A Primer For Computational Biology

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A Primer for Computational Biology

Shawn T. O'Neil
A Primer for Computational Biology Book PDF

Author : Shawn T. O'Neil
Publisher : Unknown
Page : 0 pages
File Size : 48,9 Mb
Release : 2017-12-21
Category : Science
ISBN : 0870719262

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A Primer for Computational Biology by Shawn T. O'Neil Pdf

A Primer for Computational Biology aims to provide life scientists and students the skills necessary for research in a data-rich world. The text covers accessing and using remote servers via the command-line, writing programs and pipelines for data analysis, and provides useful vocabulary for interdisciplinary work. The book is broken into three parts: Introduction to Unix/Linux: The command-line is the "natural environment" of scientific computing, and this part covers a wide range of topics, including logging in, working with files and directories, installing programs and writing scripts, and the powerful "pipe" operator for file and data manipulation. Programming in Python: Python is both a premier language for learning and a common choice in scientific software development. This part covers the basic concepts in programming (data types, if-statements and loops, functions) via examples of DNA-sequence analysis. This part also covers more complex subjects in software development such as objects and classes, modules, and APIs. Programming in R: The R language specializes in statistical data analysis, and is also quite useful for visualizing large datasets. This third part covers the basics of R as a programming language (data types, if-statements, functions, loops and when to use them) as well as techniques for large-scale, multi-test analyses. Other topics include S3 classes and data visualization with ggplot2.

Bioinformatics and Computational Biology

Basant K. Tiwary
Bioinformatics and Computational Biology Book PDF

Author : Basant K. Tiwary
Publisher : Springer Nature
Page : 239 pages
File Size : 40,5 Mb
Release : 2021-11-23
Category : Medical
ISBN : 9789811642418

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Bioinformatics and Computational Biology by Basant K. Tiwary Pdf

This textbook introduces fundamental concepts of bioinformatics and computational biology to the students and researchers in biology, medicine, veterinary science, agriculture, and bioengineering . The respective chapters provide detailed information on biological databases, sequence alignment, molecular evolution, next-generation sequencing, systems biology, and statistical computing using R. The book also presents a case-based discussion on clinical, veterinary, agricultural bioinformatics, and computational bioengineering for application-based learning in the respective fields. Further, it offers readers guidance on reconstructing and analysing biological networks and highlights computational methods used in systems medicine and genome-wide association mapping of diseases. Given its scope, this textbook offers an essential introductory book on bioinformatics and computational biology for undergraduate and graduate students in the life sciences, botany, zoology, physiology, biotechnology, bioinformatics, and genomic science as well as systems biology, bioengineering and the agricultural, and veterinary sciences.

Practical Applications of Computational Biology and Bioinformatics, 13th International Conference

Florentino Fdez-Riverola,Miguel Rocha,Mohd Saberi Mohamad,Nazar Zaki,José A. Castellanos-Garzón
Practical Applications of Computational Biology and Bioinformatics 13th International Conference Book PDF

Author : Florentino Fdez-Riverola,Miguel Rocha,Mohd Saberi Mohamad,Nazar Zaki,José A. Castellanos-Garzón
Publisher : Springer
Page : 184 pages
File Size : 45,7 Mb
Release : 2019-06-21
Category : Technology & Engineering
ISBN : 9783030238735

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Practical Applications of Computational Biology and Bioinformatics, 13th International Conference by Florentino Fdez-Riverola,Miguel Rocha,Mohd Saberi Mohamad,Nazar Zaki,José A. Castellanos-Garzón Pdf

This book features 21 papers spanning many different sub-fields in bioinformatics and computational biology, presenting the latest research on the practical applications to promote fruitful interactions between young researchers in different areas related to the field. Next-generation sequencing technologies, together with other emerging and diverse experimental techniques, are evolving rapidly, creating numerous types of omics data. These, in turn, are creating new challenges for the expanding fields of bioinformatics and computational biology, which seek to analyse, process, integrate and extract meaningful knowledge from such data. This calls for new algorithms and approaches from fields such as databases, statistics, data mining, machine learning, optimization, computer science, machine learning and artificial intelligence. Clearly, biology is increasingly becoming a science of information, requiring tools from the computational sciences. To address these challenges, we have seen the emergence of a new generation of interdisciplinary scientists with a strong background in the biological and computational sciences. In this context, the interaction of researchers from different scientific areas is, more than ever, vital to boost the research efforts in the field and contribute to the training of the new generation of interdisciplinary scientists.

