Bioinformatics with Python Cookbook

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781789349986
Pages : 360 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.4/5 (349 users download)


Download Bioinformatics with Python Cookbook by Tiago Antao PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics with Python Cookbook by Tiago Antao. This book is available in ePub and PDF format with a single click unlimited downloads. Discover modern, next-generation sequencing libraries from Python ecosystem to analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most important Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data. What you will learn Learn how to process large next-generation sequencing (NGS) datasets Work with genomic dataset using the FASTQ, BAM, and VCF formats Learn to perform sequence comparison and phylogenetic reconstruction Perform complex analysis with protemics data Use Python to interact with Galaxy servers Use High-performance computing techniques with Dask and Spark Visualize protein dataset interactions using Cytoscape Use PCA and Decision Trees, two machine learning techniques, with biological datasets Who this book is for This book is for Data data Scientistsscientists, Bioinformatics bioinformatics analysts, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems using a recipe-based approach. Working knowledge of the Python programming language is expected.


Bioinformatics with Python Cookbook

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781783558650
Pages : 306 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.5/5 (558 users download)


Download Bioinformatics with Python Cookbook by Tiago Antao PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics with Python Cookbook by Tiago Antao. This book is available in ePub and PDF format with a single click unlimited downloads. If you are either a computational biologist or a Python programmer, you will probably relate to the expression "explosive growth, exciting times". Python is arguably the main programming language for big data, and the deluge of data in biology, mostly from genomics and proteomics, makes bioinformatics one of the most exciting fields in data science. Using the hands-on recipes in this book, you'll be able to do practical research and analysis in computational biology with Python. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the book is the practical application of bioinformatics, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of bioinformatics data.


Bioinformatics with Python Cookbook - Second Edition

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ISBN 10 : OCLC:1103595163
Pages : 360 pages
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Rating : 4./5 ( users download)


Download Bioinformatics with Python Cookbook - Second Edition by Tiago Antao PDF/Ebook Free clicking on the below button will initiate the downloading process of Bioinformatics with Python Cookbook - Second Edition by Tiago Antao. This book is available in ePub and PDF format with a single click unlimited downloads. Discover modern, next-generation sequencing libraries from Python ecosystem to analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most important Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and more Explore various statistical and machine learning techniques for bioinformatics data analysis Book Description Bioinformatics is an active research field that uses a range of simple-to-advanced computations to extract valuable information from biological data. This book covers next-generation sequencing, genomics, metagenomics, population genetics, phylogenetics, and proteomics. You'll learn modern programming techniques to analyze large amounts of biological data. With the help of real-world examples, you'll convert, analyze, and visualize datasets using various Python tools and libraries. This book will help you get a better understanding of working with a Galaxy server, which is the most widely used bioinformatics web-based pipeline system. This updated edition also includes advanced next-generation sequencing filtering techniques. You'll also explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks such as Dask and Spark. By the end of this book, you'll be able to use and implement modern programming techniques and frameworks to deal with the ever-increasing deluge of bioinformatics data. What you will learn Learn how to process large next-generation sequencing (NGS) datasets Work with genomic dataset using the FASTQ, BAM, and VCF formats Learn to perform sequence comparison and phylogenetic reconstruction Perform complex analysis with protemics data Use Python to interact with Galaxy servers Use High-performance computing techniques with Dask and Spark Visualize protein dataset interactions using Cytoscape Use PCA and Decision Trees, two machine learning techniques, with biological datasets Who this book is for This book is for Data data Scientistsscientists, Bioinformatics bioinformatics analysts, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems using a recipe-based approach. Working knowledge of the Python programming language is expected. Downloading the example code for this book You can download the example code files for all Packt books you have purchased from your account at http://w ...


BIOINFORMATICS WITH PYTHON COOKBOOK - THIRDEDITION

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ISBN 10 : 1803236426
Pages : pages
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Rating : 4.0/5 (83 users download)


Download BIOINFORMATICS WITH PYTHON COOKBOOK - THIRDEDITION by TIAGO. ANTAO PDF/Ebook Free clicking on the below button will initiate the downloading process of BIOINFORMATICS WITH PYTHON COOKBOOK - THIRDEDITION by TIAGO. ANTAO. This book is available in ePub and PDF format with a single click unlimited downloads.


