As part of the training all ITN REMIX fellows had a chance to attend transferable skills courses in Statistical Literacy, Data Analysis and Data Visualization. These courses were organized by Rick Scavetta from Scavetta Academy and I found them very useful for my research. Knowledge of topics covered by the courses is essential for every experimental biologist. For a long time, I have been interested in increasing my knowledge of data analysis tools and shaping my research profile more towards bioinformatics. I was therefore very grateful for the opportunity to do my REMIX secondment with Rick Scavetta, to dive deeper into the knowledge of biological data science.

For the study of mitochondrial ribosome, we use a technique that employs separation of protein complexes by density gradient centrifugation followed by mass spectrometry analysis. This method produces large data sets that need to be processed. During my REMIX secondment, I worked on re-developing the pipeline for the data analysis of such experiments. The existing pipeline used by our research group is written in a combination of Python and R programming languages. Additionally, it requires the user to perform manual data manipulations in Excel and manual visualization. We decided to build upon the original workflow and upgrade it by implementing the whole data analysis pipeline and all its inputs/outputs in the R language, as well as by adding more functionality and making it more user friendly. The work carried out during the secondment can be divided into three parts: creation of data analysis workflow, visualization workflow and integration of first two parts into a graphical user interface. My skills in writing code in R as well as understanding some more complex topics in data analysis such as clustering greatly improved during the secondment. After 4 weeks of the secondment together with Rick Scavetta we created a first working draft of a pipeline. We continue the development and the final analysis software will be released as an R package.

This secondment provided me not only with the opportunity to improve my programming skills, but also to experience a different type of work environment. I spent my workdays in Berlin in a co-working space called Betahaus. Compared to usual laboratory and academic setting, here most people were either part of a start-up company or freelancers. The vibe of the place was very friendly and welcoming. One very useful lesson a scientist can learn and get inspired about in such place is how to “sell your research”.  Another aspect I enjoyed was the emphasis on community and social activities in Betahaus. Weekly events included “betabreakfast”, a morning get together where people pitched their professional ideas, afternoon yoga sessions to relieve some stress or “betabeer” to relax at the end of the week. I think this kind of activities might also help to strengthen community spirit in academic environment.

I really enjoyed my 4 weeks in Berlin. On weekends and evenings, I visited many Berlin landmarks and attractions, including Brandenburg gate, TV tower, Natural History museum and East Side gallery. It has been a month full of learning and new experiences. I am grateful to ITN REMIX for encouraging fellows to do secondments and to Rick Scavetta for agreeing to be the host of my REMIX secondment.