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You're reading from  Bioinformatics with Python Cookbook. - Second Edition

Product typeBook
Published inNov 2018
Reading LevelIntermediate
PublisherPackt
ISBN-139781789344691
Edition2nd Edition
Languages
Python
Tools
Biopython
Concepts
Bioinformatics
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Author (1)
Tiago Antao
Tiago Antao
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Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
Read more about Tiago Antao

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Introduction

Pipelines are fundamental in any data science environment. Data processing is never a single task. Many pipelines are implemented via ad hoc scripts. This can be done in a useful way, but in many cases, they fail many fundamental viewpoints: reproducibility, maintainability, and extensibility.

In bioinformatics, you can find three main types of pipeline systems:

  • Frameworks like Galaxy (https://usegalaxy.org), which are geared toward users, that is, they expose easy-to-use user interfaces, hiding most of the underlying machinery
  • Frameworks like Script of Scripts (SoS) (https://vatlab.github.io/sos-docs/), which are geared toward data analysis, with a focus on with programming knowledge
  • Finally generic workflow systems like Apache Airflow (https://airflow.incubator.apache.org/), which take a less data-centered approach to workflow management

In this chapter, we will discuss Galaxy, which is especially important for bioinformaticians who are supporting users that are less inclined to...

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Bioinformatics with Python Cookbook. - Second Edition
Published in: Nov 2018Publisher: PacktISBN-13: 9781789344691
© 2018 Packt Publishing Limited All Rights Reserved

Author (1)

author image
Tiago Antao

Tiago Antao is a bioinformatician currently working in the field of genomics. A former computer scientist, Tiago moved into computational biology with an MSc in Bioinformatics from the Faculty of Sciences at the University of Porto (Portugal) and a PhD on the spread of drug-resistant malaria from the Liverpool School of Tropical Medicine (UK). Postdoctoral, Tiago has worked with human datasets at the University of Cambridge (UK) and with mosquito whole genome sequencing data at the University of Oxford (UK), before helping to set up the bioinformatics infrastructure at the University of Montana. He currently works as a data engineer in the biotechnology field in Boston, MA. He is one of the co-authors of Biopython, a major bioinformatics package written in Python.
Read more about Tiago Antao

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