Computational Biology

Scott T. Kelley,Dennis Didulo
Computational Biology Book PDF

Author : Scott T. Kelley,Dennis Didulo
Publisher : John Wiley & Sons
Page : 181 pages
File Size : 55,5 Mb
Release : 2018-01-01
Category : Science
ISBN : 9781683673033

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Computational Biology by Scott T. Kelley,Dennis Didulo Pdf

This textbook is for anyone who needs to learn the basics of bioinformatics—the use of computational methods to better understand biological systems. Computational Biology covers the principles and applications of the computational methods used to study DNA, RNA, and proteins, including using biological databases such as NCBI and UniProt; performing BLAST, sequence alignments, and structural predictions; and creating phylogenetic trees. It includes a primer that can be used as a jumping off point for learning computer programming for bioinformatics. This text can be used as a self-study guide, as a course focused on computational methods in biology/bioinformatics, or to supplement general courses that touch on topics included within the book. Computational Biology's robust interactive online components “gamify” the study of bioinformatics, allowing the reader to practice randomly generated problems on their own time to build confidence and skill and gain practical real-world experience. The online component also assures that the content being taught is up to date and accurately reflects the ever-changing landscape of bioinformatics web-based programs.

Computational Modeling of Genetic and Biochemical Networks

James M. Bower,Hamid Bolouri
Computational Modeling of Genetic and Biochemical Networks Book PDF

Author : James M. Bower,Hamid Bolouri
Publisher : MIT Press
Page : 386 pages
File Size : 45,5 Mb
Release : 2001
Category : Computers
ISBN : 0262524236

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Computational Modeling of Genetic and Biochemical Networks by James M. Bower,Hamid Bolouri Pdf

How new modeling techniques can be used to explore functionally relevant molecular and cellular relationships.

Kernel Methods in Computational Biology

Bernhard Schölkopf,Koji Tsuda,Jean-Philippe Vert
Kernel Methods in Computational Biology Book PDF

Author : Bernhard Schölkopf,Koji Tsuda,Jean-Philippe Vert
Publisher : MIT Press
Page : 428 pages
File Size : 55,5 Mb
Release : 2004
Category : Computers
ISBN : 0262195097

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Kernel Methods in Computational Biology by Bernhard Schölkopf,Koji Tsuda,Jean-Philippe Vert Pdf

A detailed overview of current research in kernel methods and their application to computational biology.

Cellular Biophysics and Modeling

Greg Conradi Smith
Cellular Biophysics and Modeling Book PDF

Author : Greg Conradi Smith
Publisher : Cambridge University Press
Page : 395 pages
File Size : 47,9 Mb
Release : 2019-03-14
Category : Mathematics
ISBN : 9781107005365

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Cellular Biophysics and Modeling by Greg Conradi Smith Pdf

What every neuroscientist should know about the mathematical modeling of excitable cells, presented at an introductory level.

A Primer on Scientific Programming with Python

Hans Petter Langtangen
A Primer on Scientific Programming with Python Book PDF

Author : Hans Petter Langtangen
Publisher : Springer
Page : 942 pages
File Size : 54,6 Mb
Release : 2016-07-28
Category : Computers
ISBN : 9783662498873

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A Primer on Scientific Programming with Python by Hans Petter Langtangen Pdf

