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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.
This textbook has been conceptualized to provide a detailed
description of the various aspects of Systems and Synthetic
Biology, keeping the requirements of M.Sc. and Ph.D. students in
mind. Also, it is hoped that this book will mentor young scientists
who are willing to contribute to this area but do not know from
where to begin. The book has been divided into two sections. The
first section will deal with systems biology - in terms of the
foundational understanding, highlighting issues in biological
complexity, methods of analysis and various aspects of modelling.
The second section deals with the engineering concepts, design
strategies of the biological systems ranging from simple DNA/RNA
fragments, switches and oscillators, molecular pathways to a
complete synthetic cell will be described. Finally, the book will
offer expert opinions in legal, safety, security and social issues
to present a well-balanced information both for students and
scientists.
Genome Engineering via CRISPR-Cas9 Systems presents a compilation
of chapters from eminent scientists from across the globe who have
established expertise in working with CRISPR-Cas9 systems.
Currently, targeted genome engineering is a key technology for
basic science, biomedical and industrial applications due to the
relative simplicity to which they can be designed, used and
applied. However, it is not easy to find relevant information
gathered in a single source. The book contains a wide range of
applications of CRISPR in research of bacteria, virus, algae, plant
and mammalian and also discusses the modeling of drosophila, zebra
fish and protozoan, among others. Other topics covered include
diagnosis, sensor and therapeutic applications, as well as ethical
and regulatory issues. This book is a valuable source not only for
beginners in genome engineering, but also researchers, clinicians,
stakeholders, policy makers, and practitioners interested in the
potential of CRISPR-Cas9 in several fields.
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