Dr Tung Nguyen's profile

I am an active programmer, software engineer, research assistant and the mad Dad as a workaholic of two cute sons. When not playing with my family, I passionately discover crazy ideas in the software industry and strive to carry them out.

I'm Nguyễn Vũ Ngọc Tùng

'Nguyễn Vũ Ngọc Tùng' is my full name in Vietnamese form. To ease conversation, you call me Tùng or Tung (without the grave accent) or Tom for the easier pronunciation.

I am a software designer, full stack developer and web developer creating dynamic websites for companies of all sizes around the world. Let's start learning more about me.

About me

I am an enthusiastic, self-motivated, reliable, responsible and hardworking person. I am honest and punctual. I am a mature team worker and adaptable to all challenging situations. I am able to work well both in a team environment and using my own initiative. I am able to work well under pressure and adhere to strict deadlines.

My Curriculum Vitae | My hobbies

Experience

European Bioinformatics Institute | EMBL-EBI at Hinxton, Cambridgeshire, United Kingdom.

Senior Software Engineer, BioModels — Molecular Networks Team (Oct 2019 — Sep 2025)

Developed new features for BioModels service and improved throughput significantly.
Demonstrated my ability to work with different technologies in the migration of different legacy services from the traditional deployment environment to the cloud on Kubernetes cluster without any interruption.
Responsible for keeping good communications with our users as well as liaising with the internal and external collaborative work to link external resources, for example, worked OmicsDI team to integrate Omics Specs for BioModels, biomodels project with the Center for Reproducible Biomedical Modelling and researchers from COMBINE community.
Have effectively played the role of a tech lead to communicate with other teams to boost our work moving faster.
Programming languages working with: Java and Python.

Software Engineer, BioModels — Molecular Networks Team (Nov 2015 — Sep 2019)

Upgraded BioModels based on JUMMP open source and develop new features.
Taken part in building a model repository, a deliverable of DDMoRe project.
SBML, PharmML, MDL,...
Model Repository
Gene Ontology, Metadata
Solr, BioSolr, indexing-based search
Java, Grails, Groovy, Spring, Spring Boot, Python
SQL, MySQL, LDAP, Oracle
Agile Development, Git, JIRA
Front-End technologies: JavaScript, jQuery, Backbone, Underscore, Node, AngularJS 1.0, Angular 8, React, Foundation CSS Framework 6.0, Bootstrap 4

Hoa Sen University | HSU in Ho Chi Minh city, Vietnam.

Senior Lecturer, Faculty of Science and Technology (Aug 2004 - May 2015)

Built and updated syllabuses of Microsoft Office courses such as Microsoft Word, Excel, Access, PowerPoint and taught these courses for students in Information Technology, Economics and Business Affairs.
Responsible for courses about Web Design with Dreamweaver, Presentation Design with PowerPoint.
Created and collaborated two new courses in Software Engineering: Software Architecture and Usability Engineering.
Published a book "Microsoft Excel 2010" in 2010 in Vietnamese.
Played a role of a webmaster for the Department of Math and Information Technology’s website from 2005-2006.
Web Development with PHP, ASP and .NET full stack.

Education

Université de Bordeaux, France
Doctor of Philosophy (Ph.D.), Computer Science, Bioinformatics, Doctorate (2010 – 2015)

Metabolic network is a linked series of biochemical reactions that begins with a particular molecule and converts it into some other molecule or molecules in a carefully defined fashion in living organisms. Studying these networks is one of the current challenges in the field of biology, computer science, statistics and related other disciplines. We are working with a technique in graph theory to inhibit the production of a certain objective product in the network. The obtained results are really huge.
Classification of these results can be considered as a way to gain in-depth insight into a few of the specific functions. For instance, how do we find the solutions to obstruct the production of starch in plant cell metabolism.
Finding new methods to model, analyse and predict biological functions in Metabolic Networks.
My PhD dissertation supervised by MdC. Marie Beurton-Aimar is publicly accessible here.

