Distributed flux balance analysis simulations of serial biomass fermentation by two organisms

Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms. BioLego enables the simultaneous analysis of multiple fermentation scenarios and the comparison of fermentation potential of multiple feedstock compositions. Thanks to the effective use of cloud computing it further allows resource intensive analysis and exploration of media and organism modifications. We use BioLego to obtain biological and validation results, including (1) exploratory search for the optimal utilization of corn biomasses – corn cobs, corn fiber and corn stover – in fermentation biorefineries; (2) analysis of the possible effects of changes in the composition of...旨在同时兼顾生物质原料（biomass feedstock）组成与发酵微生物（fermentation microorganisms）特性的智能生物炼制（biorefinery）设计，可依托专用计算模拟（computational simulation）与计算机辅助优化（computer-assisted optimization）工具实现效能提升。本研究提出一款基于微软Azure云（Microsoft Azure Cloud）的BioLego Vn2.0框架（BioLego Vn2.0），该框架可支持针对两种不同微生物介导的生物质串联发酵过程开展大规模模拟。BioLego Vn2.0框架可同时分析多种发酵场景，并对比不同原料组成的发酵潜力。依托高效的云计算（cloud computing）能力，该框架还可开展资源密集型分析，并对培养基（medium）与微生物改造（organism modifications）方案进行探索。我们通过BioLego Vn2.0框架获取了生物学验证结果，包括：(1) 探索性筛选玉米生物质——玉米芯（corn cobs）、玉米纤维（corn fiber）与玉米秸秆（corn stover）——在发酵生物炼制中的最优利用方案；(2) 分析组成变化可能带来的影响……