About
I’m Alexandru (Alex) Mahmoud – an independent cloud & research software engineer focused on reproducible, automated, open science infrastructure.
SIREN: 990 047 938
Core Open Science Roles
- Bioconductor Core Engineer (https://bioconductor.org): container & cloud architecture, build / binary modernization, workshop + identity platforms, multi-cloud deployment pipelines.
- Galaxy Project team member (https://galaxyproject.org): Kubernetes & Helm stacks, CVMFS‑CSI integration, scalable CI/CD, secure on-demand platforms for genomics workflows.
- NHGRI AnVIL Project (https://anvilproject.org): Led integration of Bioconductor & Galaxy into Terra (GCP/Azure) secure research environments; cross-team coordination, architecture, automation.
Selected Systems & Platforms I Built / Maintain
| Area | Highlights |
|---|---|
| Training & Identity | Bioconductor Workshop Platform (ephemeral environments), Keycloak IAM customization, automated provisioning |
| Containers & Binaries | bioc2u Debian packaging pipeline, multi-arch container stacks, container binary builder (GPU/Jupyter/RStudio variants) |
| Deployment Stacks | Bioconductor & Galaxy Helm charts, Galaxy Kubernetes runner backend, CVMFS-CSI Helm integration |
| Modernization | Shift from static always-on infra to ephemeral, automated, testable pipelines (GitHub Actions, multi-cloud CI) |
| Data / Access | Hubs ingestion automation, secure cloud object storage routing, status & observability endpoints |
Approach & Engineering Philosophy
- Automation First – CI/CD, reproducible builds, dependency transparency.
- Ephemeral by Default – reduce manual drift and lingering state.
- Security & Maintainability – lean images, minimized permissions, declarative configs.
- Open Standards – leverage community ecosystems instead of bespoke reinvention.
Publications (Selected)
- Galaxy Helm chart: standardized deployment of production Galaxy (Bioinformatics, 2024)
- Bioconductor community infrastructure & teaching (arXiv 2024)
- Galaxy platform 2022 NAR update (Nucleic Acids Research, 2022)
- NHGRI AnVIL cloud genomics platform (Cell Genomics, 2022)
- GalaxyCloudRunner scalable bursting (Bioinformatics, 2020)
Languages (Communication)
English · Français · Română · العربية
Technical Expertise (Extensive)
- Containerization & Orchestration: Kubernetes (GKE, AKS, EKS, K3s, RKE2), Helm, Docker, Rancher
- Cloud & Infrastructure: GCP, AWS, Azure, Jetstream2 / OpenStack; S3/object storage, networking, multi-cloud deployment tests, elastic & serverless bursting (scaling auxiliary compute outside primary clusters)
- Automation & CI/CD: GitHub Actions, Ansible, Travis; internal monitoring & build pipelines (multi-arch, GPU, package binary generation)
- Programming: Python, Bash/sh, R (tooling, automation, backend glue)
- Platforms & Services: Galaxy, Bioconductor, RStudio, Jupyter, Keycloak IAM, CVMFS, NFS, RClone-CSI
- Data / Reproducibility: Container + deb packaging (bioc2u), environment provenance, repeatable pipeline design
- Security / Hardening: Minimal base images, scoped permissions, supply-chain transparency, infrastructure audits
- LLMs & AI (support tooling): Ollama, Open WebUI, llamaindex, langchain, RAG patterns (for internal enablement workflows)
Familiar (working knowledge): Go, Java, JavaScript (Vue/Angular/React basics), HTML/CSS, Jenkins, Argo CD, Perl, Matlab.
Example Engagements / Project Types
- Galaxy Instance Deployment & Operations – Production-ready or training-focused Galaxy with autoscaling, CSI-backed storage, CVMFS integration, secure identity.
- Bioconductor Cloud Modernization – Binary/container build pipelines (GPU variants), Helm deployment strategy, reproducible workshop environments.
- Workshop & Training Platform – Ephemeral multi-tenant clusters with automated provisioning and Keycloak-backed authentication.
- Infrastructure Modernization Audit – Assessment of existing servers; migration plan to automated, testable Kubernetes/Helm stack.
- Container Supply Chain Hardening – Image slimming, deb/r2u-based packaging (bioc2u), reproducible multi-arch & GPU build pipelines.
- Identity & Access Integration – Keycloak setup, role mapping, SSO integration for research platforms.
- Architecture & Roadmapping – Translate scientific goals into incremental, measurable engineering milestones & backlog refinement.
- CI/CD Pipeline Design – Multi-cloud test matrix, artifact provenance, automated validation and deployment promotion.
- Elastic / Serverless Bursting Enablement – Strategy & implementation for overflow/episodic workloads using managed or transient compute alongside core clusters.
- Data Platform Migration – Move bespoke or snowflake environments to standardized, versioned container / Helm workflows.
If your need touches open science platforms, reproducible analytics, or cloud-native research infrastructure, I can likely: (a) help you clarify & scope; (b) design the architecture; (c) implement & operationalize; and (d) hand off with durable documentation.
Contact
Email: almahmoud.research@gmail.com
GitHub: https://github.com/almahmoud
LinkedIn: https://www.linkedin.com/in/alexmahmoud