کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
2076744 1079462 2008 15 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Rule-based computing system for microbial interactions and communications: Evolution in virtual bacterial populations
موضوعات مرتبط
مهندسی و علوم پایه ریاضیات مدل‌سازی و شبیه سازی
پیش نمایش صفحه اول مقاله
Rule-based computing system for microbial interactions and communications: Evolution in virtual bacterial populations
چکیده انگلیسی

We have developed a novel rule-based computing system of microbial interactions and communications, referred to as COSMIC-Rules, for simulating evolutionary processes within populations of virtual bacteria. The model incorporates three levels: the bacterial genome, the bacterial cell and an environment inhabited by such cells. The virtual environment in COSMIC-Rules can contain multiple substances, whose relative toxicity or nutrient status is specified by the genome of the bacterium. Each substance may be distributed uniformly or in a user-defined manner. The organisms in COSMIC-Rules possess individually-defined physical locations, size, cell division status and genomes. Genes and/or gene systems are represented by abstractions that may summate sometimes complex phenotypes. Central to COSMIC-Rules is a simplified representation of bacterial species, each containing a functional genome including, where desired, extrachromosomal elements such as plasmids and/or bacteriophages. A widely applicable computer representation of biological recognition systems based on bit string matching is essential to the model. This representation permits, for example, the modelling of protein–protein interactions, receptor–ligand interactions and DNA–DNA transactions. COSMIC-Rules is intended to inform studies on bacterial adaptation and evolution, and to predict behaviour of populations of pathogenic bacteria and their viruses. The framework is constructed for parallel execution across a large number of machines and efficiently utilises a 64 processor development cluster. It will run on any Grid system and has successfully tested simulations with millions of bacteria, of multiple species and utilising multiple substrates. The model may be used for large-scale simulations where a genealogical record for individual organisms is required.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Biosystems - Volume 91, Issue 1, January 2008, Pages 216–230
نویسندگان
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