The book serves as a first introduction to computer programming of scientific applications, using the high-level Python language. The exposition is example and problem-oriented, where the applications are taken from mathematics, numerical calculus, statistics, physics, biology and finance. The book teaches "Matlab-style" and procedural programming as well as object-oriented programming. High school mathematics is a required background and it is advantageous to study classical and numerical one-variable calculus in parallel with reading this book. Besides learning how to program computers, the reader will also learn how to solve mathematical problems, arising in various branches of science and engineering, with the aid of numerical methods and programming. By blending programming, mathematics and scientific applications, the book lays a solid foundation for practicing computational science. From the reviews: Langtangen ... does an excellent job of introducing programming as a set of skills in problem solving. He guides the reader into thinking properly about producing program logic and data structures for modeling real-world problems using objects and functions and embracing the object-oriented paradigm. ... Summing Up: Highly recommended. F. H. Wild III, Choice, Vol. 47 (8), April 2010 Those of us who have learned scientific programming in Python ‘on the streets’ could be a little jealous of students who have the opportunity to take a course out of Langtangen’s Primer.” John D. Cook, The Mathematical Association of America, September 2011 This book goes through Python in particular, and programming in general, via tasks that scientists will likely perform. It contains valuable information for students new to scientific computing and would be the perfect bridge between an introduction to programming and an advanced course on numerical methods or computational science. Alex Small, IEEE, CiSE Vol. 14 (2), March /April 2012 “This fourth edition is a wonderful, inclusive textbook that covers pretty much everything one needs to know to go from zero to fairly sophisticated scientific programming in Python...” Joan Horvath, Computing Reviews, March 2015

Computational Genomics with R

Altuna Akalin
Computational Genomics with R Book PDF

Author : Altuna Akalin
Publisher : CRC Press
Page : 462 pages
File Size : 55,8 Mb
Release : 2020-12-16
Category : Mathematics
ISBN : 9781498781862

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Computational Genomics with R by Altuna Akalin Pdf

Computational Genomics with R provides a starting point for beginners in genomic data analysis and also guides more advanced practitioners to sophisticated data analysis techniques in genomics. The book covers topics from R programming, to machine learning and statistics, to the latest genomic data analysis techniques. The text provides accessible information and explanations, always with the genomics context in the background. This also contains practical and well-documented examples in R so readers can analyze their data by simply reusing the code presented. As the field of computational genomics is interdisciplinary, it requires different starting points for people with different backgrounds. For example, a biologist might skip sections on basic genome biology and start with R programming, whereas a computer scientist might want to start with genome biology. After reading: You will have the basics of R and be able to dive right into specialized uses of R for computational genomics such as using Bioconductor packages. You will be familiar with statistics, supervised and unsupervised learning techniques that are important in data modeling, and exploratory analysis of high-dimensional data. You will understand genomic intervals and operations on them that are used for tasks such as aligned read counting and genomic feature annotation. You will know the basics of processing and quality checking high-throughput sequencing data. You will be able to do sequence analysis, such as calculating GC content for parts of a genome or finding transcription factor binding sites. You will know about visualization techniques used in genomics, such as heatmaps, meta-gene plots, and genomic track visualization. You will be familiar with analysis of different high-throughput sequencing data sets, such as RNA-seq, ChIP-seq, and BS-seq. You will know basic techniques for integrating and interpreting multi-omics datasets. Altuna Akalin is a group leader and head of the Bioinformatics and Omics Data Science Platform at the Berlin Institute of Medical Systems Biology, Max Delbrück Center, Berlin. He has been developing computational methods for analyzing and integrating large-scale genomics data sets since 2002. He has published an extensive body of work in this area. The framework for this book grew out of the yearly computational genomics courses he has been organizing and teaching since 2015.

