Final degree project

The Internship

It was the end of January 2020 when I got to know about the InterMine project. I found it interesting by the first moment. I was studying the third year of my Bsc in Biomedical Engineering and I had heard about the impact of bioinformatics research. Applying for a position as an intern was my first experience with open source. We are used to work with free software, so the idea of being at the other side contributing back into an open-source project was very appealing. During the internship, I have incorporated all the necessary functions to the core of the InterMineR to make it easier for users to work with list objects. Recently, my work on the list manager has been merged and released to the Bioconductor version of InterMineR.

I appreciated the warm welcome into the community, introduced enthusiastically by Yo Yehudi with lovely meetings with the rest of interns each week. Those made working remotely less hard. I had previously worked with R and Shiny and I was comfortable with them. However, the work during the summer months, that has been extended until the begining of 2021, has been very demmanding. I am very grateful to Rachel Lyne, being there and guiding me during the internship, but also for her invaluable help in my final degree project writing. I cannot fail in my remarks to express appreciation for the coworking with Daniela Butano and Adrián Bazaga.

Altogether, the guidance, the meetings, the project results and the level of satisfaction with them make me be looking towards joining other big projects!

InterMineR Cytoscape Interface

Cytoscape is the most preferred tool for biological graph analysis. Networks provide a good way to visualise large biological datasets. Although InterMineR and Cytoscape were perfectly functional separately, the lack of a user interface between them was making tedious to use them together. InterMineR Cytoscape Interface is the first version of this Shiny application. The first requierements for the user interface were to make possible to run queries with InterMineR and then visualise the results with Cytoscape node/edge graph-based visualisations. Those requierements have been satisfied. Many more functionalities such as continuous mapping with size and colour gradients, have been incorporated.

Enjoy a walkthrough of all the applications of the app in the following tutorials! Or read my Final Degree Project.