Welcome to Bio-Object homepage
　　Recently, biologists learned that transport and degradation of transcribed mRNA and protein degradation are critically important steps for the regulation of gene expression through the extensive studies of RNAi (RNA interference), NMD (none-sense mediated decay) and ubiquitination. To provide a new computational framework to simulate such post-transcriptional regulations, we newly developed a stochastic bio-system simulator, Bio-Object (Biological Objective Model).
Basic concept of Bio-Object
　　A living cell is a system of thousands of chemical reactions and the collision of molecules is essential for the chemical reactions, which are under the influence of diffusion and activation energy of the molecules. A chemical reaction starts when each movable molecule interacts with its partner. In the case of gene expression, mRNA is produced when RNA polymerase and transcription factors make an appro-priate complex on the promoter region of a gene. The tran-scribed mRNA (premature mRNA) is processed (capping polyA addition and splicing) by RNA-binding proteins and changed to the mature mRNA. The mature mRNA is trans-located to cytoplasm, and bound by ribosomes. Then genetic information is translated to a protein.
　　 Bio-Object prepares a virtual cell with a (x, y) coordinate plane on which molecules move around. Biochemical reactions occur when a moving molecule meets its partner molecule. A virtual cell is composed of a square and a circle mimicking the area of a cell and a nucleus, respectively as shown in Fig. 1A. In order to detect access of molecules, the area is separated by latticework into meshes, and each mesh is named as “Matrix”. Multiple molecules exist within the Matrix, and the occurrence of reaction is decided for every molecule in the same Matrix. Various events occur by the reaction, and the events of transcription, translation and complex formation are shown respectively in each visual cell of Fig. 1B.

Fig. 1.? Basic concept of Bio-Object. The virtual cell is illustrated in Fig. 1A. Various events occur in the virtual cell are shown in Fig. 1B. (1) mRNA is produced at the transcription site in the nucleus under the regulation of a transcription factor. (2) The mRNA migrates to the cytoplasm, and then ‘protein A’ is produced when the mRNA meets a ribosome. (3) Protein A moves around the cytoplasm, and then a complex is produced when protein A meets its reaction partner, protein B. And the formation of the complex alters properties of these proteins. Each molecule in the Bio-Object has its own lifetime and it disappears by that. (Table 1). In the visual cell, the number and distribution of these molecules are changed by the events as time passes.
 

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