| Genome Informatics 14: 641--642 (2003) 641 SIMDEB-ECS : E-CELL Static Model Debugger (2008) | |||||||||||||
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| Introduction E-CELL[1, 2, 3] has been developed for whole chemical reaction in a cell simulation. In order to help debugging cell model we developed and E-CELL static model debugger it analyzes the cell model before starting simulation using physical constraint such as a number of atoms. 2 Method and Results E-CELL is an simulation engine based on Substance-Reactor model. Here Substances are molecule, ion, radical, or any material, and Reactors are subjects of chemical reaction such as enzymes. In the cell model Substance and Reactor are described by rule files, for example; SUBSTANCE Substance /CELL/CYTOPLASM:ADO [C00212] Adenosine Quantity 72265.6404 Here, "ADO" is entry name and "[C00212]" is keyword to search KEGG database. REACTOR MichaelisUniUniReactor /CELL/CYTOPLASM:E-ADA Adenosine_deaminase Substrate /CELL/CYTOPLASM:ADO 1 Product /CELL/CYTOPLASM:INO 1 Catalyst /CELL/CYTOPLASM:E-ADA Effector /CELL/CYTOPLASM:AC-ADA Km 0.052 Vm 20 This rule entry for a Reactor describes a c | |||||||||||||
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