Towards a Serverless Bioinformatics Cyberinfrastructure Pipeline

Function-as-a-Service (FaaS) and the serverless computing model offer a powerful abstraction for supporting large-scale applications in the cloud. A major hurdle in this context is that it is non-trivial to transform an application, even an already containerized one, to a FaaS implementation. In this paper, we take the first step towards supporting easier and efficient application transformation to FaaS. We present a systematic scheme to transform applications written in Python into a set of functions that can then be automatically deployed atop platforms such as AWS Lamda. We target a Bioinformatics cyberinfrastructure pipeline, CIWARS, that provides waste-water analysis for the identification of antibiotic-resistant bacteria and viruses such as SARS-CoV-2. Based on our experience with enabling FaaS-based CIWARS, we develop a methodology that would help the conversion of other similar applications to the FaaS model. Our evaluation shows that our approach can correctly transform CIWARS to FaaS, and the new FaaS-based CIWARS incurs only negligible(≤2%) less than 2% overhead for representative workloads.