Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines

As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud-based research continue to expand. Besides the potential for accelerated and diverse biomedical discovery that comes from a harmonized data ecosystem, the cloud also presents a shift away from the standard practice of duplicating data to computational clusters or local computers for analysis. However, despite these benefits, researcher migration to the cloud has lagged, in part due to insufficient educational resources to train biomedical scientists on cloud infrastructure. There exists a conceptual lack especially around the crafting of custom analytic pipelines that require software not pre-installed by cloud analysis platforms. We here present three fundamental concepts necessary for custom pipeline creation in the cloud. These overarching concepts are workflow and cloud provider agnostic, extending the utility of this education to serve as a foundation for any computational analysis running any dataset in any biomedical cloud platform. We illustrate these concepts using one of our own custom analyses, a study using the case-parent trio design to detect sex-specific genetic effects on orofacial cleft (OFC) risk, which we crafted in the biomedical cloud analysis platform CAVATICA.