Computational Methods in Synthetic Biology

Computational Methods in Synthetic Biology
Author: Mario Andrea Marchisio
Publisher: Humana
Total Pages: 255
Release: 2021-11-27
Genre: Science
ISBN: 9781071608241

This second edition book provides complete coverage of the computational approaches currently used in Synthetic Biology. New chapters detail computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Computational Methods in Synthetic Biology, Second Edition aims to feature a broad overview of the research areas that can be met in the area of in silico Synthetic Biology.

Computational Methods for Estimating the Kinetic Parameters of Biological Systems

Computational Methods for Estimating the Kinetic Parameters of Biological Systems
Author: Quentin Vanhaelen
Publisher: Humana
Total Pages: 0
Release: 2022-12-24
Genre: Science
ISBN: 9781071617694

This detailed book provides an overview of various classes of computational techniques, including machine learning techniques, commonly used for evaluating kinetic parameters of biological systems. Focusing on three distinct situations, the volume covers the prediction of the kinetics of enzymatic reactions, the prediction of the kinetics of protein-protein or protein-ligand interactions (binding rates, dissociation rates, binding affinities), and the prediction of relatively large set of kinetic rates of reactions usually found in quantitative models of large biological networks. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that leads to successful results. Authoritative and practical, Computational Methods for Estimating the Kinetic Parameters of Biological Systems will be of great interest for researchers working through the challenge of identifying the best type of algorithm and who would like to use or develop a computational method for the estimation of kinetic parameters.

Biodefense in the Age of Synthetic Biology

Biodefense in the Age of Synthetic Biology
Author: National Academies of Sciences, Engineering, and Medicine
Publisher: National Academies Press
Total Pages: 189
Release: 2019-01-05
Genre: Technology & Engineering
ISBN: 0309465184

Scientific advances over the past several decades have accelerated the ability to engineer existing organisms and to potentially create novel ones not found in nature. Synthetic biology, which collectively refers to concepts, approaches, and tools that enable the modification or creation of biological organisms, is being pursued overwhelmingly for beneficial purposes ranging from reducing the burden of disease to improving agricultural yields to remediating pollution. Although the contributions synthetic biology can make in these and other areas hold great promise, it is also possible to imagine malicious uses that could threaten U.S. citizens and military personnel. Making informed decisions about how to address such concerns requires a realistic assessment of the capabilities that could be misused. Biodefense in the Age of Synthetic Biology explores and envisions potential misuses of synthetic biology. This report develops a framework to guide an assessment of the security concerns related to advances in synthetic biology, assesses the levels of concern warranted for such advances, and identifies options that could help mitigate those concerns.

Algorithms in Structural Molecular Biology

Algorithms in Structural Molecular Biology
Author: Bruce R. Donald
Publisher: MIT Press
Total Pages: 497
Release: 2023-08-15
Genre: Science
ISBN: 0262548798

An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Over the past decade, novel algorithms have been developed both for analyzing biological data and for synthetic biology problems such as protein engineering. This book explains the algorithmic foundations and computational approaches underlying areas of structural biology including NMR (nuclear magnetic resonance); X-ray crystallography; and the design and analysis of proteins, peptides, and small molecules. Each chapter offers a concise overview of important concepts, focusing on a key topic in the field. Four chapters offer a short course in algorithmic and computational issues related to NMR structural biology, giving the reader a useful toolkit with which to approach the fascinating yet thorny computational problems in this area. A recurrent theme is understanding the interplay between biophysical experiments and computational algorithms. The text emphasizes the mathematical foundations of structural biology while maintaining a balance between algorithms and a nuanced understanding of experimental data. Three emerging areas, particularly fertile ground for research students, are highlighted: NMR methodology, design of proteins and other molecules, and the modeling of protein flexibility. The next generation of computational structural biologists will need training in geometric algorithms, provably good approximation algorithms, scientific computation, and an array of techniques for handling noise and uncertainty in combinatorial geometry and computational biophysics. This book is an essential guide for young scientists on their way to research success in this exciting field.

An Introduction to Computational Systems Biology

An Introduction to Computational Systems Biology
Author: Karthik Raman
Publisher: CRC Press
Total Pages: 359
Release: 2021-05-30
Genre: Computers
ISBN: 0429944527

This book delivers a comprehensive and insightful account of applying mathematical modelling approaches to very large biological systems and networks—a fundamental aspect of computational systems biology. The book covers key modelling paradigms in detail, while at the same time retaining a simplicity that will appeal to those from less quantitative fields. Key Features: A hands-on approach to modelling Covers a broad spectrum of modelling, from static networks to dynamic models and constraint-based models Thoughtful exercises to test and enable understanding of concepts State-of-the-art chapters on exciting new developments, like community modelling and biological circuit design Emphasis on coding and software tools for systems biology Companion website featuring lecture videos, figure slides, codes, supplementary exercises, further reading, and appendices: https://ramanlab.github.io/SysBioBook/ An Introduction to Computational Systems Biology: Systems-Level Modelling of Cellular Networks is highly multi-disciplinary and will appeal to biologists, engineers, computer scientists, mathematicians and others.

