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A New Kind of Computational Biology

Cellular Automata Based Models for Genomics and Proteomics

  • Parimal Pal Chaudhuri
  • Soumyabrata Ghosh
  • Adip Dutta
  • Somshubhro Pal Choudhury
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Table of contents

  1. Front Matter
    Pages i-xx
  2. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 1-65
  3. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 67-100
  4. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 101-202
  5. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 203-289
  6. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 291-325
  7. Parimal Pal Chaudhuri, Soumyabrata Ghosh, Adip Dutta, Somshubhro Pal Choudhury
    Pages 327-335

About this book

Introduction

This book reflects more than three decades of research on Cellular Automata (CA), and nearly a decade of work on the application of CA to model biological strings, which forms the foundation of 'A New Kind of Computational Biology' pioneered by the start-up, CARLBio. After a brief introduction on Cellular Automata (CA) theory and functional biology, it reports on the modeling of basic biological strings with CA, starting with the basic nucleotides leading to codon and anti-codon CA models. It derives a more involved CA model of DNA, RNA, the entire translation process for amino acid formation and the evolution of protein to its unique structure and function. In subsequent chapters the interaction of Proteins with other bio-molecules is also modeled. The only prior knowledge assumed necessary is an undergraduate knowledge of computer programming and biology.

The book adopts a hands-on, “do-it-yourself” approach to enable readers to apply the method provided to derive the CA rules and comprehend how these are related to the physical ‘rules’ observed in biology. In a single framework, the authors have presented two branches of science – Computation and Biology. Instead of rigorous molecular dynamics modeling, which the authors describe as a Bottoms-Up model, or relying on the Top-Down new age Artificial Intelligence (AI) and Machine Language (ML) that depends on extensive availability of quality data, this book takes the best from both the Top-Down and Bottoms-up approaches and establishes how the behavior of complex molecules is represented in CA. The CA rules are derived from the basic knowledge of molecular interaction and construction observed in biological world but mapped to a few subset of known results to derive and predict results.

This book is useful for students, researchers and industry practitioners who want to explore modeling and simulation of the physical world complex systems from a different perspective. It raises the inevitable the question – ‘Are life and the universe nothing but a collection of continuous systems processing information’.

Keywords

In-silico Cellular Automata (CA) CA Evolution Attractor Basin Transition and Cyclic States Bioinformatics Computational Biology Proteomics Genomics Codon

Authors and affiliations

  • Parimal Pal Chaudhuri
    • 1
  • Soumyabrata Ghosh
    • 2
  • Adip Dutta
    • 3
  • Somshubhro Pal Choudhury
    • 4
  1. 1.CARLBio Pvt. Ltd.KolkataIndia
  2. 2.CARLBio Pvt. Ltd.KolkataIndia
  3. 3.CARLBio Pvt. Ltd.KolkataIndia
  4. 4.CARLBio Pvt. Ltd.KolkataIndia

Bibliographic information

  • DOI https://doi.org/10.1007/978-981-13-1639-5
  • Copyright Information Springer Nature Singapore Pte Ltd. 2018
  • Publisher Name Springer, Singapore
  • eBook Packages Computer Science
  • Print ISBN 978-981-13-1638-8
  • Online ISBN 978-981-13-1639-5
  • Buy this book on publisher's site