The ESPACE Cloud – A snapshot

The ESPACE Cloud – A snapshot
News16 March 2022

Dr. Sven Twardziok is a bioinformatician working at the Center of Digital Health at the Charité, where he’s leading a team focused on bioinformatics and data management. In this role, he is involved in ESPACE’s Work Package 5 ‘Data Management – DCP Pancreas’, work with the implementation of single-cell analysis pipelines and is responsible for the ESPACE cloud. The ESPACE communications team caught up with him to learn more about the ESPACE cloud.

The cloud is a key component of the ESPACE study, allowing members of different institutes to access and analyze shared data in a common computing environment equipped with large processing and memory capacity. All data resulting from single cell analyses and imaging by the ESPACE team as well as all relevant metadata from the study’s samples are uploaded to the cloud.

Dr. Twardziok and his colleagues began work on the ESPACE cloud in early 2021 and invited the first users from the ESPACE consortium to the platform in October of the same year. The team has deployed and configured existing cloud and software solutions to develop the ESPACE cloud and tailor it for the ESPACE consortium’s needs. The operating system used in the cloud is Kubernetes and software called JupyterHub has been used to build up the working space.

User-centricity embedded into every stage of the design process

The thought users of the ESPACE cloud were being involved early in the design process to ensure that its design and functionality is rooted in user needs. The users of the cloud have also met regularly since the cloud was launched in October last year to discuss their work in the cloud and how different functionalities and the overall design can be optimized. Dr. Twardziok and his team gather the feedback and use it when they evaluate how the cloud can be further developed.

ESPACE is coming to an end on June 31 this year. The goal is that the ESPACE cloud will be used by members of the consortium also after the project runtime as the data generated by the ESPACE team will continue to be available to users in the cloud. In addition, Dr. Twardziok and his team are currently looking into the possibility of providing the pancreas and single-cell community access to ESPACE’s data via apps developed in the cloud.