Summary

With over 20 years of professional experience, I'm driven to leverage my expertise in full-stack development, cutting-edge back-end and front-end technologies, cloud-based solutions to drive product innovation. Enthusiastic, good work ethics, reliable. Independently and professionally manages BioModels production system across the large codebase. Good task prioritisation. Proactive. Very approachable, always eager to support database curators or external users. Excellent work in preparing an archival instance of BioModels in BioStudies, including good collaboration with BioStudies team. In the process also intensified collaboration with other EBI resources like EuropePMC, identifiers.org, and Reactome.

Professional Skills

Work Experience

Senior Software Engineer
EMBL-EBI  Oct 2019 — Sep 2025 Cambridge, United Kingdom

• Focused projects: BioModels on Kubernetes and interconnected distributed services - implementing security design principles.
• Advanced in Java: Multithreading, Threadpools, Synchronisation, Concurrency and CompletableFuture, Rich Standard Libraries, Simplified Syntax with Lambda expressions and Stream API;
• Software Design and Architecture: GoF Design Patterns, DDD, DTOs, MVC, Microservices, Message Queues/Streams (with Redis Stream, Apache Camel),
• Cloud-based solutions: Docker, CI/CD pipelines with GitLab; migrated BioModels services and its legacies (in PHP, Node.js, MongoDB, NoSQL, etc.) to EBI's Kubernetes cloud.
• Microservices: a service with Spring Boot 2.0 to create CombineArchive files, a service using Flask to download and upload large files over 1GB, a service using FastAPI combining to Slurm to exchange the requests between BioModels and EBI's High-Performance Computing (HPC) Cluster.
• Extended REST API to allow programmatic submissions and supported our collaborators to update over 1000 curated models using the API.
• Developed Python pipelines to submit BioModels content to BioStudies as a mirror repository. Worked with GitHub actions, huge data submissions, Redis cache, Bash script.
• Refactored the large codebase of BioModels to speed up Kubernetes cloud deployment, reducing from 12 to 3 minutes.
• Technologies updated: React, Vue (worked with BioStudies), MongoDB.
• Always go the extra mile when supporting end users, collaborators, and our database curators.

Software Engineer
EMBL-EBI   Nov 2015 — Sep 2019 Cambridge, United Kingdom

• Projects: DDMoRe, BioModels, and DeepOC
• Java skills: Object-Oriented Programming (Encapsulation, Inheritance, Polymorphism and Abstraction), JVM tuning: JVM arguments and options, Automatic Garbage Collection, Exception Handling, Security Manager, Logging and Monitoring frameworks; Testing: Unit testing (JUnit, Mockito), integration testing, end-to-end testing; Hibernate/JPA: ORM (Object-Relational Mapping), entity relationships, caching strategies.
• Mostly employed the principles of Software Development: SOLID, DRY, KISS, and more.
• Heavily used the best practices for implementing coding standards and clean code such as: naming conventions, formatting and indentation, comments and documentation, error handling, and DRY Principle.
• Primarily upgraded BioModels using JUMMP written in Grails Groovy and Java. Maintained the existing business implementations and added new features.
• Model Repositories: support various community standards and formats for computational models such as SBML, PharmML, MDL, etc. Worked with Ontologies, Metadata RDF, FAIRness.
• Searching and High-Performance Computing (HPC): Solr, BioSolr, indexing-based search, IBM Spectrum LSF
• Programming: Spring, Java, Grails 2.x, Groovy, MySQL, LDAP, Bash script
• Agile Development, Git, JIRA, Maven, Gradle
• JavaScript, jQuery, Backbone, Underscore, ReactJS, Node, AngularJS 1.0
• FrontEnd technologies: Angular 8, Foundation CSS Framework 5.0, 6.0, Bootstrap 4, 5
• Taken part in building a model repository using an open source project, called JUMMP, a deliverable of the DDMoRe project

PhD Student
LaBRI   Oct 2010 — Feb 2015 Bordeaux, France

• Investigated and proposed a potential approach to analyse the enormous sets of elementary flux modes in metabolic plant cell networks, then integrate the analysed results for finding motifs: employed Minimal Cut Sets into analysing feasible pathways. Studied methods of complex network analysis, clustering algorithms.
• Built and modelled biological graphs. Researched solutions for the project and completed the final report as the doctoral thesis.
• Participated in conferences, workshops and gave two talks on related works.
• Used C++, Python, and R programming language massively.

Software Developer — Trainee
LaBRI   Jun 2009 — Nov 2009 Bordeaux, France

• Researched and implemented a Graph Editor in 3D using Common Lisp programming language to manage metabolic networks. It allows users to visualise graphs in 3D and interact with their graphical elements.

University Lecturer
Hoa Sen University   Aug 2004 — Oct 2010 Ho Chi Minh City, Vietnam

• Be responsible for the syllabuses of the courses about Microsoft Office suite, the courses about Web Design with Dreamweaver and Presentation Design with PowerPoint. Delivered these courses as well as supervised students.
• Designed and delivered new Software Engineering courses: Software Architecture using Design Patterns and Usability Engineering.
• Supervised research groups and supported students through a pastoral or advisory role.
• Participated in staff training activities.
• Published a book on Microsoft Excel 2010 in 2010 in Vietnamese.
• Webmaster for the Department of Maths and Information Technology’s website.

Projects

DDMoRe (A Drug Disease Model Resources)
Maintain and enhance the published open-source DDMoRe standards and tools to deliver and improve the quality, efficiency and cost-effectiveness of Model-Informed Drug Discovery & Development (MID3) and Therapeutic Use. I contributed to developing and delivering its model repository, and it is an open source project named JUMMP (JUst a Model Management Platform).

BioModels using JUMMP
A repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely accessible models published in the scientific literature.

DeepOC
Developed a Deep Learning model to classify the models deposited in BioModels based on their Gene Ontology information using Deep Learning. The deliverables are a Deep Learning model implemented in Tensorflow and an D3 zoomable sunburst chart to facilitate browsing models based classes, automating the classification and predicting new classes.

Education

PhD in Computer Science
Université de Bordeaux, Oct 2010 — Feb 2015 Talence, France

Master's in Software Engineering
Université de Bordeaux Sep 2007 — Dec 2009 Ho Chi Minh City, Vietnam

Bachelor's in Computer Science
University of Quy Nhon Sep 2000 — Jun 2004 Quy Nhon, Vietnam

General Skills

Agile Methodologies, Exhibit Leadership and mentorship, Problem-solving, Time Management, Priority, Teamwork, Communication, Software Development, Software Architecture Design, Debugging, Microservices architecture, Technological literacy, Organisation, Adaptability, Empathy, Data analysis, Dependability

Certifications

Application Development using Microservices and Serverless
(Issued on Dec 27, 2024 by Coursera)
Advanced and detailed study of creating microservices using various methodologies and running the applications on the IBM Cloud Code Engine with Openshift.
Continuous Integration and Continuous Delivery (CI/CD)
(Issued on Nov 23, 2024 by Coursera)
Revised the key features of CI, explore social coding, and the Git Feature Branch Workflow. Grasped how to build and run a CI/CD pipeline to an OpenShift Kubernetes cluster, also discovered standard CD tools.
See more certifications: https://tinyurl.com/tomcerts

Languages

Hobbies

References