For a successful study, design and development of the enterprise architecture, a thorough insight into the essence of the work and operation of an enterprise, is a crucial factor. As the well-known Zachman and other modern frameworks illustrate, enterprise processes and process modeling are one of the fundamental components of enterprise architecture for providing such an insight. Like building construction in which construction drawings or blueprints play crucial roles, enterprise process models are critical in developing enterprise architecture. Moreover, one may argue that the role of business process modeling in enterprise architecture is similar to the floor plan that defines the boundaries of a building to be constructed. Therefore, a suitable enterprise process modeling approach that could capture the essential operations and reflect the cross-enterprise (cross-departmental) processes is a needed component to complement enterprise architecture. In this chapter, authors study, discuss, and review the practical role of enterprise process modeling in enterprise architecture using a real life organization-based case study. Authors introduce a modeling methodology that captures essential activities not only within a process but also from the enterprise perspective where cross departmental or enterprise processes are represented.

Tile emphasis o.fthis paper is on IIsing Fillile Automata (FA) as a lIIodeling tool to lIIodel, sililulate alld ana�vze the process o.fprofein production. There is tremendous potential for mathematical alld compulational appro(iches in leading to .limdamellla! inSights and important practical benefits in research 011 hiological systems. Mathematical and cOl1lpulalional approaches have long been appreCiated in physics and ill the last twenty years have ph�ved an ever-increasing role ill chemistry. Now more and 1//01'1.' moleclilar biologist and biochemists are interested if/llsing compuler science applications and mathematical app/'Oaches in tlIfir work. In the first section, we introdllce the basic concept o/hioinjo17natics and modeling tools in Biology. In the second mid third sections Ihe molecular eve!1ls a/prolein /)/'OdIlCtioll process is exp lained and then based on the lIIo/eell/ar events, G Finite AlIlomGla lIIodel is constructed During the latter half of the 20th century, biology was dominated by reductionism approaches thaI successfully allowed for the generation of information about individual cellular components and their functions. Over the past decade , thiS proces� has been greatly accelerated due to the emergence 01' gcnomics. We now have entire DNA sequences for a growing numbe r of organisms and are c ontinually defining their gene portfolios. Also Molecular processes are complex, dynamic and invisible. This complexity makes them difficult to explain, teach, demonstrate and understand, Further more, any laboratory experiment ofbiologicaJ process/reaction is a (ilbe consuming business. Many biological experiments require days or weeks, before the dynamic behavior of reaction, process or the expected result can be obs erved . Even then many biological experiments tail to get the desired or expeoted resull by carrying the experiment once. So the repetitions of the experiments not only make it time consuming business, but also costly business. Pharmaciutical companies are trying to lo wer 'the risk and financial burden of clinical trials, so technologies that use compllters to model and simulate biological systems are revolutionizing the drug discovery field. Though clinical trials are in no inm1ediate danger of replacement by simulation tecimologies, pharmaceutical companies are eagerly adopting new means of accelerating the drug discovery and development process. This study analy£es the emerging markets for technologies that enable researchers to model and simuhlle biological pathways, cells, tissue, and diseases. It examines upcoming products, pricing strategies, and competitive pressures. With such in depth coverage, your company will be well prepared to capitalize on a burgeoning industry. Modeling the struc1ure of Biological molecules and processes are critical for understanding how these structures and processes perform their function. Furthermore, these models can be u,ed for designing compounds to modify or enhance the functions of biological molecules for medical or industrial purpose, or ...

A ne~a upplication area of Petri nets is introduced in this paper. In purticalar it show's how, bv means of Petri nets, the protein production process can be modeled and ana!vzed. In order to develop a Petri net model of the protein production process, Jrst(v the paper describes the protein production process from DNA. Although the aim qf this puper is to develop a Petri net model of protein production rather then the molecular events und chemical reuctions that occur during this process, .some basic information ahout the molec~ilar events, and precwsors/molecules thut are required for each .step of the protein production process are described in both part one and purr hw of this paper, prior to the Petri net model construction. After constructing u Petri net model of the protein production processes, bused on information contained in it, there are some program modules developed. These progrum modules are bvritten in u pseudo ftmctional language, which can be easi1.v translated into any high level programming or simulution langtruges for,final implementation.

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