Computational Methods in Systems Biology

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Publisher : Springer
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ISBN 10 : 9783319674711
Pages : 332 pages
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Rating : 4.7/5 (674 users download)


Download Computational Methods in Systems Biology by Jérôme Feret PDF/Ebook Free clicking on the below button will initiate the downloading process of Computational Methods in Systems Biology by Jérôme Feret. This book is available in ePub and PDF format with a single click unlimited downloads. This book constitutes the refereed proceedings of the 15th International Conference on Computational Methods in Systems Biology, CMSB 2017, held in Darmstadt, Germany, in September 2017. The 15 full papers, 4 tool papers and 4 posters presented together with 1 invited talk were carefully reviewed and selected from 41 regular paper submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verication, 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.


Introduction to Bioinformatics

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ISBN 10 : 9780198794141
Pages : 432 pages
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Rating : 4.9/5 (794 users download)


Download Introduction to Bioinformatics by Arthur Lesk PDF/Ebook Free clicking on the below button will initiate the downloading process of Introduction to Bioinformatics by Arthur Lesk. This book is available in ePub and PDF format with a single click unlimited downloads. The ideal text for biology students encountering bioinformatics for the first time, Introduction to Bioinformatics describes how recent technological advances in the field can be used as a powerful set of tools for receiving and analyzing biological data.


Mastering Numerical Computing with NumPy

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781788996846
Pages : 248 pages
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Rating : 4.9/5 (996 users download)


Download Mastering Numerical Computing with NumPy by Umit Mert Cakmak PDF/Ebook Free clicking on the below button will initiate the downloading process of Mastering Numerical Computing with NumPy by Umit Mert Cakmak. This book is available in ePub and PDF format with a single click unlimited downloads. Enhance the power of NumPy and start boosting your scientific computing capabilities Key Features Grasp all aspects of numerical computing and understand NumPy Explore examples to learn exploratory data analysis (EDA), regression, and clustering Access NumPy libraries and use performance benchmarking to select the right tool Book Description NumPy is one of the most important scientific computing libraries available for Python. Mastering Numerical Computing with NumPy teaches you how to achieve expert level competency to perform complex operations, with in-depth coverage of advanced concepts. Beginning with NumPy's arrays and functions, you will familiarize yourself with linear algebra concepts to perform vector and matrix math operations. You will thoroughly understand and practice data processing, exploratory data analysis (EDA), and predictive modeling. You will then move on to working on practical examples which will teach you how to use NumPy statistics in order to explore US housing data and develop a predictive model using simple and multiple linear regression techniques. Once you have got to grips with the basics, you will explore unsupervised learning and clustering algorithms, followed by understanding how to write better NumPy code while keeping advanced considerations in mind. The book also demonstrates the use of different high-performance numerical computing libraries and their relationship with NumPy. You will study how to benchmark the performance of different configurations and choose the best for your system. By the end of this book, you will have become an expert in handling and performing complex data manipulations. What you will learn Perform vector and matrix operations using NumPy Perform exploratory data analysis (EDA) on US housing data Develop a predictive model using simple and multiple linear regression Understand unsupervised learning and clustering algorithms with practical use cases Write better NumPy code and implement the algorithms from scratch Perform benchmark tests to choose the best configuration for your system Who this book is for Mastering Numerical Computing with NumPy is for you if you are a Python programmer, data analyst, data engineer, or a data science enthusiast, who wants to master the intricacies of NumPy and build solutions for your numeric and scientific computational problems. You are expected to have familiarity with mathematics to get the most out of this book.


