OpenProblems.bio
NumFOCUS Sponsored Project since 2025OpenProblems.bio is a community-driven project aiming to identify and benchmark computational methods for analyzing single-cell data. It provides a framework for evaluating different algorithms on well-defined tasks, using standardized metrics and datasets. The ultimate goal is to accelerate progress in single-cell research by highlighting the most effective tools and identifying key open challenges in the field.
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Industry
Higher Education, Healthcare and Life Sciences
Language
Python, R, C++, Scala
Features
Benchmarking, Method evaluation, Dataset aggregation, Model Zoo
Open Problems is a platform for centralized benchmarking of methods in single-cell analysis. The platform enables method developers to upload their code to a centralized repository, where it is evaluated on a set of standardized datasets and metrics. Results are displayed on continuously updated leaderboards at https://openproblems.bio/.
Open Problems is a generalized framework for living benchmarking. Here, we apply this framework to the life sciences, with a focus on single-cell analysis workflows. The scope of our applications is continually expanding as new contributors implement new tasks to new biological domains.
