Bioinformatician

Naturalis seeks to recruit a Bioinformatician for the eDentity Project
- Bachelor degree- Fulltime (32 - 36 hours per week)- Fixed term- € 3.187 - € 4.141**About**

**Naturalis**:

- Naturalis Biodiversity Center in Leiden is the Dutch national research institute for biodiversity and systematics. With our collection of 43 million specimens, one of the world's largest natural history collections, and our state-of-the-art research facilities we offer the (inter)national research infrastructure for species identification and monitoring (for example in the ARISE and DiSSCo projects). We closely collaborate with many Dutch universities, research institutes, industry, and government. We host over 120 researchers including 15 academia embedded professors, 50 PhD students and 20 postdoctoral fellows. We present the history of our planet, and the diversity of life on Earth, through permanent and temporary museum exhibitions, educational programmes, and online presence, with more than 400,000 visitors per year. All in all, a unique combination of science and culture in the Netherlands and elsewhere in the world_

**Position**:
The position is part of the eDentity project. With this project, Naturalis will build a research infrastructure specifically aimed at large-scale identification and monitoring of biodiversity using small amounts of environmental DNA in soil, water and air samples. Our goal will be achieved by exploiting recent advances in DNA sequencing technologies (e.g. establishing high-throughput DNA sequencing pipelines) and machine-learning. The services to be built within eDentity will make biodiversity monitoring accessible for researchers, industry, policy and citizens. Having such knowledge readily available will drive the future of biodiversity and our planet.

**Tasks and**

**responsibilities**:

- Refine and optimize existing analysis toolkits and pipelines and develop new ones for metabarcode sequencing of mixed environmental samples, calculation of alpha and beta diversity metrics including phylogenetic diversity, sequence classification with machine learning and AI, and for updating and curating molecular reference databases;
- Deploy and maintain pipelines on workflow management systems (e.g. Galaxy, SnakeMake) running on cloud-based and bare-metal high-performance computing infrastructure;
- Integrate pipelines in a larger information architecture that manages relevant metadata, so that analysis parameterization (e.g. which primers were used) and raw data is obtained from the environment (LIMS, S3 buckets) as much as possible, and outcomes move easily downstream to our information products (e.g. as implemented in DataBricks);
- Integrate said pipelines in a data management and staging infrastructure so that different storage tiers are used optimally while maintaining FAIR principles.

**Profile**:

- Bioinformatics background (at least HBO / Univ. Appl. Sci.), especially in high-throughput DNA sequence analysis techniques, DNA metabarcoding, taxonomy/phylogenetics;
- Good verbal and written communicator; multidisciplinary team player;
- Self-motivated, independent, solution-oriented;
- Demonstrable experience with high-performance, Linux-based, computing systems and workflow management systems such as Galaxy and SnakeMake;
- Awareness of the FAIR principles and the requirements of reproducible open science;
- Demonstrable programming skills in Python and R, including supporting technologies such as version control systems (git), unit testing, continuous integration, and project and issue tracking systems (JIRA). Experience with various databasing approaches (e.g. SQL / NoSQL);
- Experience in working with distributed systems and the technologies to integrate these, e.g. via RESTful web services

**Our offer**:
**Procedure**:

- **If you are a recruiting agent, please do not contact us**_