FEDGEN Testbed: A Federated Genomics Private Cloud Infrastructure for Precision Medicine and Artificial Intelligence Research

Abstract

The cloud computing space is enjoying a renaissance. Not long ago, cloud computing was confined to the wall of high-revenue companies, but in recent times a growing number of businesses, public and private institutions are turning to the cloud computing platform to reap the benefits of a self-service, scalable, and flexible infrastructure. Moreover, with the increased implementation, advantages, and popularity of artificial intelligence, the demand for computing environments to solve age-old problems such as malaria and cancer is on the rise. This paper presents the implementation of a cloud computing infrastructure, the FEDerated GENomics (FEDGEN) Testbed, to provide an adequate IT environment for cancer and malaria researchers. The cloud computing environment is built using Openstack middleware. OpenStack is deployed using Metal-As-A-Service (MAAS) and Juju. Virtual Machines (Instances) were deployed, and services (JupiterHub) were installed on the FEDGEN testbed. The built infrastructure would allow the running of models requiring high computing power and would allow for collaboration among teams.

Personalizing medicine in Africa: current state, progress and challenges

“…CApIC-ACE seeks to develop new diagnostic biomarkers for prostate and breast cancers. They are also building a federated genomics (FEDGEN) infrastructure customized to process and analyze indigenous genomic data ( Adetiba, E. et al, 2022 ). The MRC/UVRI and LSHTM Uganda Research Unit is promoting the genetic epidemiology of both communicable and non-communicable diseases (NCDs) in Uganda.…”

“…The study's findings reported that aspirin could be considered as a good preventive agent for colorectal cancer in group of pateints with Lynch syndrome. In 2022, Mathers et al (2022 subjected participants with Lynch syndrome to a randomized doubleblind treatment with 30 g resistant starch (RS) (n = 463) daily or placebo (n = 455) for up to 4 years. Upon following up with the participant for up to 20 years, they concluded that 30 g daily RS confers substantial protection against non-colorectal cancers for the group of patients with Lynch syndrome.…”

FEDARGOS-V1: A Monitoring Architecture for Federated Cloud Computing Infrastructures

“…The FEDGEN testbed [58] makes use of a Broker to manage resource negotiations between end-users and CSPs within the federated cloud environment. The testbed is built with Open-Stack middleware.…”