Reproducible Bioinformatics With Python
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Reproducible Bioinformatics With Python
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Author : Ken Youens-Clark
language : en
Publisher:
Release Date : 2021
Reproducible Bioinformatics With Python written by Ken Youens-Clark and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021 with categories.
Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained--usually by students and postdoc researchers who've never learned basic programming skills. This practical guide shows how to exploit the best parts of Python for solving problems in biology while also creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates how to write effective Python code and how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools--such as linters, formatters, type checkers, and tests--to write documented and tested programs. Create command-line Python programs that document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures (strings, lists, and sets) and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA, FASTQ, and SwissProt Find patterns of text using regular expressions Use higher-order functions in Python like filter() and map().
Implementing Reproducible Research
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Author : Victoria Stodden
language : en
Publisher: CRC Press
Release Date : 2018-12-14
Implementing Reproducible Research written by Victoria Stodden and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-12-14 with Mathematics categories.
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.
Mastering Python For Bioinformatics
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Author : Ken Youens-Clark
language : en
Publisher: "O'Reilly Media, Inc."
Release Date : 2021-05-05
Mastering Python For Bioinformatics written by Ken Youens-Clark and has been published by "O'Reilly Media, Inc." this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-05-05 with Computers categories.
Life scientists today urgently need training in bioinformatics skills. Too many bioinformatics programs are poorly written and barely maintained, usually by students and researchers who've never learned basic programming skills. This practical guide shows postdoc bioinformatics professionals and students how to exploit the best parts of Python to solve problems in biology while creating documented, tested, reproducible software. Ken Youens-Clark, author of Tiny Python Projects (Manning), demonstrates not only how to write effective Python code but also how to use tests to write and refactor scientific programs. You'll learn the latest Python features and tools including linters, formatters, type checkers, and tests to create documented and tested programs. You'll also tackle 14 challenges in Rosalind, a problem-solving platform for learning bioinformatics and programming. Create command-line Python programs to document and validate parameters Write tests to verify refactor programs and confirm they're correct Address bioinformatics ideas using Python data structures and modules such as Biopython Create reproducible shortcuts and workflows using makefiles Parse essential bioinformatics file formats such as FASTA and FASTQ Find patterns of text using regular expressions Use higher-order functions in Python like filter(), map(), and reduce()
Advances In Bioinformatics
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Author : Vijai Singh
language : en
Publisher: Springer Nature
Release Date : 2024-02-05
Advances In Bioinformatics written by Vijai Singh and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-02-05 with Computers categories.
The second edition of Advances in Bioinformatics presents the latest developments in bioinformatics in gene discovery, genome analysis, genomics, transcriptomics, proteomics, metabolomics, metabolic flux analysis, drug discovery, and drug repurposing. It includes advancements in the applications of bioinformatics in the analysis of non-coding RNA, next-generation sequencing, genome-scale modelling, high throughput drug screening, precision medicine, automation and artificial intelligence, and machine learning. The chapter also summarizes the technologies and concepts that form the basis of this functional genomics approach. Additionally, the book highlights some of the areas in which bioinformatics resources and methods are being developed to support the drug discovery pipeline. The chapter also discusses the role of bioinformatics in modelling and simulations of molecular biology systems in pathways identification and design. It is a valuable source of information for beginners in bioinformatics and students, researchers, scientists, clinicians, practitioners, policymakers, and stakeholders who are interested in harnessing the potential of bioinformatics in biomedical and allied sciences.
Computational Intelligence Methods For Bioinformatics And Biostatistics
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Author : Claudia Angelini
language : en
Publisher: Springer
Release Date : 2016-07-30
Computational Intelligence Methods For Bioinformatics And Biostatistics written by Claudia Angelini and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2016-07-30 with Computers categories.
This book constitutes the thoroughly refereed post-conference proceedings of the 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2015, held in Naples, Italy, in September, 2015. The 21 revised full papers presented were carefully reviewed and selected from 24 submissions. They present problems concerning computational techniques in bioinformatics, systems biology and medical informatics discussing cutting edge methodologies and accelerate life science discoveries, as well as novel challenges with an high impact on molecular biology and translational medicine.
Modern Python Bio Informatics
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Author : Dr. Amarendra Alluri
language : en
Publisher: RK Publication
Release Date : 2024-09-20
Modern Python Bio Informatics written by Dr. Amarendra Alluri and has been published by RK Publication this book supported file pdf, txt, epub, kindle and other format this book has been release on 2024-09-20 with Computers categories.
Modern Python Bioinformatics is an insightful guide merging Python programming with bioinformatics, designed for both beginners and seasoned professionals in computational biology. This book covers essential Python skills and advanced bioinformatics concepts, including DNA/RNA sequencing, protein structure analysis, and data visualization. It emphasizes practical applications with examples and projects that demonstrate how to handle biological data, perform statistical analyses, and develop efficient bioinformatics workflows. With accessible explanations and code snippets, it equips readers to tackle real-world challenges in bioinformatics research and development.
