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Leiden University of Applied Sciences

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Abstract 2018-2019: Development of an interactive application for transcriptome analysis 

The Leiden Centre of Applied Bioscience’s bioinformatics lab is responsible for the bioinformatics support of different lectorates. Currently, each gene expression analysis project is analyzed in with custom methods. An RNA-seq analysis is performed for each dataset, and the best method for doing this is evaluated. This however results in variation between the processed datasets, which makes comparing these needlessly difficult. Because of the large amounts of data the LCAB has to process, the creation of a standard application for the RNA-seq analysis that gives a standardized output is necessary. Additionally, this application has to be compatible with the existing application AVIDE, which visualizes RNA-seq data in a statistical manner. Through the use of R-shiny and with AVIDE as a reference, AIDEA was created. Its user interface was directly inspired by that of AVIDE, and it expands on the data processing functions already present in said application. AIDEA requires a “sample sheet” and a “fragments per gene” file to be uploaded, which it uses to calculate various variables by using the DESeq2 and edgeR package. The user can choose which package to use. Output is generated in the form of several data tables, which can be downloaded in either .tsv or .csv format. Genes of interest can be selected, stored in a separate table, and downloaded as well. 


Zernikestraat 10
2300 AJ Leiden


Traineeship supervisor
Floyd F.Wittink
Traineeship supervisor
Stephen S. Pieterman

Testimony Tibbert Van Den Eynde (2018-2019)

I have really enjoyed my time in Leiden. This marks the first time I’ve studied abroad and it is also the first time I’ve been living on my own. The freedom I experienced from getting to decide what to eat and when to eat it was refreshing, and all the daily chores that need doing are a whole lot less annoying to do when you decide yourself to do them. Likewise, I had the good fortune to get sliding workhours, so I could start and stop when I wanted to. Which means that for once I wasn’t a sleep deprived zombie the first couple hours of the day, and I could be productive instead of trying and failing not to nod off to sleep at my desk. Leiden itself is of course a city where a lot of students (both native to the Netherlands, and from around the world) gather, so you will never be starved for parties or other activities. The International student network of Leiden organizes a party every Wednesday at the Einstein pub, so if you don’t know where to go, go there. If you’re not one for parties, there are also a lot of museums to visit, with my personal recommendation being the Museum Volkenkunde (the museum of ethnology). When I was there, they had a collection of gorgeous Japanese armors and other recognizable objects. Leiden also has a lot of parks to walk through and sit in, and while most are not very large, they certainly are beautiful. Personal recommendations are the Van der Werfpark and the Wondertuin. So yeah, I have had a wonderful time here in Leiden, so I’d encourage everyone who’s considering a traineeship abroad to pick Leiden.


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