| Artificial Life is a very important researching field in Bioinformatics, which means some systems'behavior holding basic life features. Basic life features generally include self-reproduction, evolution, and self-organization. When Artificial Life was born in the middle of 1980s, Artificial Life has attracted many experts from various domains to join in the field, who hoped to reveal the secret of life. The researching fields of Artificial Life are various, and recent years, different life systems are introduced in computer system. As one of the most important researching field in Artificial Life, E-Cell was born in 1997. E-Cell mostly simulates the main course of cell's life activities on computer platform, including cell's growth, development, reproduction and apoptosis. It involves the internal and external environment of cells and cell-related material on the life activities of the role of performance, such as physical activity inside and outside the cell and biochemical reactions, gene expression, protein interactions, such as the kinetic energy of reproduction. There are also medical, pharmaceutical, biological functions is E-Cell researching fields.E-Cell technology research and modeling is of important significance. In medical, building normal and pathological E-Cell, can not only simulate the physiological mechanisms of cell's birth, activities and regulation, but also understand and reveal disease process find effective pathogenic elements and molecular markers for the early warning disease diagnosis, prevention and intervention measures, design and test new drugs. With respect to scientific research, E-Cells can be used for all kinds of scientific research, experiment can be realized which in the actual conditions is difficult to achieve, predict the results of the pilot tests, find that some cells in a real experiment it is difficult to observe the phenomenon and the law, coupled with the certification. And E-Cell's systematic, can make us from the perspective of the overall study; the E-Cell intuitive, help researchers understanding of the issues. We can set all kinds of complex experimental conditions, intervene all aspects, and simplify the experiment, save the experimental materials and time. In social life, by using of E-Cells, we can observe environmental factors on the role of the human body and its means to control measures; E-Cells can be simulated through nutrition, drugs, poisons on the role of cells, and avoid the direct adverse consequences on human and animals; can simulate the structure of genes and proteins, and predict the function of genes and proteins.Analog-Cell is a model of E-Cell blueprint that is imitative of genetic expression. The current models of E-Cell blueprint seem to be over-simplified and Analog-Cell is therefore constructed to supply the gap. Analog-Cell simulates transcription, posttranscriptional processing, translation, mRNA degradation and gene mutations of eukaryotic cell, as well as in the five process, related enzymes and regulatory factors control mechanism. These regulation mechanisms consist: the role of DNA gyrase in DNA helicase; the role of RNA polymerase in DNA transcription; the role of aminoacyl-tRNA synthetase in the tRNA aminoacylation loading amino acids; Peptide-transferase in mRNA translation, catalytic polypeptide chain formation; the role of RNase in mRNA dissociation when translation was completed; the role of eIF-2 in guiding met-tRNA to the mRNA translation start codon; the role of eIF-3 in the ribosome identify mRNA's cap; the role of eIF-5 in translation; the role of eEF-1 in guiding aminoacyl-tRNA to the corresponding codon; the role of eEF-2 in ribosomes'sliding in mRNA; the role of eRF-1 in the identification of the terminal codon; the role of eRF-3 in translation termination. In addition, Analog-Cell also simulates eukaryotic cells in looking for promoter, transcription start site and translation initial site.Analog-Cell is developed by MFC and VC + + 6.0 by using the state-controlled mechanism. The reactions in gene expression and its regulation are very plenty and complex. The paper involves more than ten reactions and dozens of reaction substrate and related enzymes. The main work includes, improving transcription reaction, translation reaction, degradation and gene mutation reaction in Analog-Cell, adding related enzymes and regulators and their mechanism reactions, and adding the DNA helicase reaction, transcription initiation reaction, mRNA capping increases, the aminoacylation reaction, the initial reaction of translation, translation termination reaction, as well as DNA interception algorithm using poromoter predicting. There are four algorithms improved and seven original algorithms added in total. Through these algorithms, although Analog-Cell can't simulate all reactions in gene expression and regulation, but basically describe a detailed process. Analog-Cell is the first domestic E-Cell model. As E-Cell technology was come out in a shorter time, the study abroad is in the initial stage, and so far no domestic E-Cell model published, the emergence of Analog-Cell model can promote domestic E-Cell technology. Analog-Cell contains rich image information. Because the existing E-Cell models are weak in graphics display, and not conducive to observe intracellular biochemical reaction process, Analog-Cell was designed as a vivid, containing rich graphics display image information model. So Analog-Cell can do something significant in E-Cell model's graphics display. Analog-Cell simulates gene mutation. Analog-Cell was simulated on molecule level, and gene sequence is made by lots of nucleotides. This kind of model is fit for researching single gene, and very comfortable to simulate gene mutation. Gene Mutation is one of the important means in biological evolution. So Analog-Cell model plays a certain role in studying the evolution of genes. Analog-Cell simulates gene expression regulation. Analog-Cell involves a variety of enzyme and regulatory factors, and it can really simulate them how to control the process of gene expression in eukaryotic cells. So Analog-Cell can promote the research in gene expression regulation as well as the principles of related enzymes and regulatory factors. Analog-Cell joined the promoter prediction function. As promoter prediction belong to gene prediction areas, we can also add other important sequence prediction in gene expression to Analog-Cell. So promoter prediction's successful adding pave the way for other sequence prediction's adding, and will drive the development of gene prediction.
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