Managing Your Biological Data With Python

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

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.

Hands-on Data Science for Biologists using Python has been conceptualized to address the massive data handling needs of modern-day biologists. With the advent of high throughput technologies and consequent availability of omics data, biological science has become a data-intensive field. This hands-on textbook has been written with the inception of easing data analysis by providing an interactive, problem-based instructional approach in Python programming language. The book starts with an introduction to Python and steadily delves into scrupulous techniques of data handling, preprocessing, and visualization. The book concludes with machine learning algorithms and their applications in biological data science. Each topic has an intuitive explanation of concepts and is accompanied with biological examples. Features of this book: The book contains standard templates for data analysis using Python, suitable for beginners as well as advanced learners. This book shows working implementations of data handling and machine learning algorithms using real-life biological datasets and problems, such as gene expression analysis; disease prediction; image recognition; SNP association with phenotypes and diseases. Considering the importance of visualization for data interpretation, especially in biological systems, there is a dedicated chapter for the ease of data visualization and plotting. Every chapter is designed to be interactive and is accompanied with Jupyter notebook to prompt readers to practice in their local systems. Other avant-garde component of the book is the inclusion of a machine learning project, wherein various machine learning algorithms are applied for the identification of genes associated with age-related disorders. A systematic understanding of data analysis steps has always been an important element for biological research. This book is a readily accessible resource that can be used as a handbook for data analysis, as well as a platter of standard code templates for building models.

In biological research, we''re currently in a golden age of data. It''s never been easier to assemble large datasets to probe biological questions. But these large datasets come with their own problems. How to clean and validate data? How to combine datasets from multiple sources? And how to look for patterns in large, complex datasets and display your findings? The solution to these problems comes in the form of Python''s scientific software stack. The combination of a friendly, expressive language and high quality packages makes a fantastic set of tools for data exploration. But the packages themselves can be hard to get to grips with. It''s difficult to know where to get started, or which sets of tools will be most useful. Learning to use Python effectively for data exploration is a superpower that you can learn. With a basic knowledge of Python, pandas (for data manipulation) and seaborn (for data visualization) you''ll be able to understand complex datasets quickly and mine them for biological insight. You''ll be able to make beautiful, informative charts for posters, papers and presentations, and rapidly update them to reflect new data or test new hypotheses. You''ll be able to quickly make sense of datasets from other projects and publications - millions of rows of data will no longer be a scary prospect! In this book, Dr. Jones draws on years of teaching experience to give you the tools you need to answer your research questions. Starting with the basics, you''ll learn how to use Python, pandas, seaborn and matplotlib effectively using biological examples throughout. Rather than overwhelm you with information, the book concentrates on the tools most useful for biological data. Full color illustrations show hundreds of examples covering dozens of different chart types, with complete code samples that you can tweak and use for your own work. This book will help you get over the most common obstacles when getting started with data exploration in Python. You''ll learn about pandas'' data model; how to deal with errors in input files and how to fit large datasets in memory. The chapters on visualization will show you how to make sophisticated charts with minimal code; how to best use color to make clear charts, and how to deal with visualization problems involving large numbers of data points. Chapters include: Getting data into pandas: series and dataframes, CSV and Excel files, missing data, renaming columns Working with series: descriptive statistics, string methods, indexing and broadcasting Filtering and selecting: boolean masks, selecting in a list, complex conditions, aggregation Plotting distributions: histograms, scatterplots, custom columns, using size and color Special scatter plots: using alpha, hexbin plots, regressions, pairwise plots Conditioning on categories: using color, size and marker, small multiples Categorical axes:strip/swarm plots, box and violin plots, bar plots and line charts Styling figures: aspect, labels, styles and contexts, plotting keywords Working with color: choosing palettes, redundancy, highlighting categories Working with groups: groupby, types of categories, filtering and transforming Binning data: creating categories, quantiles, reindexing Long and wide form: tidying input datasets, making summaries, pivoting data Matrix charts: summary tables, heatmaps, scales and normalization, clustering Complex data files: cleaning data, merging and concatenating, reducing memory FacetGrids: laying out multiple charts, custom charts, multiple heat maps Unexpected behaviours: bugs and missing groups, fixing odd scales High performance pandas: vectorization, timing and sampling Further reading: dates and times, alternative syntax

Powerful, flexible, and easy to use, Python is an ideal language for building software tools and applications for life science research and development. This unique book shows you how to program with Python, using code examples taken directly from bioinformatics. In a short time, you'll be using sophisticated techniques and Python modules that are particularly effective for bioinformatics programming. Bioinformatics Programming Using Python is perfect for anyone involved with bioinformatics -- researchers, support staff, students, and software developers interested in writing bioinformatics applications. You'll find it useful whether you already use Python, write code in another language, or have no programming experience at all. It's an excellent self-instruction tool, as well as a handy reference when facing the challenges of real-life programming tasks. Become familiar with Python's fundamentals, including ways to develop simple applications Learn how to use Python modules for pattern matching, structured text processing, online data retrieval, and database access Discover generalized patterns that cover a large proportion of how Python code is used in bioinformatics Learn how to apply the principles and techniques of object-oriented programming Benefit from the "tips and traps" section in each chapter

This book introduces Python as a powerful tool for the investigation of problems in computational biology, for novices and experienced programmers alike.

Discover modern, next-generation sequencing libraries from the powerful Python ecosystem to perform cutting-edge research and analyze large amounts of biological data Key Features Perform complex bioinformatics analysis using the most essential Python libraries and applications Implement next-generation sequencing, metagenomics, automating analysis, population genetics, and much 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, and this book will show you how to manage these tasks using Python. This updated third edition of the Bioinformatics with Python Cookbook begins with a quick overview of the various tools and libraries in the Python ecosystem that will help you convert, analyze, and visualize biological datasets. Next, you'll cover key techniques for next-generation sequencing, single-cell analysis, genomics, metagenomics, population genetics, phylogenetics, and proteomics with the help of real-world examples. You'll learn how to work with important pipeline systems, such as Galaxy servers and Snakemake, and understand the various modules in Python for functional and asynchronous programming. This book will also help you explore topics such as SNP discovery using statistical approaches under high-performance computing frameworks, including Dask and Spark. In addition to this, you'll explore the application of machine learning algorithms in bioinformatics. By the end of this bioinformatics Python book, you'll be equipped with the knowledge you need to implement the latest programming techniques and frameworks, empowering you to deal with bioinformatics data on every scale. What you will learn Become well-versed with data processing libraries such as NumPy, pandas, arrow, and zarr in the context of bioinformatic analysis Interact with genomic databases Solve real-world problems in the fields of population genetics, phylogenetics, and proteomics Build bioinformatics pipelines using a Galaxy server and Snakemake Work with functools and itertools for functional programming Perform parallel processing with Dask on biological data Explore principal component analysis (PCA) techniques with scikit-learn Who this book is for This book is for bioinformatics analysts, data scientists, computational biologists, researchers, and Python developers who want to address intermediate-to-advanced biological and bioinformatics problems. Working knowledge of the Python programming language is expected. Basic knowledge of biology will also be helpful.

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.