ACHR.cu: GPU-accelerated sampling of metabolic networks

Abstract

The in silico modeling of biological organisms consists of the mathematical representation of key functions of a biological system and the study of its behavior in different conditions and environments. It serves as a tool to support wet lab experiments and to generate hypotheses about the functioning of the subsystems. Among the many biological products, metabolism is the most amenable to modeling because it is directly related to key biological functions and processes. Moreover, public data resources of several metabolites and their abundances have been developing rapidly in recent years thereby enabling applications in many areas. In biotechnology, the metabolic modeling of ethanol-producing bacteria allows finding key interventions, such as substrate optimization, that would increase the yield in the bioreactor and improve its efficiency (Mahadevan, Burgard, Famili, Dien, & Schilling, 2005).