Building a dashboard application to track DNA analysis for biodiversity

ARISE (Authoritative and Rapid Identification System for Essential biodiversity information) is a research infrastructure with a mission to provide semi-automated identification of all multicellular species in the Netherlands and innovate on biodiversity monitoring solutions. By applying DNA barcoding, artificial intelligence for species recognition based on images, sound and radar, and monitoring technology ARISE will be able to radically speed up the inventory of life on earth.

DNA barcoding is a technique that allows for monitoring of biodiversity at a molecular level. Naturalis is developing work processes for DNA barcoding at high-throughput scale. These processes encompass the entire chain from physical specimen collection, to lab work, DNA sequencing, bioinformatics, and data publishing. To monitor part of these processes, a web-based dashboard application is needed.

DNA barcoding is a technique that allows for monitoring of biodiversity at a molecular level. Naturalis is developing work processes for DNA barcoding at high-throughput scale. These processes encompass the entire chain from physical specimen collection, to lab work, DNA sequencing, bioinformatics, and data publishing. To monitor part of these processes, a web-based dashboard application is needed.

The interface should enable scientists to follow the status of their ongoing experiments, track their projects, 96-well lab plates and samples along the automated processing pipelines. The interface should also serve to browse sample metadata and provide easy ways for users to download raw and processed data. If time permits, adding the possibility to track the status of processing pipelines and options to (re)start them from the UI will be added.

The project is conceived as a long internship compatible with graduation projects at BSc or MSc level at universities and universities of applied sciences. The expected outcome would therefore be both tangible deliverables (i.e. source code and web application assets) as well as reporting, where the latter is expected to include an exploration of user interaction design illustrated with mockups based on research performed at the outset of the project. The exact duration of the components of the project and how they are evaluated is to be determined in consultation with the candidate’s educational institution.

Successful completion of the practical part of the project requires:

• a productive knowledge of javascript, HTML, CSS
• previous experience in working with web frameworks (React, Vue.js)
• an interest in working with DNA sequencing data

In addition, an interest in visual analytics and UI/UX design would be a great asset.