I had an opportunity to visit Basel, Switzerland for a month between mid-July to mid-August. The first week began with the ISMB/ECCB Conference 2019, which was a 5 days event. The average temperature was 35 °C with a hottest day reaching up to 39 °C, which was rather too hot compared to a British weather. This weather was perfect to try out ‘floating’ in the Rhine river, which I missed the opportunity to, but would highly recommend it if anyone is visiting Basel in the future.

The highlight of the conference was a presentation given by Professor Bonnie Berger from MIT regarding “Biomedical Data Sharing and Analysis at Scale”. She addressed the need for secure data sharing and analysis at scale due to exponential growth of the sequence data available worldwide. In her talk, she described three key challenges in research involving biomedical big data: 1) secure genome-wide association studies (GWAS) across multiple diverse datasets; 2) secure collaboration of pharmacological data to predict new drug candidates; 3) consortium-scale integration for single-cell data analysis. She presented a novel computational approach (based on their paper), which allows for secure multiparty computation while secretly sharing data. This methodology securely enables genomics data to be combined in multiple remote locations whilst preserving genetic data privacy and returning GWAS statistics. The protocol for GWAS could be scaled up to a million individuals.

After the conference, I have spent three weeks working at Roche to analyze the clinical data together with conducting data analytics to obtain genetics data from the scientific literature. Below is my favourite view of the city of Basel from Roche’s tower, which is 178 meters above ground level.

For those visiting Basel in the future, if you would like to learn more about the history of paper, typography, and writing, I highly recommend visiting the Basel Paper Mill Museum (thanks to our group’s colleague, Lyuba, for letting me know about this place).