Using Computer Algebra for Developmental Biology英文电子书.pdfVIP

CSSB-2004 Using Computer Algebra for Developmental Modeling: Introduction to Signal Transduction, Cellerator, and the Computable Plant Bruce E. Shapiro Abstract In any given cell (with very few exceptions) hundreds to thousands of different chemical species undergo a continual dance. The movements at times seem to be random, and at other times ordered. The partners sometimes wait shyly in place, at other times meet and interact, moving here and there, sometimes alone, sometimes as joined pairs, sometimes trading places, at other times trading parts of themselves. When two (or more) species meet, they undergo information-exchanging chemical interaction. Between interactions, a species may remain in place, waiting, or may move to another location; in either case, the entity continues to bear information that can be transferred to its next partner. In some cases the information is allowed to leave the cell; its ultimate target may lie within the intercellular medium or may, in fact, be within another cell. In other cases, chemical entities travel between regions or compartments within a cell. There is considerable evidence that this dance is modular, i.e., that the signal transduction circuits can often be represented in terms of functional interacting modules such as cascades, switches, amplifiers, filters, and oscillators, that occur widely in nature with very little variation. This is the dance of signal tradsduction. We will focus on the deterministic representation of some key classes of modules in terms of differential equations, and then consider how developmental systems might be built from these modules. The lecture will focus on the use of Cellerator notation to generate computational models that can be numerically solved to predict