Overview

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes.[1]Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous snapshot of the physiology of that cell.

In our project, we investigate the origin of formaldehydemetabolism using computer simulation ofbiochemical networks in tobacco. By utilizing the genetic engineering, threepathways of formaldehyde metabolism in tobacco were taken into account and three models of regulatory mechanism were established for these pathways. After that, we combined them by considering three pathways systematically and an integrated model was obtained.Below, let us describe the mathematical principles and all the procedures one by one.

Mathematical Principles

一切化学反应都服从定比定律。假设各个反应的反应式为：

vi(l)为化学反应组元Ai在第l个反应中的化学定比，通过m个反应相互转化。vi(l)>0的组元为生成物，反之为反应物。令ϛl代表反应的“进行度”，其定义为：当ϛl=1时有关组元各自增加vi(l) mol。所以当进行度为dϛl时，由于反应l导致各组元增加的摩尔数dni为：