Machine Learning in Biotechnology and Life Sciences

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781801815673
Pages : 408 pages
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Rating : 4.1/5 (815 users download)


Download Machine Learning in Biotechnology and Life Sciences by Saleh Alkhalifa PDF/Ebook Free clicking on the below button will initiate the downloading process of Machine Learning in Biotechnology and Life Sciences by Saleh Alkhalifa. This book is available in ePub and PDF format with a single click unlimited downloads. Explore all the tools and templates needed for data scientists to drive success in their biotechnology careers with this comprehensive guide Key Features Learn the applications of machine learning in biotechnology and life science sectors Discover exciting real-world applications of deep learning and natural language processing Understand the general process of deploying models to cloud platforms such as AWS and GCP Book Description The booming fields of biotechnology and life sciences have seen drastic changes over the last few years. With competition growing in every corner, companies around the globe are looking to data-driven methods such as machine learning to optimize processes and reduce costs. This book helps lab scientists, engineers, and managers to develop a data scientist's mindset by taking a hands-on approach to learning about the applications of machine learning to increase productivity and efficiency in no time. You'll start with a crash course in Python, SQL, and data science to develop and tune sophisticated models from scratch to automate processes and make predictions in the biotechnology and life sciences domain. As you advance, the book covers a number of advanced techniques in machine learning, deep learning, and natural language processing using real-world data. By the end of this machine learning book, you'll be able to build and deploy your own machine learning models to automate processes and make predictions using AWS and GCP. What you will learn Get started with Python programming and Structured Query Language (SQL) Develop a machine learning predictive model from scratch using Python Fine-tune deep learning models to optimize their performance for various tasks Find out how to deploy, evaluate, and monitor a model in the cloud Understand how to apply advanced techniques to real-world data Discover how to use key deep learning methods such as LSTMs and transformers Who this book is for This book is for data scientists and scientific professionals looking to transcend to the biotechnology domain. Scientific professionals who are already established within the pharmaceutical and biotechnology sectors will find this book useful. A basic understanding of Python programming and beginner-level background in data science conjunction is needed to get the most out of this book.


Artificial Intelligence with Python Cookbook

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781789137965
Pages : 468 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.3/5 (137 users download)


Download Artificial Intelligence with Python Cookbook by Ben Auffarth PDF/Ebook Free clicking on the below button will initiate the downloading process of Artificial Intelligence with Python Cookbook by Ben Auffarth. This book is available in ePub and PDF format with a single click unlimited downloads. If you are looking to build next-generation AI solutions for work or even for your pet projects, you’ll find this cookbook useful. With the help of easy-to-follow recipes, this book will take you through the advanced AI and machine learning approaches and algorithms that are required to build smart models for problem-solving.


R Bioinformatics Cookbook

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Publisher : Packt Publishing Ltd
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ISBN 10 : 9781789955590
Pages : 316 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.5/5 (955 users download)


Download R Bioinformatics Cookbook by Dan MacLean PDF/Ebook Free clicking on the below button will initiate the downloading process of R Bioinformatics Cookbook by Dan MacLean. This book is available in ePub and PDF format with a single click unlimited downloads. Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you’ll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you’ll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.


R Bioinformatics Cookbook

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ISBN 10 : 1789950694
Pages : 316 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.8/5 (789 users download)


