ProSt: computing, storing and visualizing attributes of prokaryotic genomes

TL;DR

ProSt is a flexible computational system that efficiently computes, stores, and visualizes attributes of prokaryotic genomes, supporting incremental updates, multiple programming languages, and metadata tracking.

Contribution

It introduces a novel system for batch computation, storage, and visualization of prokaryotic genome attributes with plugin support and data provenance features.

Findings

Supports parallel batch computation of genome attributes

Allows incremental updates with new genome data

Supports multiple programming languages for attribute plugins

Abstract

Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding repository of information, we introduce ProSt, a computational system designed for the batch computation, storage, and interactive visualization of the values of attributes of prokaryotic genomes. The system allows for parallel attribute value batch computation, dynamically designed to incrementally integrate new attribute values as additional genomes become available. ProSt is flexible permitting the definition of attributes by implementing attribute value computation plugins, supporting several languages (Python, Nim, Rust and Bash). This allows the system to continually evolve in accordance with changing research needs and developments. Additionally, our computation and storage systems maintain comprehensive metadata, thereby enabling data provenance tracking for the computed attribute values.