Summary

I am passionate about coding, software design, and digital creation,
and acquired diverse IT engineering skills since high school to postdoc.
My current work is in Computer Science to support Cancer Research.

After my MSc. in Theoretical Physics and my MSc. in Computer Science, I got my PhD in Computational Biotechnology for creating various software applications in cooperation with molecular biologists. I continued this work as I moved from Belgium to Norway, where I engineered a unique web platform for comprehensive scientific knowledge accumulation.

Among many interests I'm primarily a:
1. Software engineer, who loves web-applications, tough algorithms, semantics;
2. Scientist in Computer & Life Sciences, trained in IT, Physics, Biotech;
3. Photographer;
4. Entrepreneurial spirit.

As a software engineer, I have years of experience with JavaScript, Java, C++, PHP, MySQL, and now also full-stack web development skills including Node.js, Aurelia, AngularJS, Express, jQuery, MongoDB, Backbone, Browserify, Stripe, Agile, git, gulp, Amazon Web Services (AWS), etc.

As a scientist, I help Life Scientists deal with large amounts of diverse knowledge. I am driven to find and apply ways to improve computer intelligence that supports their activities. For example I designed the technology VSM, that lets bioscientists capture extremely comprehensive and context-rich information from text, using a method that mimics natural language but can be queried and parsed semantically. I used this as the basis to build the web-app SciCura.

As a photography enthusiast, I love street portraits and meeting new people.

As for entrepreneurship, I'm interested in startups, and led a team of students in the intensive Take Off course at NTNU School of Entrepreneurship.


Software Projects

SciCura

Collecting sense from Bioscience literature. (JS/PHP)

SciCura is a web-platform where life-scientists gather complex and diverse bio-information, and can then apply semantic search and processing.

The web-app supports versatile information collection: one can capture facts on any topic, while also storing all essential biological context.
Note that collection of detailed structured facts, called 'curation', happens manually because of AI limitations.

SciCura stores facts as semantic sentences, built from simple rules, yet enabling complexity like natural language.

The platform’s development involves iterative front-end & back-end design and implementation, challenging graph-algorithms (for semantic pattern-matching and syntax visualization), webserver operation, and close cooperation with life-scientist users.

2012 - present


WordVis & OLSVis

Visualizing semantic dictionaries. (JS/HTML5/PHP)

I built an animated graph-visualizer & editor in JavaScript, connected it to various semantic dictionaries, and packed this into desktop web-applications.

  • WordVis lets you explore the English dictionary,
    see synonyms grouped by meaning, and browse them in a fluid, interactive web of words and meanings.
  • OLSVis lets you browse complex life-science ontologies (=terminology hierarchies).

2010-2011


Notable Earlier Work

  • SIM-plex: Gene Network Simulator. (Java)
  • MineMap: Text curation platform to cooperatively extract facts from bioscience literature. (Java/PHP)
  • Agenda: Multi-user app for scheduling meetings, holidays, and reservations at Becewa. (C++)
  • Database apps for billing/logistics. (Access/VBScript)
  • Physics+3D simulation engine in high school. (C/C++)

1994-2010


Research Positions

Researcher / Software Engineer

NTNU, Trondheim, Norway

  • Computer Science for Cancer Research.
  • Design of a Knowledge Commons, a basis to model & predict cancer cells' response to drug combinations.
  • Expand VSM & SciCura.

2016 - present


Researcher / Software Engineer

Independent, Associated with NTNU

  • IT-engineer & close cooperation in Cancer Research.
  • SciCura web-app: iterative design & implementation.
  • Start-up case-study.

2012 - 2015


Postdoctoral researcher

Norwegian University of Science and Technology, Trondheim

  • Design of a general semantic format and visual interface, which bridges natural language used by people, and database formats used by algorithms. (VSM/UltraRel).
  • Development of WordVis and OLSVis.

2008-2011


Education

Full Stack Web Developer

(Self-directed learning)

Sabbatical year, using various online resources.

  • Advanced JavaScript front&back-end, Aurelia, Angular, NodeJS, NoSQL, etc.
  • Around 20 different Amazon Web Services.
  • DevOps tools.