Université de Bordeaux, France
Master of Science (M.Sc.), Computer Software Engineering (Sep 2007 – Dec 2010)

Equipped learners with the latest knowledge of technology and framework in the software industry. We were studied courses in Compiler Design, Advanced Database System, Software Design, Formal Method and Design, Distributed Application.
Graduated with Honours in English. Received Scholarship at LaBRI, 2009.
Dissertation titled “Developing a Biological Graph Editor in 3D”. Marked: 17/20
Final grade: 14.29/20

University of Quy Nhon, Vietnam
Bachelor of Science (B.Sc.), Computer Science (Sep 2000 – Jun 2004)

Awarded: one of the best students
Final grade: 7.93/10

Certificates

Coursera Specialization Certificate: Full-Stack Web Development with React funded by EBML-EBI.
Front-End Web UI Frameworks and Tools: Bootstrap 4
Front-End Web Development with React
Multiplatform Mobile App Development with React Native
Server-side Development with Node.js, Express and MongoDB

Soft Skills

Problem-Solving, Adaptability, Collaboration, Teamwork.

Publications

[1]	M. Beurton-Aimar, T. V.-N. Nguyen, and S. Colombié, ‘Metabolic Network Reconstruction and Their Topological Analysis’, in Plant Metabolic Flux Analysis: Methods and Protocols, M. Dieuaide-Noubhani and A. P. Alonso, Eds. Totowa, NJ: Humana Press, 2014, pp. 19–38.
[2]	V. N. T. Nguyen, ‘Analysis of biochemical reaction graph: application to heterotrophic plant cell metabolism’, phdthesis, Université de Bordeaux, 2015.
[3]	M. Glonț et al., JUst Model Management Platform. Zenodo, 2016.
[4]	L. Harnisch, I. Matthews, J. Chard, and M. O. Karlsson, ‘Drug and Disease Model Resources: A Consortium to Create Standards and Tools to Enhance Model-Based Drug Development’, CPT Pharmacomet. Syst. Pharmacol., vol. 2, no. 3, p. e34, Mar. 2013, doi: 10.1038/psp.2013.10.
[5]	M. Glont et al., ‘BioModels: expanding horizons to include more modelling approaches and formats’, Nucleic Acids Res., vol. 46, no. D1, pp. D1248–D1253, Jan. 2018, doi: 10.1093/nar/gkx1023.
[6]	R. S. Malik-Sheriff et al., ‘BioModels—15 years of sharing computational models in life science’, Nucleic Acids Res., vol. 48, no. D1, pp. D407–D415, Jan. 2020, doi: 10.1093/nar/gkz1055.
[7]	M. Glont, C. Arankalle, K. Tiwari, T. V. N. Nguyen, H. Hermjakob, and R. S. Malik-Sheriff, ‘BioModels Parameters: a treasure trove of parameter values from published systems biology models’, Bioinformatics, doi: 10.1093/bioinformatics/btaa560.
[8]	K. Tiwari et al., ‘Reproducibility in systems biology modelling’, bioRxiv, p. 2020.08.07.239855, Aug. 2020, doi: 10.1101/2020.08.07.239855.
[9]	Shaikh, Bilal, et al. “BioSimulators: A Central Registry of Simulation Engines and Services for Recommending Specific Tools.” Nucleic Acids Research, vol. 50, no. W1, July 2022, pp. W108–14, https://doi.org/10.1093/nar/gkac331.
[10]	Ramachandran, K.; König, M.; Scharm, M.; Nguyen, T.V.N.; Hermjakob, H.; Waltemath, D.; Malik Sheriff, R.S. FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast . Preprints 2022, 2022060137 (doi: 10.20944/preprints202206.0137.v1).
[11]	TransQST: Translational quantitative systems toxicology to improve the understanding of the safety of medicines, http://transqst.org/.

My recent projects

View my digital name card: eNameCard

Contact Details

Dr Tung Nguyen
Linton, Cambridge, Cambridgeshire
The United Kingdom
(+44) 7784 XXX XXX
nguyenvungoctung@gmail.com

Dr Tung Nguyen Senior Software Engineer | Full Stack Developer at European Bioinformatics Institute | EMBL-EBI