The interdisciplinary field of molecular systems biology aims to understand the behavior and mechanisms of biological processes composed of individual molecular components. As we gain more qualitative and quantitative information of complex intracellular processes, biochemical modeling and simulation become indispensable not only to uncover the molecular mechanisms of the processes, but to perform useful predictions. To this end, the E-Cell System, a multi-algorithm, multi-timescale object-oriented simulation platform, can be used to construct predictive virtual biological systems. Gene regulatory and biochemical networks that constitute a sub- or a whole cellular system can be constructed using the E-Cell System to perform qualitative and quantitative analyses. The purpose of E-Cell System: Basic Concepts and Applications is to provide a comprehensive guide for the E-Cell System version 3 in terms of the software features and its usage. While the publicly available E-Cell Simulation Environment version 3 User's Manual provides the technical details of model building and scripting, it does not describe some of the underlying concepts of the E-Cell System. The first part of the book addresses this issue by providing the basic concepts of modeling and simulation with the E-Cell System.

The Generalized LR parsing algorithm (some call it "Tomita's algorithm") was originally developed in 1985 as a part of my Ph.D thesis at Carnegie Mellon University. When I was a graduate student at CMU, I tried to build a couple of natural language systems based on existing parsing methods. Their parsing speed, however, always bothered me. I sometimes wondered whether it was ever possible to build a natural language parser that could parse reasonably long sentences in a reasonable time without help from large mainframe machines. At the same time, I was always amazed by the speed of programming language compilers, because they can parse very long sentences (i.e., programs) very quickly even on workstations. There are two reasons. First, programming languages are considerably simpler than natural languages. And secondly, they have very efficient parsing methods, most notably LR. The LR parsing algorithm first precompiles a grammar into an LR parsing table, and at the actual parsing time, it performs shift-reduce parsing guided deterministically by the parsing table. So, the key to the LR efficiency is the grammar precompilation; something that had never been tried for natural languages in 1985. Of course, there was a good reason why LR had never been applied for natural languages; it was simply impossible. If your context-free grammar is sufficiently more complex than programming languages, its LR parsing table will have multiple actions, and deterministic parsing will be no longer possible.

Parsing Efficiency is crucial when building practical natural language systems. 'Ibis is especially the case for interactive systems such as natural language database access, interfaces to expert systems and interactive machine translation. Despite its importance, parsing efficiency has received little attention in the area of natural language processing. In the areas of compiler design and theoretical computer science, on the other hand, parsing algorithms 3 have been evaluated primarily in terms of the theoretical worst case analysis (e.g. lXn", and very few practical comparisons have been made. This book introduces a context-free parsing algorithm that parses natural language more efficiently than any other existing parsing algorithms in practice. Its feasibility for use in practical systems is being proven in its application to Japanese language interface at Carnegie Group Inc., and to the continuous speech recognition project at Carnegie-Mellon University. This work was done while I was pursuing a Ph.D degree at Carnegie-Mellon University. My advisers, Herb Simon and Jaime Carbonell, deserve many thanks for their unfailing support, advice and encouragement during my graduate studies. I would like to thank Phil Hayes and Ralph Grishman for their helpful comments and criticism that in many ways improved the quality of this book. I wish also to thank Steven Brooks for insightful comments on theoretical aspects of the book (chapter 4, appendices A, B and C), and Rich Thomason for improving the linguistic part of tile book (the very beginning of section 1.1).

Parsing technologies are concerned with the automatic decomposition of complex structures into their constituent parts, with structures in formal or natural languages as their main, but certainly not their only, domain of application. The focus of Recent Advances in Parsing Technology is on parsing technologies for linguistic structures, but it also contains chapters concerned with parsing two or more dimensional languages. New and improved parsing technologies are important not only for achieving better performance in terms of efficiency, robustness, coverage, etc., but also because the developments in areas related to natural language processing give rise to new requirements on parsing technologies. Ongoing research in the areas of formal and computational linguistics and artificial intelligence lead to new formalisms for the representation of linguistic knowledge, and these formalisms and their application in such areas as machine translation and language-based interfaces call for new, effective approaches to parsing. Moreover, advances in speech technology and multimedia applications cause an increasing demand for parsing technologies where language, speech, and other modalities are fully integrated. Recent Advances in Parsing Technology presents an overview of recent developments in this area with an emphasis on new approaches for parsing modern, constraint-based formalisms on stochastic approaches to parsing, and on aspects of integrating syntactic parsing in further processing.

The Generalized LR parsing algorithm (some call it "Tomita's algorithm") was originally developed in 1985 as a part of my Ph.D thesis at Carnegie Mellon University. When I was a graduate student at CMU, I tried to build a couple of natural language systems based on existing parsing methods. Their parsing speed, however, always bothered me. I sometimes wondered whether it was ever possible to build a natural language parser that could parse reasonably long sentences in a reasonable time without help from large mainframe machines. At the same time, I was always amazed by the speed of programming language compilers, because they can parse very long sentences (i.e., programs) very quickly even on workstations. There are two reasons. First, programming languages are considerably simpler than natural languages. And secondly, they have very efficient parsing methods, most notably LR. The LR parsing algorithm first precompiles a grammar into an LR parsing table, and at the actual parsing time, it performs shift-reduce parsing guided deterministically by the parsing table. So, the key to the LR efficiency is the grammar precompilation; something that had never been tried for natural languages in 1985. Of course, there was a good reason why LR had never been applied for natural languages; it was simply impossible. If your context-free grammar is sufficiently more complex than programming languages, its LR parsing table will have multiple actions, and deterministic parsing will be no longer possible.

Parsing Efficiency is crucial when building practical natural language systems. 'Ibis is especially the case for interactive systems such as natural language database access, interfaces to expert systems and interactive machine translation. Despite its importance, parsing efficiency has received little attention in the area of natural language processing. In the areas of compiler design and theoretical computer science, on the other hand, parsing algorithms 3 have been evaluated primarily in terms of the theoretical worst case analysis (e.g. lXn", and very few practical comparisons have been made. This book introduces a context-free parsing algorithm that parses natural language more efficiently than any other existing parsing algorithms in practice. Its feasibility for use in practical systems is being proven in its application to Japanese language interface at Carnegie Group Inc., and to the continuous speech recognition project at Carnegie-Mellon University. This work was done while I was pursuing a Ph.D degree at Carnegie-Mellon University. My advisers, Herb Simon and Jaime Carbonell, deserve many thanks for their unfailing support, advice and encouragement during my graduate studies. I would like to thank Phil Hayes and Ralph Grishman for their helpful comments and criticism that in many ways improved the quality of this book. I wish also to thank Steven Brooks for insightful comments on theoretical aspects of the book (chapter 4, appendices A, B and C), and Rich Thomason for improving the linguistic part of tile book (the very beginning of section 1.1).