2015


PhD in Biotechnology

(Computational, Integrative, Systems Biology)

VIB (Flanders Institute for Biotechnology) / UGent

Multidisciplinary work-environment. Building bridges between IT-tools and bio-scientists. For example:

  • Knowledge management: Building tools to help scientists cooperatively collect information from Bioscience literature.
  • Gene network analysis: Building a network simulator, applying it to unravel the logical wiring of plant cell division.

2003-2008


MSc in Computer Science

Ghent University

Software Development: graduated with Distinction.
Parallel BSc and MSc completed in just 2 years.

2000-2002


MSc in Physics

Ghent University

Theoretical Physics: graduated with High Distinction.

1996-2000


Scientific Publications

  1. A simple, graphical way to construct the semantic meaning of complex information. Vercruysse S, Kuiper M. (in preparation).
  2. Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Tripathi S, Vercruysse S, et al. Database. 2016.
  3. Jointly creating digital abstracts: dealing with synonymy and polysemy. Vercruysse S, Kuiper M. BMC Res Notes. 2012.
  4. Putting Semantics in Systems Biology. Kuiper M, ..., Vercruysse S, et al. Meta. 2012.
  5. OLSVis: an animated, interactive visual browser for bio-ontologies. Vercruysse S, Venkatesan A, et al. BMC Bioinformatics. 2012.
  6. WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. Vercruysse S, Kuiper M. IHCI Conf. 2011.
  7. The Arabidopsis leaf as a model system for investigating the role of cell cycle regulation in organ growth. Beemster GT, Vercruysse S, et al. J Plant Res. 2006.
  8. Genome-wide analysis of gene expression profiles associated with cell cycle transitions in growing organs of Arabidopsis. Beemster GT, De Veylder L, Vercruysse S, et al. Plant Physiol. 2005.
  9. The cyclin-dependent kinase inhibitor KRP2 controls the onset of the endoreduplication cycle during Arabidopsis leaf development through inhibition of mitotic CDKA;1 kinase complexes. Verkest A, Manes CL, Vercruysse S, et al. Plant Cell. 2005.
  10. Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Hilson P, ..., Vercruysse S, et al. Genome Res. 2004.
  11. Transcript profiling of early lateral root initiation. Himanen K, ..., Vercruysse S, et al. Proc Natl Acad Sci USA. 2004.
  12. Simulating genetic networks made easy: network construction with simple building blocks. Vercruysse S, Kuiper M. Bioinformatics. 2005.


Photography

To be added.


Skills

JavaScript, Node.js, Aurelia, AngularJS, Express, jQuery, MongoDB, Browserify, Backbone, git, GitHub, gulp, npm, templating, Stripe, Agile, test-driven development, Bootstrap, responsive design, UI/UX, HTML5, CSS3, SASS, Amazon Web Services.

PHP, MySQL, Java, C++, VB, asm.

Photoshop, Illustrator, 123D Design, AutoHotkey, SublimeText, CMS, MS Access, audio-video-image editing, and 100+ software tools. Familiar with computer security, AI.

Creative. Perseverant. Thorough. Open-minded. Critical thinking. Self-reflection and improvement. Independent, proactive, enthusiastic spirit.


Languages

Proficient: English, Dutch.
Intermediate: Norwegian, French.
Notions: German, Spanish.


Activities

Hiking in Norway's mountains
Mindfulness meditation
Dancing, various styles
Travelling


Awards

Idea-Leader for Start-up, NTNU Take-Off (2014)

Selected as 1 of 6 in idea-leadership role in intensive entrepreneurship course.

Personal Postdoc grant, FUGE (2008)

Based on written project proposal.

Personal PhD grant, IWT (2003)

Based on written project proposal and two oral defenses.


Endorsements

Martin Kuiper

Professor in Systems Biology

Steven is extremely creative, not shy to adopt unconventional approaches, and has a good eye for identifying what biologists would like to see in software that should support their research.

Astrid Lægreid

Prof. in Functional Genomics

I have known and worked with Steven for nearly 10 years focusing on extraction and management of biological background knowledge from literature. During these years, I have come to highly appreciate Steven’s innovative and goal-oriented approaches.

European Commission

Future & Emerging Techn.

(...) has potential to represent a significant contribution to simplified knowledge representation needed for effective crowd-sourcing, data management, database querying and reasoning.
The approach is ambitious and demonstrates a general understanding of the challenges, with original approaches to address these.

S.

Anonymous friend

I like how you're always so happy and joyful about things!