(Lead) Developer

Scagliola / Brakkee Atrium Neutelings Riedijk Architects

A key position to the development of the pan-European DiSSCo research infrastructure, that will digitally unify the natural scientific collections in Europe through a FAIR Digital Object infrastructure.

Are you a back-end or full stack application developer who likes to pioneer and experiment with the latest technologies to develop data infrastructure for biodiversity related science? Are you interested in making technical choices and piloting towards applications that will be instrumental in tackling societal challenges like biodiversity loss and climate change? Then we have the right job for you!

Naturalis is looking for a Lead developer for the development of DiSSCo Digital Specimen Architecture pilots (2 years, 32- 36 hours a week).

Introduction

Naturalis Biodiversity Center in Leiden is the Dutch national institute for biodiversity and systematics. With our collection of 42 million specimens Naturalis provides one of the world's largest natural history collections, and Naturalis provides state-of-the-art facilities and digital infrastructure for research.

Data derived from collection specimens is fundamental to scientific biodiversity and geodiversity research aimed at the understanding and conservation of the natural riches of our Earth. In Europe, Naturalis leads the development of the Distributed System of Scientific Collections (DiSSCo), 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 1.5 billion physical objects held in European collections. With implementation beginning in 2024, DiSSCo’s full operations are planned to commence in 2026. Nevertheless, DiSSCo is already starting to work on early e-Services and pilots to demonstrate the added value and feasibility of its plans for a Digital Specimen Architecture (DSArch).

Position

The vacancy is for the key role of lead developer of DiSSCo but also open to full-stack or back-end application developers which do not yet have the seniority to be a lead developer. The initial focus of the role will be, but not limited to, developing a Digital Specimen pilot to showcase and test the novel principles of a FAIR Digital Object infrastructure (FAIR DO) for specimens, which should enable linkages between digital specimen and derived or related information such as genomic information or species interactions, and which should enable global community curation and annotation.

Development will include:

  • support the development of the openDS specification for Digital Specimens (digital objects served as JSON-LD) by trial implementation in the nsidr.org demonstrator (open source java application based on Cordra
  • Transitioning of the demonstrator into a pilot with real datasets implementing pipelines to ingest data from multiple sources. This may require migration from MongoDB to Amazon S3 to scale up
  • Connecting to external APIs and provision of APIs and microservices to serve DiSSCo services
  • Piloting development of annotation services for humans and machines by implementing annotation standards
  • Implementation of Elastic Search based data indexing and search functions and experimentation with machine learning techniques for advanced indexing
  • Experimentation with implementation of machine-actionable metadata
  • Documentation of developed components and configurations

Optionally the work may include:

  • Assisting in development of the openDS specification by definition of e.g. data type and JSON schemas
  • Support for developers or researchers wanting to make use of the pilot implementation or contribute to it
  • Implementation of graph visualisations of the data

Required
qualifications, experience and skills (must-have)

The vacancy is for the key role of lead developer of DiSSCo but also open to full-stack or back-end application developers which do not yet have the seniority to be a lead developer. The initial focus of the role will be, but not limited to, developing a Digital Specimen pilot to showcase and test the novel principles of a FAIR Digital Object infrastructure (FAIR DO) for specimens, which should enable linkages between digital specimen and derived or related information such as genomic information or species interactions, and which should enable global community curation and annotation.

Development will include:

  • support the development of the openDS specification for Digital Specimens (digital objects served as JSON-LD) by trial implementation in the nsidr.org demonstrator (open source java application based on Cordra
  • Transitioning of the demonstrator into a pilot with real datasets implementing pipelines to ingest data from multiple sources. This may require migration from MongoDB to Amazon S3 to scale up
  • Connecting to external APIs and provision of APIs and microservices to serve DiSSCo services
  • Piloting development of annotation services for humans and machines by implementing annotation standards
  • Implementation of Elastic Search based data indexing and search functions and experimentation with machine learning techniques for advanced indexing
  • Experimentation with implementation of machine-actionable metadata
  • Documentation of developed components and configurations

Optionally the work may include:

  • Assisting in development of the openDS specification by definition of e.g. data type and JSON schemas
  • Support for developers or researchers wanting to make use of the pilot implementation or contribute to it
  • Implementation of graph visualisations of the data

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

  • Have experience in search engines and graph data processing, preferably with Elasticsearch, SPARQL, Neo4J
  • Be able to present and pitch architectural concepts and implementation choices to both technical and non-technical audiences
  • Familiar with the concept of Persistent Identifiers, e.g. Handles, DOIs, DO, DOIPv2, ORCID iDs
  • Have experience with continuous integration, dev-ops, Docker, Kubernetes, AWS;
  • Have experience in open source programming and engineering 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)
  • Affinity with user-friendly GUIs

We
offer

A contract (36 hours per week, 32 is possible) for a period of one year, to be extended with one year after a successful first year evaluation, and a monthly gross salary between € 3,405 and € 4,576, 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. 

Procedure

Applicants are invited to submit their application, including a cover letter and CV, 26th September at the latest, by using this application form. Feel free to contact Wouter Addink (coördinator Research-data & E-infrastructure) with questions about the position: wouter.addink@naturalis.nl.

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.