Download R Bioinformatics Cookbook by Dan MacLean PDF/Ebook Free clicking on the below button will initiate the downloading process of R Bioinformatics Cookbook by Dan MacLean. This book is available in ePub and PDF format with a single click unlimited downloads. Over 60 recipes to model and handle real-life biological data using modern libraries from the R ecosystem Key Features Apply modern R packages to handle biological data using real-world examples Represent biological data with advanced visualizations suitable for research and publications Handle real-world problems in bioinformatics such as next-generation sequencing, metagenomics, and automating analyses Book Description Handling biological data effectively requires an in-depth knowledge of machine learning techniques and computational skills, along with an understanding of how to use tools such as edgeR and DESeq. With the R Bioinformatics Cookbook, you'll explore all this and more, tackling common and not-so-common challenges in the bioinformatics domain using real-world examples. This book will use a recipe-based approach to show you how to perform practical research and analysis in computational biology with R. You will learn how to effectively analyze your data with the latest tools in Bioconductor, ggplot, and tidyverse. The book will guide you through the essential tools in Bioconductor to help you understand and carry out protocols in RNAseq, phylogenetics, genomics, and sequence analysis. As you progress, you will get up to speed with how machine learning techniques can be used in the bioinformatics domain. You will gradually develop key computational skills such as creating reusable workflows in R Markdown and packages for code reuse. By the end of this book, you'll have gained a solid understanding of the most important and widely used techniques in bioinformatic analysis and the tools you need to work with real biological data. What you will learn Employ Bioconductor to determine differential expressions in RNAseq data Run SAMtools and develop pipelines to find single nucleotide polymorphisms (SNPs) and Indels Use ggplot to create and annotate a range of visualizations Query external databases with Ensembl to find functional genomics information Execute large-scale multiple sequence alignment with DECIPHER to perform comparative genomics Use d3.js and Plotly to create dynamic and interactive web graphics Use k-nearest neighbors, support vector machines and random forests to find groups and classify data Who this book is for This book is for bioinformaticians, data analysts, researchers, and R developers who want to address intermediate-to-advanced biological and bioinformatics problems by learning through a recipe-based approach. Working knowledge of R programming language and basic knowledge of bioinformatics are prerequisites.


The Digital Research Skills Cookbook

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Publisher : Research Platforms Services
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ISBN 10 : 9781549698521
Pages : 218 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.9/5 (698 users download)


Download The Digital Research Skills Cookbook by Dejan Jotanovic PDF/Ebook Free clicking on the below button will initiate the downloading process of The Digital Research Skills Cookbook by Dejan Jotanovic. This book is available in ePub and PDF format with a single click unlimited downloads. Research Platform Services is excited to announce the publication of The Digital Research Skills Cookbook: An Introduction to the Research Bazaar Community. This new publication is a guide to learning and teaching digital research tools. It also explains how to build your own research community. Each chapter includes introductory information about the latest digital tools and 'challenges' that encourage innovative and effective pedagogy. Material is organized to facilitate practical application of digital research skills and to encourage 'learning by doing'. The book includes step-by-step, visual introductions to learning and teaching the following tools: Python, R Studio, Matlab, Twitter Scraping, Textual Analysis with NLTK, TinkerCAD, Inventor, Fusion360, 3D Slicer, Omeka and LaTeX. Employing the latest pedagogical practices, the Digital Research Skills CookBook ensures learning is open and accessible to all. Whether you want to teach yourself or start your own Research Bazaar, this is the book for you!


Python in Neuroscience

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Publisher : Frontiers Media SA
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ISBN 10 : 9782889196081
Pages : pages
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Rating : 4.9/5 (196 users download)


Download Python in Neuroscience by Eilif Muller PDF/Ebook Free clicking on the below button will initiate the downloading process of Python in Neuroscience by Eilif Muller. This book is available in ePub and PDF format with a single click unlimited downloads. Python is rapidly becoming the de facto standard language for systems integration. Python has a large user and developer-base external to theneuroscience community, and a vast module library that facilitates rapid and maintainable development of complex and intricate systems. In this Research Topic, we highlight recent efforts to develop Python modules for the domain of neuroscience software and neuroinformatics: - simulators and simulator interfaces - data collection and analysis - sharing, re-use, storage and databasing of models and data - stimulus generation - parameter search and optimization - visualization - VLSI hardware interfacing. Moreover, we seek to provide a representative overview of existing mature Python modules for neuroscience and neuroinformatics, to demonstrate a critical mass and show that Python is an appropriate choice of interpreter interface for future neuroscience software development.


