Pipelining and Infrastructure
An essential part of bioinformatics is to interface different tools, such that the user has a simple way of inputting their data and receive the information they are interested in. Installing the tools themselves can already be quite cumbersome and interfacing them with each other can be quite challenging as well. Additionally, each tool comes with its own set of parameters, often requiring careful adjustment. However, once such pipelines are in place, especially wet-lab scientists benefit a lot from them, as cumbersome manual work can be replaced by automatic processing pipelines.
Most of our internal processing pipelines are written in bash, R and Python and oftentimes are combined with a graphical user interface, e.g through a webpage built as a Shiny app in R. In addition to interfacing existing tools, your project might also contain elements to explore alternative tools as well as implementing specific processing steps from scratch.
- LIMS triggered processing - BA, Internship
- Database search engine pipeline - BA, Internship