Duitsland – Onderzoek en ontwikkeling, en aanverwante adviezen – Project "anndataR: Native R access to the standard single-cell data format"

This service agreement concerns the FOSS‌ library "anndataR", covering the work needed to bring this implementation in R of the bioinformatics library up to compliance with the most recent edition of the reference implementation. To achieve this, a gap analysis must be performed to identify the deviation between the current implementation and the most recent edition of the reference implementation. Research must then be conducted to arrive at the best method to implement the lacking functionality within the defining capabilities and programming paradigm of the R language and its ecosystem of libraries and modules.

Moreover, research and design work is required to devise solutions to several issues and limitations that are already identified within the existing implementation, by examining the relevant issue reports submitted by users, and comparing the proposed solutions in order to select the best in each case and implement it. Additionally, optimising and improving the performance of the library, which processes huge amounts of data in each run, entail profiling the resulting implementation and measuring its performance to identify bottlenecks, then design solutions to mitigate them. Finally, the design and implementation of CI/CD tests ensures the continuous validity and compliance with future editions of the reference implementation.

The overall aim of this work is to maintain FOSS infrastructure components used to utilise the large datasets that are critical building blocks in the field of bioinformatics, by keeping it updated as per the state-of-the-art in the field, in terms of capabilities and performance.