27/05/2020

Today, the Chan Zuckerberg Initiative (CZI) announced $3.8 million in funding for 23 grants to support open-source software projects essential to biomedical research, enabling software maintenance, growth, development, and community engagement.  Software by the lab of Prof. Yvan Saeys (VIB-UGent Center for Inflammation Research) for the analysis and visualization of single-cell data is one of the projects that will receive funding as part of CZI’s Essential Open Source Software for Science (EOSS) program. 

Open and transparent

Open-source software is crucial to modern scientific research, advancing biology and medicine while providing reproducibility and transparency. Yet even the most widely used research software often lacks dedicated funding. The EOSS program enables scientists to hire additional developers, improve documentation, address usability, improve compatibility, attract contributors, convene communities, and more. 

One of the selected projects was the dynverse project developed by the Saeys lab. Prof. Yvan Saeys (VIB-UGent Center for Inflammation Research) explains: “The dynverse project provides an ecosystem of open-source software for analyzing and interpreting dynamic cellular processes measured at single-cell resolution. The project is spearheaded by postdocs Robrecht Cannoodt and Wouter Saelens, whose work in developing and benchmarking single-cell software has greatly impacted the field.”

Visualizing single-cell data
Dr. Robrecht Cannoodt recalls the first steps of the project: “During our extensive review of software tools for analyzing cellular dynamics we developed a large library of internal tools to visualize single-cell data. We strongly believe in open-sourcing research projects from the get-go. Indeed, already long before the publication of our research in Nature Biotechnology, we received interest from other researchers in using the dynverse packages to enhance their analyses.”

Dr. Wouter Saelens adds: “Good software is one of the driving forces behind current biomedical research. More than ever, biological researchers need tools that are open, freely available, and trustworthy. Classical funding channels are often hesitant with software development projects because of the low research component. But in the long run, these tools will push the biomedical field even further. I'm really happy that the Chan Zuckerberg Initiative has recognized this, as their support will allow us to further refine our software and start new collaborations with research groups.” 

Related publication
Saelens, W., Cannoodt, R., Todorov, H., Saeys, Y. (2019) A comparison of single-cell trajectory inference methods.  Nat. Biotechnol. 37(5):547-554 
DOI: http://dx.doi.org/10.1038/s41587-019-0071-9
Software packages: https://dynverse.org   ​

 

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