Personal details

Work experience

1. Lead Software Developer

   Swiss Institute of Bioinformatics, Geneva, Switzerland

   February 2008 - current

   Worked with the team on

   • Redesigning the UniProt consortium web presence with user experience experts in HTML 5
   • Meeting the demands of the growing database (110x growth in 7 years)

   I am directly responsible for: www.uniprot.org and sparql.uniprot.org. The www.uniprot.org website is one of the most popular websites in the life science community with over 900,000 monthly users and in the top 13,0000 of most popular websites in the world. Sparql.uniprot.org is the largest, public and free to use graph database on the internet.

   • Monthy code and data releases
   • JSON-LD and RDF data representation
   • Berkley-DB/je upgrade and finally removal for custom key value store
   • Lucene full text search and indexing strategies
   • Multi site resilience and fail over setup
   • Java 1.5 -> 1.11 migrations
   • Deployment strategies, considering multiple institutes, data centres and set ups

2. Java Software Engineer

   Ordina, Groningen, Netherlands

   May 2005 - January 2008

   At Ordina I worked as part of a team developing and maintaining a Electronic Medical File system named Kidos, for recording information of children aged 0-19, implemented a J2EE application based on Struts and EJB 2. I introduced continuous integration to assist in guaranteeing software quality as well as reintroduced JUnit based testing. I have taught courses in Java based technology to new employees as well as retraining others with an Oracle Forms/Designer background.

   Worked with the team on

   • Migrating the application from a BEA stack to an Oracle J2EE environment and from Java 1.4 to Java 5.
   • Maintained code using EJB2, Struts, Xslt and Oracle databases.

   Was directly responsible for:

   • New functionality to track and register warning signs from multiple sources. e.g. a doctor reports suspicion of child abuse.
   • Updating the generation of automatic reports and forms using Apache FOP.

Education

1. Bachelor in Bioinformatics

   Hanze University of Applied Sciences, Groningen, Netherlands

   2002-2007

   A broad education in bio-informatics. Project orientated education dealing with questions derived from real academic or industry problems. For example in-silico modeling of micro-array probe cross hybridisation of a micro-array. Broad experience with a broad spectrum of languages and API's to solve problems such as Python, Java, Perl and dialects of SQL.

2. Bachelor in Bioinformatics internship

   European Bioinformatics Institute (EBI), Cambrige, United Kingdom

   2005-2006

   Comparative study of a number of automated methods to functionally annotate proteins on the basis of knowledge in the Swiss-Prot part of the UniProtKB database. Implemented and compared (data-mining) algorithms in Java as well as part of the data based parallelization work. Part of a strong team using test driven development to deliver high performance software. Parts of my work in the team included assisting in building a possible new front end for the UniProt website using a Java based web front-end using the Tapestry framework.

Skills

1. Programming Languages

   1. Java
   2. SPARQL
   3. SQL
   4. Javascipt
   5. BASH

2. Languages

   1. Dutch (Fluent)
   2. English (Fluent)
   3. French (Basic)