The services to be built within ARISE will make species recognition and biodiversity monitoring accessible for researchers, industry, policy and citizens. Having such knowledge readily available will drive the future of biodiversity and our planet
The ARISE programme demands substantial development of automated bioinformatics pipelines for DNA sequence analysis. These pipelines will integrate in the larger ARISE infrastructure, such that provenance of study results can be tracked, data can be managed following FAIR principles, and relevant metadata is obtained automatically from upstream in the infrastructure, rather than entered manually. This all in the interest of scalability, reproducibility and user-friendliness, so that non-technical users can enact analysis pipelines by themselves. To this end, we are seeking a bioinformatician with significant skills in software development and the integration of disparate system components. The main tasks and responsibilities of the successful candidate will therefore be:
- To refine and optimize existing analysis pipelines and develop new ones for i) sequencing DNA barcodes using third-generation sequencing platforms (PacBio and/or Oxford Nanopore), ii) metabarcode sequencing of mixed environmental samples, iii) genome skimming for the purpose of taxonomic identification and phylogenomics; iv) updating and curating molecular reference databases.
- To deploy and maintain said pipelines on workflow management systems (e.g. Galaxy) running on cloud-based high-performance computing infrastructure.
- To integrate said pipelines in a larger infrastructure that manages relevant metadata, such that analysis parameterization (e.g. which primers were used) is obtained from the environment as much as possible.
- To integrate said pipelines in a data management and staging infrastructure such that different storage tiers are used optimally while maintaining FAIR principles.
General requirementsand skills
The ideal candidate for this position will meet the following criteria:
- Bioinformatics background (at least HBO / Univ. Appl. Sci.), especially in high-throughput DNA sequence analysis techniques, genomics, taxonomy/phylogenetics
- Good verbal and written communicator; multidisciplinary team player
- Self-motivated, independent, solution-oriented
- Demonstrable programming skill in Python and R, including supporting technologies such as version control systems (git), unit testing, continuous integration, and project and issue tracking systems (JIRA).
- Demonstrable programming skill in various databasing approaches (e.g. SQL / NoSQL)
- Demonstrable programming skill working with distributed systems and the technologies to integrate these, e.g. via RESTful web services and/or semantic web technologies
- Demonstrable experience with high-performance, Linux-based, computing systems
- Awareness of the FAIR principles and the requirements of reproducible open science
A role in a dynamic working environment that is embarking on an exciting ‘moon shot’-level programme. Between € 2,840 - and € 3,718.- (scale 9 under evaluation) gross remuneration on the basis of 36 hr / week. Initial appointment will be for the period of 12 months.
Please use this form for your application no later than 9 August 2021 17.00 h CEST.
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.