I am a PhD computer scientist (my thesis focused on machine learning) with 15+ years of software development experience across academia and industry in the UK and USA.
I currently lead an open source container runtime project, with involvement in development, managing roadmaps, commercial LTS, and mentoring junior and mid-level developers.
I have deep knowledge of scientific computing including HPC, containerization, and cloud, especially in the context of my background in bioinformatics and computational proteomics research with 30+ peer-reviewed publications.
I'm comfortable leading greenfield and brownfield projects, and take pride in delivering pragmatic solutions to difficult problems with a strong focus on UX for less-technical users.
Please get in touch if you have any questions or would like to discuss potential opportunities.
Education
PhD, Computer Science
2008University of Exeter, Exeter, UK
Development of novel neural networks for the classification of protein sequence data.
BSc (Hons), Computer Science — 1st Class
2004University of Exeter, Exeter, UK
Experience
Sylabs Inc. / QLAD
Remote, USA & UK
Software Engineer, QLAD Confidential Containers Platform
2025 – Present- Development in Go of backend REST API server and in-cluster agent with gRPC communication for QLAD - a confidential containers platform for kubernetes, supporting confidential computing on EKS/AKS/GKE and local SEV-SNP confidential computing hardware.
Software Engineer, Lead for SingularityCE & PRO
2019 – Present- Lead for SingularityCE open-source HPC container runtime written in Go, and SingularityPRO commercial LTS. Covering all aspects of the project including roadmap, development, support, and interaction with customers and the open-source community.
- Drove improved QA processes with end-to-end testing across Linux distributions and HPC-like test environments, to deliver a regular six-monthly open source / annual LTS release cycle and reduction of support incidents.
- Conceived and developed Singularity's OCI-mode, for improved compatibility with OCI-compliant runtimes and standards (e.g. CDI) in modern HPC environments.
- Navigated the project and community spaces through a fork (Singularity -> SingularityCE & Apptainer), with minimal disruption to users and customers, while mentoring junior and mid-level developers.
Software Developer, Singularity & Container Services
2018- Led design and development of the Sylabs container library cloud service to alpha stage.
- Contributed to design and development of authn / authz / token services.
- Contributed to development of Singularity container runtime & rewrite from C/Python to Go.
UT Southwestern Medical Center
Dallas, TX, USA
Computer Scientist, BioHPC
2018 – 2019- Led multiple web and scientific software development projects in Python, supervising junior developers. Co-ordinated fellowship program. Contributed to HPC system administration and user support. Delivered HPC training and Python nano-course sessions.
- Responsible for the initial development of Astrocyte, a web-based platform for the publication of Nextflow workflows, and R/Shiny visualization tools developed by expert bioinformatics groups. Git-based workflow publication, HPC workflow execution, Python/Django front-end for ease of use by non-computational researchers.
Computational Scientist / Scientific Programmer III
2014 – 2018- Member of the UTSW BioHPC high-performance computing team. Led web and scientific software projects. Co-ordinated and delivered training. Contributed to user support, scientific collaborations, and administration of the HPC cluster.
- Developed features for the BioHPC portal - a web-based platform for interacting with HPC resources. Tasks included conversion to django CMS for content publication. Integration with institutional LDAP directory systems. Creation of SLURM submission / monitoring tools, usage accounting, web-VNC based interactive desktop access with GPU OpenGL acceleration. Python with Django.
Instructor / Assistant Professor (Research Track)
2011 – 2014- Computational proteomics research, scientific software development, and data analysis support for proteomics service.
- Further developed the Central Proteomics Facilities Pipeline, to leverage cloud and HPC resources for large-scale datasets. Received an AWS in education research grant.
University of Oxford
Oxford, UK
Bioinformatician in Proteomics
2008 – 2011- Computational proteomics research, scientific software development, and data analysis support for proteomics service and Ratcliffe laboratory.
- Developed the Central Proteomics Facilities Pipeline (CPFP), a web-based platform for the analysis of proteomics data, targeted at the needs of core facilities.
Technical Skills
Languages
Primarily Go (7 years). Additional experience across Python, Perl, R, shell scripting, Java, C.
Operating Systems
Linux (Debian/Ubuntu, RHEL family, SLES) including systems level development, advanced troubleshooting, and rpm packaging. macOS.
Containers & Virtualization
Singularity, Docker/OCI, KVM/QEMU.
Cloud & Infrastructure
AWS, Azure, GCP. Terraform, Ansible. Kubernetes, KubeVirt.
HPC
SLURM, MPI, InfiniBand, Lustre, GPFS/Spectrum Scale, GPUs.
CI / CD
CircleCI, GitHub Actions.
Web & Frameworks
Echo, REST APIs, Django, HTML/CSS.
Databases
PostgreSQL, MySQL, SQLite, MongoDB.
Bioinformatics
Shotgun proteomics LC-MS/MS data analysis pipelines, RNA-Seq analysis, Nextflow workflow development, R/Shiny visualization tools.
Soft Skills
- Remote Work: 7 years experience with a fully-remote company. Comfortable working across timezones, managing asynchronous communication, and balancing independent and team working.
- Writing / Communication: First or co-author of over 30 peer-reviewed scientific publications. Contributed to multiple scientific grant applications. Led open source community spaces & project documentation.
- Training / Mentoring: Enjoy giving training on basic and technical topics. Have successfully mentored multiple junior & mid-level developers.
Memberships, Awards & Service
- Member, British Computer Society.
- Fedora / EPEL Packager.
- AWS in Education Research Grant ($10,000, 2011-2013).
- Honorary Life Member, University of Exeter Guild of Students.
Selected Publications
See all →- Salomon D, Klimko JA, Trudgian DC, Kinch LN, Grishin NV, Mirzaei H, Orth K. Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria. PLoS Pathog. 2015 Aug 25;11(8):e1005128.
- Guo X, Trudgian DC, Lemoff A, Yadavalli S, Mirzaei H. Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics. Mol Cell Proteomics. 2014 Jun;13(6):1573-84.
- Trudgian DC, Fischer R, Guo X, Kessler BM, Mirzaei H. GOAT--a simple LC-MS/MS gradient optimization tool. Proteomics. 2014 Jun;14(12):1467-71.
- Howden AJ, Geoghegan V, Katsch K, Efstathiou G, Bhushan B, Boutureira O, Thomas B, Trudgian DC, Kessler BM, Dieterich DC, Davis BG, Acuto O. QuaNCAT: quantitating proteome dynamics in primary cells. Nat Methods. 2013 Apr;10(4):343-6.
- Trudgian DC, Mirzaei H. Cloud CPFP: a shotgun proteomics data analysis pipeline using cloud and high performance computing. J Proteome Res. 2012 Dec 7;11(12):6282-90.
- Masson N, Singleton RS, Sekirnik R, Trudgian DC, Ambrose LJ, Miranda MX, Tian YM, Kessler BM, Schofield CJ, Ratcliffe PJ. The FIH hydroxylase is a cellular peroxide sensor that modulates HIF transcriptional activity. EMBO Rep. 2012 Mar 1;13(3):251-7.
- Fischer R, Trudgian DC, Wright C, Thomas G, Bradbury LA, Brown MA, Bowness P, Kessler BM. Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis. Mol Cell Proteomics. 2012 Feb;11(2):M111.013904.