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© 2018

A New Kind of Computational Biology

Cellular Automata Based Models for Genomics and Proteomics

Textbook

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

  1. 1.CARLBio Pvt. Ltd.KolkataIndia
  2. 2.CARLBio Pvt. Ltd.KolkataIndia
  3. 3.CARLBio Pvt. Ltd.KolkataIndia
  4. 4.CARLBio Pvt. Ltd.KolkataIndia

About the authors

Prof Parimal Pal Chaudhuri is the Chief Scientific Officer and Founder of CARLBio. He is a renowned academician and researcher on Cellular Automata for over 30 years. He started his career at IBM back in the early 60’s and shifted to academia in the mid 70’s where he founded the Computer Science Department of Indian Institute of Technology (IIT) Kharagpur. He was the Head of Department for several years where he pioneered industry-academia research in India and initiated the research in Cellular Automata. He was a Visiting Research Professor at Intel Research Labs, Oregon, USA where his CA research was applied in testing of asynchronous circuits of Intel chips. On his return to India, he joined his alma mater, Bengal Engineering and Science University where he continued his CA research focusing on end applications in partnership with several MNCs. He held several assignments on sabbaticals - as a consultant to Cadence Design Systems and as a Visiting Professor at University of Illinois, Urbana Champaign, USA. He has supervised research of 20 Ph D students, authored 2 books and over 200 research publications. He is a Fellow of National Academy of Engineers (India) and was awarded the Thomas Ward Memorial Gold Medal by Institution of Engineers (India). 

Soumyabrata Ghosh is the Founder & Director of Research at CARLBio. He received his PhD degree from IIEST (Indian Institute of Engineering Science and Technology, Shibpur, formerly Bengal Engineering and Science University ). He did his MSc in Biophysics and Bioinformatics from University of Calcutta. He has more than 10 years of industrial experience in the field of data analytics, machine learning, and computational biology. His research interest includes predictive analytics, cognitive computing and AI.

Adip Dutta is a Senior Researcher at CARLBio. For more than thirty-three years, Adip Dutta has worked in diverse domains - developing algorithms, smart devices, sensor networks, power conversion, automation, motion control and instrumentation. Adip was DRDO (Defence Research and Development Organization) Scientist for several years working on high power LASER systems, thermal Imaging and optimal control algorithms. He worked with Raman Research Institute and ISRO (Indian Space Research Organization). Adip was the chief of R&D division in National Instruments and was Senior architect in the advanced technology division of Portalplayer, the designer of the first SOC used in Apple’s iPOD. He was the Chief Knowledge Officer of Hamilton Research and was a Research Consultant to nComputing Inc. USA. Since 2012 he is associated with the development of CA applications in biology pioneered by CARLBio. He completed his graduation in Physics in 1982 and B Tech (1985) in Electronics.

Somshubhro (Som) Pal Choudhury is an investor, advisor and director at CARLBio. He is a Partner at Bharat Innovations Fund, a $100M fund focused on building disruptive and innovation led startups out of India. He is a thought leader in Internet of Things (IoT) space, formerly a board and executive council member of India Electronics and Semiconductor Association (IESA),  co-founder and co-chair of India’s premier IoT event, IoTNext and ecosystem building initiative, IoTForum. Som was previously the Managing Director for Analog Devices India, wholly owned subsidiary of a US based $3.5B semiconductor MNC, Analog Devices. He was based for almost 2 decades in Silicon Valley in various roles: Global Director of Product Mgmt and Marketing of Consumer Business Unit at NETGEAR, first employee of an early M2M/IoT company in the energy management and Smart grid space, American Grid and held several management and engineering roles at Cadence Design Systems. He is a Wharton-UPenn MBA, and engineering degrees from Indian Institute of Technology (IIT) Kharagpur and North Carolina State University.

Bibliographic information

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