Naturalis is developing work processes for DNA barcoding at high-throughput scale. To monitor part of these processes, a web-based dashboard application is needed.
Backgroundand context
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.
Objectivesand goals
The web interface to develop using modern web technology must enable scientists to follow the status of their ongoing experiments, track their projects, 96-well lab plates and samples along the automated processing pipelines. It must also allow users to browse sample metadata and provide easy ways for downloading raw and processed data. If time permits, adding the possibility to track the live status of processing pipelines and implementing functionalities such as the option to (re)start them from the UI will be added.
Methodsand approach
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.
Studentrequirements
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.