Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit

Ben Blamey, Salman Toor, Martin Dahlö, Håkan Wieslander, Philip J Harrison, Ida-Maria Sintorn, Alan Sabirsh, Carolina Wählby, Ola Spjuth, Andreas Hellander
2021 GigaScience  
Background Large streamed datasets, characteristic of life science applications, are often resource-intensive to process, transport and store. We propose a pipeline model, a design pattern for scientific pipelines, where an incoming stream of scientific data is organized into a tiered or ordered "data hierarchy". We introduce the HASTE Toolkit, a proof-of-concept cloud-native software toolkit based on this pipeline model, to partition and prioritize data streams to optimize use of limited
more » ... ing resources. Findings In our pipeline model, an "interestingness function" assigns an interestingness score to data objects in the stream, inducing a data hierarchy. From this score, a "policy" guides decisions on how to prioritize computational resource use for a given object. The HASTE Toolkit is a collection of tools to adopt this approach. We evaluate with 2 microscopy imaging case studies. The first is a high content screening experiment, where images are analyzed in an on-premise container cloud to prioritize storage and subsequent computation. The second considers edge processing of images for upload into the public cloud for real-time control of a transmission electron microscope. Conclusions Through our evaluation, we created smart data pipelines capable of effective use of storage, compute, and network resources, enabling more efficient data-intensive experiments. We note a beneficial separation between scientific concerns of data priority, and the implementation of this behaviour for different resources in different deployment contexts. The toolkit allows intelligent prioritization to be 'bolted on' to new and existing systems – and is intended for use with a range of technologies in different deployment scenarios.
doi:10.1093/gigascience/giab018 pmid:33739401 pmcid:PMC7976223 fatcat:2ytlje4u2jfulg7gquwiffn3me