Managing Your Biological Data with Python

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Publisher : CRC Press
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ISBN 10 : 9781439880944
Pages : 560 pages
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Rating : 4.8/5 (88 users download)


Download Managing Your Biological Data with Python by Allegra Via PDF/Ebook Free clicking on the below button will initiate the downloading process of Managing Your Biological Data with Python by Allegra Via. This book is available in ePub and PDF format with a single click unlimited downloads. Take Control of Your Data and Use Python with ConfidenceRequiring no prior programming experience, Managing Your Biological Data with Python empowers biologists and other life scientists to work with biological data on their own using the Python language. The book teaches them not only how to program but also how to manage their data. It shows how


Graph Drawing

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Publisher : Springer
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ISBN 10 : 9783540318439
Pages : 540 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.1/5 (318 users download)


Download Graph Drawing by Janos Pach PDF/Ebook Free clicking on the below button will initiate the downloading process of Graph Drawing by Janos Pach. This book is available in ePub and PDF format with a single click unlimited downloads. This book constitutes the thoroughly refereed post-proceedings of the 12th International Symposium on Graph Drawing, GD 2004, held in New York, NY, USA in September/October 2004. The 39 revised full papers and 12 revised short papers presented together with 4 posters and a report on the graph drawing context were carefully selected during two rounds of reviewing and improvement. All current aspects in graph drawing are addressed ranging from foundational and methodological issues to applications for various classes of graphs in a variety of fields.


Implementing Reproducible Research

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Publisher : CRC Press
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ISBN 10 : 9781315360393
Pages : 448 pages
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Rating : 4.6/5 (36 users download)


Download Implementing Reproducible Research by Victoria Stodden PDF/Ebook Free clicking on the below button will initiate the downloading process of Implementing Reproducible Research by Victoria Stodden. This book is available in ePub and PDF format with a single click unlimited downloads. In computational science, reproducibility requires that researchers make code and data available to others so that the data can be analyzed in a similar manner as in the original publication. Code must be available to be distributed, data must be accessible in a readable format, and a platform must be available for widely distributing the data and code. In addition, both data and code need to be licensed permissively enough so that others can reproduce the work without a substantial legal burden. Implementing Reproducible Research covers many of the elements necessary for conducting and distributing reproducible research. It explains how to accurately reproduce a scientific result. Divided into three parts, the book discusses the tools, practices, and dissemination platforms for ensuring reproducibility in computational science. It describes: Computational tools, such as Sweave, knitr, VisTrails, Sumatra, CDE, and the Declaratron system Open source practices, good programming practices, trends in open science, and the role of cloud computing in reproducible research Software and methodological platforms, including open source software packages, RunMyCode platform, and open access journals Each part presents contributions from leaders who have developed software and other products that have advanced the field. Supplementary material is available at www.ImplementingRR.org.


Managing Your Biological Data with Python

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Publisher : CRC Press
Release Date :
ISBN 10 : 9781439880937
Pages : 560 pages
File Format : PDF, EPUB, TEXT, KINDLE or MOBI
Rating : 4.8/5 (88 users download)


Download Managing Your Biological Data with Python by Allegra Via PDF/Ebook Free clicking on the below button will initiate the downloading process of Managing Your Biological Data with Python by Allegra Via. This book is available in ePub and PDF format with a single click unlimited downloads. Take Control of Your Data and Use Python with Confidence Requiring no prior programming experience, Managing Your Biological Data with Python empowers biologists and other life scientists to work with biological data on their own using the Python language. The book teaches them not only how to program but also how to manage their data. It shows how to read data from files in different formats, analyze and manipulate the data, and write the results to a file or computer screen. The first part of the text introduces the Python language and teaches readers how to write their first programs. The second part presents the basic elements of the language, enabling readers to write small programs independently. The third part explains how to create bigger programs using techniques to write well-organized, efficient, and error-free code. The fourth part on data visualization shows how to plot data and draw a figure for an article or slide presentation. The fifth part covers the Biopython programming library for reading and writing several biological file formats, querying the NCBI online databases, and retrieving biological records from the web. The last part provides a cookbook of 20 specific programming "recipes," ranging from secondary structure prediction and multiple sequence alignment analyses to superimposing protein three-dimensional structures. Tailoring the programming topics to the everyday needs of biologists, the book helps them easily analyze data and ultimately make better discoveries. Every piece of code in the text is aimed at solving real biological problems.


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