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Foundations of Systems Biology

Using Cell Illustrator and Pathway Databases

  • Textbook
  • © 2009

Overview

Authors:
  1. Masao Nagasaki
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  2. Ayumu Saito
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  3. Atsushi Doi
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  4. Hiroshi Matsuno
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  5. Satoru Miyano
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  • A concise, easy-to-follow text, serving as a valuable introduction to contemporary cell biology and offering insight into the key research directions in the field
  • Introduces the current big bio-databases, and why and how they can be used to develop and support systems biology research
  • Includes supplementary material: sn.pub/extras

Part of the book series: Computational Biology (COBO, volume 13)

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Table of contents (6 chapters)

  1. Front Matter

    Pages i-xii
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  2. Introduction

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 1-4

  3. Pathway Databases

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 5-18

  4. Pathway Simulation Software

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 19-24

  5. Starting Cell Illustrator

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 25-74

  6. Pathway Modeling and Simulation

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 75-125

  7. Computational Platform for Systems Biology

    • Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano
    Pages 127-144

  8. Back Matter

    Pages 145-155
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Keywords

About this book

Today, as hundreds of genomes have been sequenced and thousands of proteins and more than ten thousand metabolites have been identi?ed, navigating safely through this wealth of information without getting completely lost has become crucial for research in, and teaching of, molecular biology. Consequently, a considerable number of tools have been developed and put on the market in the last two decades that describe the multitude of potential/putative interactions between genes, proteins, metabolites, and other biologically relevant compounds in terms of metabolic, genetic, signaling, and other networks, their aim being to support all sorts of explorations through bio-data bases currently called Systems Biology. As a result, navigating safely through this wealth of information-processing tools has become equally crucial for successful work in molecular biology. To help perform such navigation tasks successfully, this book starts by providing an extremely useful overview of existing tools for ?nding (or designing) and inv- tigating metabolic, genetic, signaling, and other network databases, addressing also user-relevant practical questions like • Is the database viewable through a web browser? • Is there a licensing fee? • What is the data type (metabolic, gene regulatory, signaling, etc. )? • Is the database developed/maintained by a curator or a computer? • Is there any software for editing pathways? • Is it possible to simulate the pathway? It then goes on to introduce a speci?c such tool, that is, the fabulous “Cell - lustrator 3. 0” tool developed by the authors.

Bibliographic Information

  • Book Title: Foundations of Systems Biology

  • Book Subtitle: Using Cell Illustrator and Pathway Databases

  • Authors: Masao Nagasaki, Ayumu Saito, Atsushi Doi, Hiroshi Matsuno, Satoru Miyano

  • Series Title: Computational Biology

  • DOI: https://doi.org/10.1007/978-1-84882-023-4

  • Publisher: Springer London

  • eBook Packages: Computer Science, Computer Science (R0)

  • Copyright Information: Springer-Verlag London 2009

  • Hardcover ISBN: 978-1-84882-022-7Published: 06 April 2009

  • Softcover ISBN: 978-1-4471-6872-0Published: 30 April 2017

  • eBook ISBN: 978-1-84882-023-4Published: 21 April 2009

  • Series ISSN: 1568-2684

  • Series E-ISSN: 2662-2432

  • Edition Number: 1

  • Number of Pages: XII, 155

  • Topics: Life Sciences, general, Computational Biology/Bioinformatics, Simulation and Modeling, Cell Biology

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