Image credit: Wellcome Sanger Institute
A recent hackathon, hosted by the Wellcome Sanger Institute, brought together software developers and computational biologists working on tools to analyse data from single cells.
The ability to study the building blocks of life - the cells that make up our organs and bodies - has exploded over the last few years. DNA and RNA sequencing, protein and other measurements are now possible for an individual cell.
With some of the largest sequencing facilities in the world, Wellcome Sanger Institute scientists are applying these latest techniques to the study of millions of individual cells, as they hunt for insights into how cells function, how they organise and communicate, and how they respond to stimuli or disease.
As intricate data from single cells grow, so does the need for computational tools and methods that can process and interpret these data. Sanger Institute researchers are at the forefront of developing these technologies. However, in many cases, it is beyond the capabilities of a single person, team or even a single institute to build and maintain the complex computational pipelines that researchers use.
Instead, communities of scientists have come together to support, improve and maintain core processing and analysis software. One, the scverse community, has emerged as people pooled their expertise to enhance the computational tools needed for single-cell research. These methods, used worldwide, are the foundations of single-cell data analysis. The scverse seeks to make the tools more accessible, help data re-use, and streamline analysis for researchers.
Lisa Dratva and Emma Dann, PhD students in Sarah Teichmann’s group at the Sanger Institute, are members of the scverse community, and recently organised and hosted the fourth hackathon for the group. The event, held at the Sanger Institute and funded by CZI, was attended by 35 eager participants from academia and industry across Europe and beyond. About half of attendees were researchers from the Sanger Institute and EMBL’s European Bioinformatics Institute (EMBL-EBI).
“It was great to bring together the community again. Analysing single-cell data is complex and it is a relatively new field. To do robust science we need practical, up-to-date and well-maintained computational tools. This hackathon enabled us to leverage local expertise in single-cell technologies and improve the methods we use on a daily basis. Thanks to everyone who got involved.”
Lisa Dratva,
PhD Student, Teichmann group, Wellcome Sanger Institute
“The hackathon focused on tools for comparative analysis of multi-condition datasets in the scverse ecosystem, working on documentation, data structures, methods for statistical testing, visualisation and interpretation of differential analysis results. To maximise impact, all the code, documentation, notebooks and tutorials developed during the hackathon were immediately available open-source on Github and integrated into the scverse environment.”
Emma Dann,
PhD Student, Teichmann group, Wellcome Sanger Institute
A networking session with flash talks by both hackathon attendees and Sanger scientists was held one afternoon, and attracted over 40 people from the wider Wellcome Genome Campus.
“As part of the Human Cell Atlas initiative, we are analysing millions of individual cells, in multiple states, to map all the cell types in the human body. The project will serve as the basis for the next generation of biological research. Researchers here are also leading computational analysis efforts to interpret vast amounts of single-cell data – we’ve developed tools that can predict a cell's type, its functions and its drug response. Computational analysis is part of everyday life in biology now. Standardising the tools we use is vital if we want to do research that is accessible to all.”
Dr Sarah Teichmann,
Senior Group Leader, Teichmann Group, Wellcome Sanger Institute
