Research Software Engineer

Scagliola / Brakkee Atrium Neutelings Riedijk Architects

Naturalis is looking for a Research Software engineer, experienced in Java, Python and/or Ruby programming.

We are looking for a Research Software Engineer, for a period of two years, 36 hours a week.


Are you a back-end or full stack research software engineer and ready for a new challenge? Are you qualified to build high quality PID infrastructure for biodiversity related science? Are you interested in building a system that is instrumental in tackling societal challenges like biodiversity loss and climate change? Then we have the right job for you!

Naturalis Biodiversity Center in Leiden is the Dutch national institute for biodiversity and systematics. With our collection of 42 million specimens we house one of the world's largest natural history collections, provide state-of-the-art research facilities and our museum exhibitions receive more than 400.000 visitors per year. 

Naturalis is looking for a research software engineer to join our DiSSCo team, who has experience in writing open source software, in building applications that are reliable and scale, who has a basic understanding of data infrastructures and who has affinity with science. At Naturalis you will be part of a specialised development team with senior developers in a modern office with state of the art ICT infrastructure. 

Naturalis leads the development of DiSSCo, the Distributed System of Scientific Collections, which is a new world-class Research Infrastructure (RI) for natural science collections. DiSSCo brings together 136 museums across 21 European countries to unify and serve genomic, geographical, morphological and taxonomic knowledge for the estimated 1.5 billion physical objects held in European collections. 


In this job you will work on a task in an EC funded project called BiCIKL (Biodiversity Community Integrated Knowledge Library) to build a pan-European PID (Persistent Identifier Development) system for Digital Specimens. This system will be a key component of a digital object infrastructure for specimens, and will need to follow FAIR principles. The project includes partners from European and global research infrastructures such as GBIF, EMBL and CERN with a mission to build linkages between the infrastructures to connect different biodiversity related data classes such as specimen data, genomic data and scholarly publications. 

The PID system you will build will enable the connection of specimen data with data from other infrastructures. For the system we are experimenting with Cordra as tooling for the registry for the digital objects, indexed with Elastic Search and with Handles and DOIs as PIDs. We aim for an infrastructure that is as federated as possible and as central as needed.

Specimen data has an important role to play as anchor point for derived and related biodiversity data and the collected objects provide 'hard evidence' about biological and geological diversity. In the project you will work as part of the DiSSCo Coordination and Support office, a virtual office with staff located at different places in Europe. You will work closely together with the DiSSCo data architect and will be led by the coordinator research-data and e-infrastructure and guided by the DiSSCo technical team. The position will require occasional travelling a few days a year and is likely to be extended beyond the initial two years.

skills and edcuation

The research software engineer we are looking for will need to have the following skills:

  • Have a solid understanding of the processes, limitations and technical solutions related to data processing, linking and indexing
  • Think in innovative solutions and production quality software that is reliable, scalable and secure
  • Like to work in an international setting, with collaboration mainly through teleconferencing
  • Be able to travel internationally a few days a year
  • Excellent knowledge of the English language (written and verbal)
  • Have experience in Java programming 
  • Familiar with standard web application development (JSON, REST, APIs)
  • Be self-motivated, feel responsible, able to work independently

Desired qualifications, experience and skills (good-to-have) are:

  • Have experience in writing open source software
  • Familiar with the concept of Persistent Identifiers, e.g. Handles, DOIs, DO, DOIPv2, ORCID iDs
  • Have experience in developing in Python and Ruby
  • Have experience with JSON-LD and GraphQL implementation
  • Have experience in search engines and graph data processing, preferably with Elasticsearch, SPARQL, Neo4J
  • Have experience with continuous integration, dev-ops, Docker, Kubernetes, AWS
  • Have experience in working in complex international science innovation or infrastructure projects
  • Hold a university degree, preferably in software engineering or similar technical study
  • Knowledge of the Dutch language
  • Have affinity with the community and field of natural sciences and biology
  • Familiar with Research Data Alliance recommendations and TDWG standards;
  • Familiar with data serialization as well as exchange and discovery solutions (such as Protobuf, Avro, Bioschemas)
  • Be able to present implementation choices to both technical and non-technical audiences
  • Affinity with user-friendly GUIs


A contract (36 hours per week) for a period of one year, to be extended with one year after a successful first year evaluation, and a monthly gross salary between € 3,099.- and € 4,053.-, depending on relevant experience. You also get an allowance for travel expenses, holiday allowance (8%) and year-end bonus (3.4%). Naturalis Biodiversity Center offers an inspiring working atmosphere and advanced ICT infrastructure. The Naturalis offices in Leiden are easily accessible by public transport from Amsterdam, Rotterdam, Utrecht and The Hague.

and information

Applicants are invited to submit their application, including a cover letter and CV, 8th November CET at the latest, by using this application form. Feel free to contact Wouter Addink (coördinator Research-data & E-infrastructure) with questions about the position:

For information concerning the procedure or HR issues please contact the HR department, or 071-7519191. 

Naturalis endorses the Cultural Diversity Code. In the case of equal suitability, preference is given to the candidate who reinforces diversity within the team.

Acquisition is not appreciated.