The Genomics Virtual Laboratory (GVL) is a cloud based suite of pre-configured genomics analysis tools and workflow platforms running on a scalable Slurm cluster. The microbial-GVL is a tailored version of the Genomics Virtual Lab workbench, pre-populated with a large suite of tools specifically for microbial -omics analysis.
There is little overlap in the tools used for microbial versus large genome model organism genomics. Thus, significant effort is needed to populate the computational analysis environment for the RDS omics platform for the data generated in the Antibiotic Resistant Pathogens (SEPSIS) initiative. The suite of tools provided in the microbial GVL is defined by the bioinformatics analyses used within the SEPSIS project itself.
Characteristics defining the microbial-GVL workbench include:
- Highly scalable computationally
- Tool- and compute- centric (as opposed to data-centric)
- Highly capable in terms of available tools and analysis options
- Controlled, in that there is a large effort in pre-configuring the GVL workbench
- Reproducible and workflow-oriented
- Flexible in that several options for data analysis platforms are offered: Workflow GUI (Galaxy); Statistical GUI (RStudio); programmatic GUI (Jupyter Python GUI); command line. Tools on the microbial GVL are available through all platform interfaces.