Data Intuitive was thrilled to be part of the very first scverse Conference, held at the Technical University of Munich (Schedule). With around 150 single-cell bioinformaticians and software developers in attendance, this inaugural event was a must-attend for us. The conference offered an invaluable opportunity to connect with the vibrant open-source community from around the world that is driving innovation in single-cell analysis. We were excited to share our insights and learn from the best in the field.
A couple of highlights from the conference:
Talks from industry leaders like Angela Oliveira Pisco (insitro), David Brocks (Immunai), Alex Wolf (Lamin), Ryan Williams (TileDB), and Maximilian Lombardo (CZI) highlighted the symbiotic relationship between companies and the single-cell community, where companies leverage research advancements and in turn contribute back with open-source software, standards, ML models, and large quantities of omics data.
Training models on atlas-scale single-cell datasets by Ryan Williams (TileDB) and Maximilian Lombardo (CZI). The CELLxGENE Discover Census workshop demonstrated the power of accessing metadata from millions of cells and being able to query and download omics data in a unified interface. Particularly, the Census Similarity Search functionality promises to be a valuable tool in leveraging the CELLxGENE Discover Census data to automatically annotate incoming datasets (demo).
From scanpy to the virtual cell: The coming-of-age of single-cell analysis by Fabian Theis (Helmholtz Munich): Fabian provided a very insightful overview of the history of scverse. His interactive poll on desired topics for the scverse Conference 2025 edition highlighted the need for continued focus on interoperability, workflows, and data management.
- Luke Zappia’s Sketchnotes: Luke captured the essence of the keynote talks through insightful sketchnotes, which can be found on his blog post here.
Poll Results: Most Requested Topics for scverse Conference 2025
Fabian Theis’ poll underscored the relevance of Data Intuitive’s contributions to the scverse ecosystem. Our presentations and workshops at the conference perfectly aligned with those topics:
Benchmarking Open Problems in Single Cell Analysis by Malte Luecken (Helmholtz Munich) and Robrecht Cannoodt (Data Intuitive): We led a workshop on fostering community engagement in creating robust benchmarks for single-cell analysis and deriving best practices from them. Link
Polyglot Programming for Single-cell Analysis by Louise Deconinck (VIB), Benjamin Rombaut (VIB), and Robrecht Cannoodt (Data Intuitive): Our presentation on polyglot programming equipped researchers and developers with strategies for seamlessly integrating diverse tools and languages in single-cell workflows. saeyslab.github.io/polygloty
anndataR: Easily Interact with anndata in R by Louise Deconinck (VIB): anndataR is an R package that streamlines working with anndata and other single-cell data formats in R. anndataR is developed and maintained by Data Intuitive. anndataR.data-intuitive.com
Conclusion
The scverse Conference 2024 was a fantastic experience, and not just for the excellent catering! We thoroughly enjoyed connecting with so many passionate individuals from the single-cell analysis community. The open and collaborative atmosphere was truly inspiring, and the commitment to open-source principles was evident throughout the event. We’re already excited about participating in the next scverse Conference in 2025!