Brooks J Paul, Burns William P, Fong Stephen S, Gowen Chris M, Roberts Seth B
Center for the Study of Biological Complexity, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA ; Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, P.O. Box 843083, Richmond, VA 23284, USA.
Adv Bioinformatics. 2012;2012:323472. doi: 10.1155/2012/323472. Epub 2012 Sep 10.
Constraint-based metabolic models are currently the most comprehensive system-wide models of cellular metabolism. Several challenges arise when building an in silico constraint-based model of an organism that need to be addressed before flux balance analysis (FBA) can be applied for simulations. An algorithm called FBA-Gap is presented here that aids the construction of a working model based on plausible modifications to a given list of reactions that are known to occur in the organism. When applied to a working model, the algorithm gives a hypothesis concerning a minimal medium for sustaining the cell in culture. The utility of the algorithm is demonstrated in creating a new model organism and is applied to four existing working models for generating hypotheses about culture media. In modifying a partial metabolic reconstruction so that biomass may be produced using FBA, the proposed method is more efficient than a previously proposed method in that fewer new reactions are added to complete the model. The proposed method is also more accurate than other approaches in that only biologically plausible reactions and exchange reactions are used.
基于约束的代谢模型是目前细胞代谢最全面的全系统模型。在构建一个生物体的计算机约束模型时会出现几个挑战，在通量平衡分析（FBA）可用于模拟之前需要解决这些挑战。这里提出了一种名为FBA-Gap的算法，该算法基于对已知在生物体中发生的给定反应列表进行合理修改，辅助构建一个可行模型。当应用于一个可行模型时，该算法给出关于在培养中维持细胞的最小培养基的假设。该算法的实用性在创建一个新的模式生物中得到了证明，并应用于四个现有的可行模型以生成关于培养基的假设。在修改部分代谢重建以便可以使用FBA产生生物质时，所提出的方法比先前提出的方法更有效，因为完成模型时添加的新反应更少。所提出的方法也比其他方法更准确，因为只使用了生物学上合理的反应和交换反应。