Engineering Genetic Circuits

Chris J. Myers
Engineering Genetic Circuits Book PDF

Author : Chris J. Myers
Publisher : CRC Press
Page : 306 pages
File Size : 50,8 Mb
Release : 2016-04-19
Category : Medical
ISBN : 1420083252

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Engineering Genetic Circuits by Chris J. Myers Pdf

An Introduction to Systems Bioengineering Takes a Clear and Systematic Engineering Approach to Systems Biology Focusing on genetic regulatory networks, Engineering Genetic Circuits presents the modeling, analysis, and design methods for systems biology. It discusses how to examine experimental data to learn about mathematical models, develop efficient abstraction and simulation methods to analyze these models, and use analytical methods to guide the design of new circuits. After reviewing the basic molecular biology and biochemistry principles needed to understand genetic circuits, the book describes modern experimental techniques and methods for discovering genetic circuit models from the data generated by experiments. The next four chapters present state-of-the-art methods for analyzing these genetic circuit models. The final chapter explores how researchers are beginning to use analytical methods to design synthetic genetic circuits. This text clearly shows how the success of systems biology depends on collaborations between engineers and biologists. From biomolecular observations to mathematical models to circuit design, it provides essential information on genetic circuits and engineering techniques that can be used to study biological systems.

A Primer in Mathematical Models in Biology

Lee A. Segel,Leah Edelstein-Keshet
A Primer in Mathematical Models in Biology Book PDF

Author : Lee A. Segel,Leah Edelstein-Keshet
Publisher : SIAM
Page : 435 pages
File Size : 42,6 Mb
Release : 2013-05-09
Category : Science
ISBN : 9781611972498

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A Primer in Mathematical Models in Biology by Lee A. Segel,Leah Edelstein-Keshet Pdf

A textbook on mathematical modelling techniques with powerful applications to biology, combining theoretical exposition with exercises and examples.

Advances in Bioinformatics and Computational Biology

Peter F. Stadler,Maria Emilia M. T. Walter,Maribel Hernandez-Rosales,Marcelo M. Brigido
Advances in Bioinformatics and Computational Biology Book PDF

Author : Peter F. Stadler,Maria Emilia M. T. Walter,Maribel Hernandez-Rosales,Marcelo M. Brigido
Publisher : Springer Nature
Page : 159 pages
File Size : 50,8 Mb
Release : 2021-11-23
Category : Science
ISBN : 9783030918149

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Advances in Bioinformatics and Computational Biology by Peter F. Stadler,Maria Emilia M. T. Walter,Maribel Hernandez-Rosales,Marcelo M. Brigido Pdf

This book constitutes the refereed proceedings of the Brazilian Symposium on Bioinformatics, BSB 2021, held in November 2021. Due to COVID-19 pandemic the conference was held virtually The 10 revised full papers and 5 short papers were carefully reviewed and selected from 28 submissions. The papers address a broad range of current topics in computational biology and bioinformatics.

Synthetic Biology — A Primer

Anonim
Synthetic Biology A Primer Book PDF

Author : Anonim
Publisher : World Scientific
Page : 196 pages
File Size : 43,5 Mb
Release : 2015-08-24
Category : Science
ISBN : 9781783268818

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Synthetic Biology — A Primer by Anonim Pdf

Synthetic Biology — A Primer (Revised Edition) presents an updated overview of the field of synthetic biology and the foundational concepts on which it is built. This revised edition includes new literature references, working and updated URL links, plus some new figures and text where progress in the field has been made. The book introduces readers to fundamental concepts in molecular biology and engineering and then explores the two major themes for synthetic biology, namely 'bottom-up' and 'top-down' engineering approaches. 'Top-down' engineering uses a conceptual framework of systematic design and engineering principles focused around the Design-Build-Test cycle and mathematical modelling. The 'bottom-up' approach involves the design and building of synthetic protocells using basic chemical and biochemical building blocks from scratch exploring the fundamental basis of living systems. Examples of cutting-edge applications designed using synthetic biology principles are presented, including: the production of novel, microbial synthesis of pharmaceuticals and fine chemicalsthe design and implementation of biosensors to detect infections and environmental waste. The book also describes the Internationally Genetically Engineered Machine (iGEM) competition, which brings together students and young researchers from around the world to carry out summer projects in synthetic biology. Finally, the primer includes a chapter on the ethical, legal and societal issues surrounding synthetic biology, illustrating the integration of social sciences into synthetic biology research. Final year undergraduates, postgraduates and established researchers interested in learning about the interdisciplinary field of synthetic biology will benefit from this up-to-date primer on synthetic biology. Contents:List of ContributorsPrefaceIntroduction to BiologyBasic Concepts in Engineering BiologyFoundational TechnologiesMinimal Cells and Synthetic LifeParts, Devices and SystemsModelling Synthetic Biology SystemsApplications of Designed Biological SystemsiGEMThe Societal Impact of Synthetic BiologyAppendices:Proforma of Common Laboratory TechniquesGlossaryIndex Readership: Students, professionals, researchers in biotechnology and bioengineering. Keywords:Synthetic Biology;Engineering Principles;Biosociety;Biological Engineering;BiotechnologyKey Features:The book is written in a way that is accessible to students and researchers from different disciplinesThe authors are part of the internationally recognised Centre for Synthetic Biology and Innovation and are among the leaders in this field

