling, and problem-solving across diverse domains
- 💎 Julia Programming: Harnessing Julia's power for scientific computing and performance-critical applications
- 📚 HPC Education: Creating accessible documentation and mentorship pathways for the next generation of HPC practitioners
South African National Bioinformatics Institute (SANBI) | Cape Town, South Africa
📅 Present
Working across multiple strategic initiatives in the HPC and bioinformatics departments:
HTC Workflows & SOP Development (PHA4GE Project):
- 🧬 Designing standardized bioinformatic workflows and Standard Operating Procedures (SOPs) for pathogen genomics
- 🌍 Developing workflows intended for implementation across epidemiology labs and institutions in Africa
- 📋 Creating reproducible, containerized workflows for high-throughput computational analysis
- 🤝 Collaborating with PHA4GE consortium partners to ensure interoperability and accessibility
HPC Infrastructure Management:
- 🖥️ Managing and maintaining HPC cluster infrastructure for computational biology research
- 🌐 Network administration and optimization for high-throughput data transfer
- 📊 Performance monitoring and system optimization using tools like Prometheus and Grafana
- 🔧 Supporting researchers with job scheduling, resource allocation, and computational workflow optimization
- 🛠️ Troubleshooting and resolving technical issues in a production HPC environment
- 📈 Contributing to infrastructure upgrades and capacity planning
Technologies Used: Slurm, Linux (Ubuntu), Singularity/Docker, Nextflow, CWL, Networking protocols, Monitoring tools, HPC optimization techniques
SI-NRF Centre of Excellence in Food Security | South Africa
📅 Present
Supporting cutting-edge research in food security through high-performance computing infrastructure.
Key Responsibilities & Achievements:
- 🖥️ HPC cluster configuration and management for food security research initiatives
- 🎮 GPU acquisition, installation, and optimization for accelerated computing workloads
- 🔧 System administration and environment optimization for diverse researcher needs
- 📚 Creating user-friendly documentation and training materials for HPC cluster access
- 🌐 Designing accessible computational environments for researchers with varying technical backgrounds
- 🚀 Performance tuning and resource allocation optimization
- 🔬 Supporting researchers in utilizing advanced computing resources for their work
Technologies Used: Linux systems administration, GPU computing (CUDA), HPC cluster management, Documentation tools
Computational Intelligence Research Group (CIRG) | South Africa
📅 Present
Conducting research on nature-inspired AI techniques and their applications across multiple domains.
Research Areas:
- 🌾 Agri-Food Systems: Optimizing agricultural processes through intelligent algorithms
- 🏥 Smart Healthcare: Developing AI solutions for healthcare optimization and resource management
- 🔭 Astronomy: Applying nature-inspired techniques to astronomical data analysis
- 💧 Water Management: Intelligent systems for water resource optimization
- ⚡ Energy Systems: Nature-inspired approaches to energy management and optimization
Technologies Used: Nature-inspired algorithms, Machine Learning, Python, Data analysis tools
CSIR CHPC Student Cluster Competition - University of the Western Cape | Cape Town, South Africa
📅 2025 - Present (Continuing from 2024)
Volunteering as Co-Lead Mentor to develop the next generation of HPC practitioners at UWC, with a focus on training mentors and equipping competition participants.
Key Responsibilities & Achievements:
- 👥 Leading UWC team through the CSIR CHPC Student Cluster Competition pipeline
- 🎓 Training and developing the next generation of mentors - equipping them with HPC knowledge and mentorship skills
- 📚 Teaching participants from Linux fundamentals through to advanced benchmarking and performance optimization
- 💻 Curriculum development: Linux basics → cluster architecture → optimization → benchmarking → performance analysis
- 📖 Creating accessible educational resources and documentation for skill progression
- 📝 Planning and executing a publication on HPC Education (2025/2026) to share best practices
- 🏆 Guiding teams to national competition success while building a sustainable mentorship pipeline
Impact: Trained 2025 team member selected for the National Team; establishing long-term HPC education culture at UWC
Technologies Used: Linux, HPC Architecture, Benchmarking tools, Technical writing, Mentorship frameworks
University of the Western Cape | Cape Town, South Africa
📅 2026 - Present
University of the Western Cape | Cape Town, South Africa
📅 2023 - 2025
| 💡 Problem Solving | 🤝 Team Collaboration | 📊 Research & Analysis |
| 🎯 Critical Thinking | 📚 Self-Learning | ⏱️ Time Management |
| 📝 Technical Writing | 🗣️ Communication | 🔍 Attention to Detail |
- 🌱 Exploring advanced parallel computing patterns in Julia
- 🎯 Implementing state-of-the-art Deep RL algorithms for HPC job scheduling
- 💡 Optimizing neural network training on distributed systems
- 📚 Contributing to open-source HPC and Julia ecosystem
- 🔬 Resource allocation and optimization in high-performance computing environments
- 🧠 Model-based reinforcement learning systems
- ⚡ Performance optimization and benchmarking
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Technologies: C, Adversarial Algorithms Description: A chess engine written in C following bluefeversoft's tutorial. This project enhanced my understanding of AI heuristics for move calculation and applied advanced C programming techniques learned during my third year. Role: Solo Developer Outcome: Functional chess engine with AI opponent capabilities |
Technologies: Java, MySQL Description: A comprehensive database management system for zoo operations, including animal tracking, feeding schedules, and visitor management. Role: Database Designer & Developer Outcome: Efficient relational database system with GUI |
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Role: Team Lead Achievement: 3rd Place (National Round) Description: Led a team in building and optimizing a small HPC cluster over 5 intensive days. Responsible for fine-tuning cluster performance and running various synthetic and application-based benchmarks to demonstrate system capabilities. Skills Applied: HPC Architecture, Performance Benchmarking, Team Leadership, Cluster Optimization |
Role: Lead Mentor Achievement: Mentored team to 4th Place (National Round) Description: Served as lead mentor, training students from preparation through to the national competition round. Personally mentored the 4th place team, with one team member being selected for the National Team - a testament to the quality of training and guidance provided. Skills Applied: Mentorship, Technical Training, HPC Education, Leadership Development |
No publications yet.
Currently working on research in HPC job scheduling optimization using deep reinforcement learning. Stay tuned for upcoming papers!
- 💻 Open Source Contributor - Julia Community & HPC Ecosystem
- 🎓 IT Society - (Member) University of the Western Cape
- 📚 HPC Society - (Mentor) University of the Western Cape
💻 I code best with a cup of coffee ☕ | ♟️ When not coding, you'll find me playing chess | 🌍 Love exploring new technologies
Thanks for visiting my profile! ⭐
Feel free to reach out if you want to collaborate on HPC, Julia, or RL projects!