Synthetic Biology

Synthetic Biology
Author: Daniel G. Gibson
Publisher: Perspectives Cshl
Total Pages: 0
Release: 2017
Genre: Science
ISBN: 9781621821182

Synthetic biology involves the rational design and construction of biological components and systemsfrom genetic elements and metabolic pathways to entirely new organisms. Progress in this field has been rapid, and it promises to significantly expand our capabilities in biotechnology, medicine, and agriculture. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines the tools and techniques employed by synthetic biologists, how these may be used to develop new drugs, diagnostic approaches, food sources, and clean energy, and what the field of synthetic biology has taught us about natural living systems. The contributors discuss advances in DNA synthesis and assembly, genome editing (e.g., CRISPR/Cas9), and artificial genetic systems. Progress in designing complex genetic switches and circuits, expanding the genetic code, modifying cellular organization, producing proteins using cell-free systems, and developing biodesign automation tools is also covered. The authors also explore ways to produce new organisms and products that have particular attributesfor example, microbial "molecular factories," synthetic organs and tissues, and plants with novel traits. This volume is an essential resource for molecular, cell, and systems biologists who seek to engineer living systems for human benefit.

Computational Methods in Systems Biology

Computational Methods in Systems Biology
Author: Eugenio Cinquemani
Publisher: Springer Nature
Total Pages: 292
Release: 2021-09-13
Genre: Science
ISBN: 303085633X

This book constitutes the refereed proceedings of the 19th International Conference on Computational Methods in Systems Biology, CMSB 2021, held in Bordeaux, France, September 22–24, 2021.*The 13 full papers and 5 tool papers were carefully reviewed and selected from 32 submissions. The topics of interest include biological process modelling; biological system model verification, validation, analysis, and simulation; high-performance computational systems biology; model inference from experimental data; multi-scale modeling and analysis methods; computational approaches for synthetic biology; machine learning and data-driven approaches; microbial ecology modelling and analysis; methods and protocols for populations and their variability; models, applications, and case studies in systems and synthetic biology. The chapters "Microbial Community Decision Making Models in Batch", "Population design for synthetic gene circuits", "BioFVM-X: An MPI+OpenMP 3-D Simulator for Biological Systems" are published open access under a CC BY license (Creative Commons Attribution 4.0 International License). * The conference was held in a hybrid mode due to the COVID-19 pandemic.

Computational Methods in Systems Biology

Computational Methods in Systems Biology
Author: Ion Petre
Publisher: Springer Nature
Total Pages: 324
Release: 2022-08-18
Genre: Science
ISBN: 3031150341

This book constitutes the refereed proceedings of the 20th International Conference on Computational Methods in Systems Biology, CMSB 2022, held in Bucharest, Romania, in September 2022. The 13 full papers and 4 tool papers were carefully reviewed and selected from 43 submissions. CMSB focuses on modeling, simulation, analysis, design and control of biological systems. The papers are arranged thematically as follows: Chemical reaction networks; Boolean networks; continuous and hybrid models; machine learning; software.

Systems Biology and Synthetic Biology

Systems Biology and Synthetic Biology
Author: Pengcheng Fu
Publisher: John Wiley & Sons
Total Pages: 672
Release: 2009-08-13
Genre: Technology & Engineering
ISBN: 9780470437971

The genomic revolution has opened up systematic investigations and engineering designs for various life forms. Systems biology and synthetic biology are emerging as two complementary approaches, which embody the breakthrough in biology and invite application of engineering principles. Systems Biology and Synthetic Biology emphasizes the similarity between biology and engineering at the system level, which is important for applying systems and engineering theories to biology problems. This book demonstrates to students, researchers, and industry that systems biology relies on synthetic biology technologies to study biological systems, while synthetic biology depends on knowledge obtained from systems biology approaches.

Computational Methods in Systems Biology

Computational Methods in Systems Biology
Author: Ezio Bartocci
Publisher: Springer
Total Pages: 361
Release: 2016-09-03
Genre: Computers
ISBN: 3319451774

This book constitutes the refereed proceedings of the 14th International Conference on Computational Methods in Systems Biology, CMSB 2016, held in Cambridge, UK, in September 2016. The 20 full papers, 3 tool papers and 9 posters presented were carefully reviewed and selected from 37 regular paper submissions. The topics include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology and parallel implementations; model inference from experimental data; model integration from biological databases; multi-scale modeling and analysis methods; and computational approaches for synthetic biology.