Systems Biology

Andreas Kremling
Systems Biology Book PDF

Author : Andreas Kremling
Publisher : CRC Press
Page : 382 pages
File Size : 51,7 Mb
Release : 2013-11-12
Category : Mathematics
ISBN : 9781466567894

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Systems Biology by Andreas Kremling Pdf

Drawing on the latest research in the field, Systems Biology: Mathematical Modeling and Model Analysis presents many methods for modeling and analyzing biological systems, in particular cellular systems. It shows how to use predictive mathematical models to acquire and analyze knowledge about cellular systems. It also explores how the models are systematically applied in biotechnology. The first part of the book introduces biological basics, such as metabolism, signaling, gene expression, and control as well as mathematical modeling fundamentals, including deterministic models and thermodynamics. The text also discusses linear regression methods, explains the differences between linear and nonlinear regression, and illustrates how to determine input variables to improve estimation accuracy during experimental design. The second part covers intracellular processes, including enzymatic reactions, polymerization processes, and signal transduction. The author highlights the process–function–behavior sequence in cells and shows how modeling and analysis of signal transduction units play a mediating role between process and function. The third part presents theoretical methods that address the dynamics of subsystems and the behavior near a steady state. It covers techniques for determining different time scales, sensitivity analysis, structural kinetic modeling, and theoretical control engineering aspects, including a method for robust control. It also explores frequent patterns (motifs) in biochemical networks, such as the feed-forward loop in the transcriptional network of E. coli. Moving on to models that describe a large number of individual reactions, the last part looks at how these cellular models are used in biotechnology. The book also explains how graphs can illustrate the link between two components in large networks with several interactions.

Fundamentals of Systems Biology

Markus W. Covert
Fundamentals of Systems Biology Book PDF

Author : Markus W. Covert
Publisher : CRC Press
Page : 367 pages
File Size : 48,9 Mb
Release : 2017-10-19
Category : Technology & Engineering
ISBN : 9781498728478

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Fundamentals of Systems Biology by Markus W. Covert Pdf

For decades biology has focused on decoding cellular processes one gene at a time, but many of the most pressing biological questions, as well as diseases such as cancer and heart disease, are related to complex systems involving the interaction of hundreds, or even thousands, of gene products and other factors. How do we begin to understand this complexity? Fundamentals of Systems Biology: From Synthetic Circuits to Whole-cell Models introduces students to methods they can use to tackle complex systems head-on, carefully walking them through studies that comprise the foundation and frontier of systems biology. The first section of the book focuses on bringing students quickly up to speed with a variety of modeling methods in the context of a synthetic biological circuit. This innovative approach builds intuition about the strengths and weaknesses of each method and becomes critical in the book’s second half, where much more complicated network models are addressed—including transcriptional, signaling, metabolic, and even integrated multi-network models. The approach makes the work much more accessible to novices (undergraduates, medical students, and biologists new to mathematical modeling) while still having much to offer experienced modelers--whether their interests are microbes, organs, whole organisms, diseases, synthetic biology, or just about any field that investigates living systems.