Unleashing Innovation On Precision Public Health Highlights From The Mcbios Maqc 2021 Joint Conference
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Author : Ramin Homayouni
language : en
Publisher: Frontiers Media SA
Release Date : 2022-07-07
Unleashing Innovation On Precision Public Health Highlights From The Mcbios Maqc 2021 Joint Conference written by Ramin Homayouni and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-07-07 with Science categories.
Rigor And Reproducibility In Genetics And Genomics
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Author :
language : en
Publisher: Academic Press
Release Date : 2023-11-08
Rigor And Reproducibility In Genetics And Genomics written by and has been published by Academic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-11-08 with Medical categories.
Rigor and Reproducibility in Genetics and Genomics: Peer-reviewed, Published, Cited provides a full methodological and statistical overview for researchers, clinicians, students, and post-doctoral fellows conducting genetic and genomic research. Here, active geneticists, clinicians, and bioinformaticists offer practical solutions for a variety of challenges associated with several modern approaches in genetics and genomics, including genotyping, gene expression analysis, epigenetic analysis, GWAS, EWAS, genomic sequencing, and gene editing. Emphasis is placed on rigor and reproducibility throughout, with each section containing laboratory case-studies and classroom activities covering step-by-step protocols, best practices, and common pitfalls. Specific genetic and genomic technologies discussed include microarray analysis, DNA-seq, RNA-seq, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis. Training exercises, supporting data, and in-depth discussions of rigor, reproducibility, and ethics in research together deliver a solid foundation in research standards for the next generation of genetic and genomic scientists. - Provides practical approaches and step-by-step protocols to strengthen genetic and genomic research conducted in the laboratory or classroom - Presents illustrative case studies and training exercises, discussing common pitfalls and solutions for genotyping, gene expression analysis, epigenetic analysis, GWAS, genomic sequencing, and gene editing, among other genetic and genomic approaches - Examines best practices for microarray analysis, DNA-seq, RNA-seq, gene expression validation, Chip-Seq, methyl-seq, CRISPR gene editing, and CRISPR-based genetic analysis - Written to provide trainees and educators with highly applicable tools and strategies to learn or refine a method toward identifying meaningful results with high confidence in their reproducibility
Enhancing Scientific Reproducibility In Biomedical Research Through Transparent Reporting
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Author : National Academies of Sciences, Engineering, and Medicine
language : en
Publisher: National Academies Press
Release Date : 2020-04-28
Enhancing Scientific Reproducibility In Biomedical Research Through Transparent Reporting written by National Academies of Sciences, Engineering, and Medicine and has been published by National Academies Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2020-04-28 with Medical categories.
Sharing knowledge is what drives scientific progress - each new advance or innovation in biomedical research builds on previous observations. However, for experimental findings to be broadly accepted as credible by the scientific community, they must be verified by other researchers. An essential step is for researchers to report their findings in a manner that is understandable to others in the scientific community and provide sufficient information for others to validate the original results and build on them. In recent years, concern has been growing over a number of studies that have failed to replicate previous results and evidence from larger meta-analyses, which have pointed to the lack of reproducibility in biomedical research. On September 25 and 26, 2019, the National Academies of Science, Engineering, and Medicine hosted a public workshop in Washington, DC, to discuss the current state of transparency in the reporting of preclinical biomedical research and to explore opportunities for harmonizing reporting guidelines across journals and funding agencies. Convened jointly by the Forum on Drug Discovery, Development, and Translation; the Forum on Neuroscience and Nervous System Disorders; the National Cancer Policy Forum; and the Roundtable on Genomics and Precision Health, the workshop primarily focused on transparent reporting in preclinical research, but also considered lessons learned and best practices from clinical research reporting. This publication summarizes the presentation and discussion of the workshop.
The Practice Of Reproducible Research
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Author : Justin Kitzes
language : en
Publisher: Univ of California Press
Release Date : 2018
The Practice Of Reproducible Research written by Justin Kitzes and has been published by Univ of California Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018 with Computers categories.
The Practice of Reproducible Research presents concrete examples of how researchers in the data-intensive sciences are working to improve the reproducibility of their research projects. In each of the thirty-one case studies in this volume, the author or team describes the workflow that they used to complete a real-world research project. Authors highlight how they utilized particular tools, ideas, and practices to support reproducibility, emphasizing the very practical how, rather than the why or what, of conducting reproducible research. Part 1 provides an accessible introduction to reproducible research, a basic reproducible research project template, and a synthesis of lessons learned from across the thirty-one case studies. Parts 2 and 3 focus on the case studies themselves. The Practice of Reproducible Research is an invaluable resource for students and researchers who wish to better understand the practice of data-intensive sciences and learn how to make their own research more reproducible.