Business & Other
Reader small image

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
Right arrow
Author (1)
Tiago Antao
Tiago Antao
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

Right arrow

Using generic pipelines with bioinformatics data

Galaxy is mostly geared toward users who are less inclined to program. Knowing how to deal with it, even if you prefer a more programmer-friendly environment, is important because of its pervasiveness. It is reassuring that an API exists to interact with Galaxy. But if you want a more programmer-friendly pipeline, there are many alternatives available.

Here, we will explore Airflow, originally from Airbnb, and currently incubating under the Apache umbrella. Airflow is somewhat at the other end of the pipeline world: it is completely subject-agnostic (actually, its development has nothing to do with bioinformatics), and it is completely geared toward programming.

Getting ready

Be careful with the sources for the installation of Airflow, as some might not be up to date. At this stage, this applies to some conda packages that are available.

At the time of writing, the best approach is probably to use a standard Python installation that either comes...

lock icon
The rest of the page is locked
Previous Page
Chapter 12 of 16, Page 6
Next Page
You have been reading a chapter from
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

Personalised recommendations for you

Based on your interests and search pattern

Engineering Manager's Handbook

Engineering Manager's Handbook

Engineering Manager's Handbook is a comprehensive guide for managers to excel in their role, foster customer-centric digital products, learn leadership, team building, and balancing technical work with management. You’ll also explore how to develop trust, authority, and collaboration to drive success and make a lasting impact.

BookSep 2023278 pages
C++ Game Animation Programming

C++ Game Animation Programming

Video game characters have a fascinating history, evolving from simple 2D sprites to high-polygon 3D models. Take a look behind the curtain and learn how to build a 3D renderer, load character models, play animations and blend between them, and create large crowds of animated people with this comprehensive C++ game animation programming guide.

BookDec 2023480 pages
Gamification for Product Excellence

Gamification for Product Excellence

This book helps you to take your product management strategy to the next level by standing out in crowded markets. Along with boosting user adoption rates by creating engaging products that incorporate playful elements, learn gamification theory and how to integrate it into your design, product development, and product management processes.

BookSep 2023350 pages
Supercharging Productivity with Trello

Supercharging Productivity with Trello

Supercharging Productivity with Trello is the ultimate guide for anyone looking to boost their productivity with digital tools. Whether you're new to Trello or a seasoned professional, this book covers everything from core features to advanced automation, and Power-Ups.

BookAug 2023342 pages
Automate It with Zapier and Generative AI

Automate It with Zapier and Generative AI

This comprehensive guide takes you through the concepts of business process automation, showing you how Zapier can facilitate it without having to write code and helping you to boost productivity. You’ll learn how to save time, reduce costs, and make your business recession-proof by using Zapier to automate tasks in your cloud-based business apps.

BookAug 2023706 pages
Scoring to Picture in Logic Pro

Scoring to Picture in Logic Pro

In this book, you’ll explore a variety of techniques to synchronize music to picture using Logic Pro. Though this is not a technical manual, it will teach you how to make the best use of Logic Pro and how to wield this technology to maximize your potential when scoring to picture.

BookSep 2023412 pages
Mastering Information Security Compliance Management

Mastering Information Security Compliance Management

This concise book equips you with the knowledge and practices needed to establish and maintain an effective information security management system. The chapters provide insights into ISO/IEC 27001/27002:2022, risk management, ISMS development, incident management, audit processes, and strategies for continuous improvement.

BookAug 2023236 pages1
Implementing Atlassian Confluence

Implementing Atlassian Confluence

Implementing Atlassian Confluence provides both a high-level overview and an insightful path for remote collaboration with Atlassian Confluence. With this multi-layered yet practical guide, you’ll be able to set up Confluence-based collaboration with minimum external consultancy services to ensure smooth and close coordination between teams.

BookSep 2023406 pages
R Bioinformatics Cookbook

R Bioinformatics Cookbook

This book takes a unique problem–solution approach to handling complex tasks in the bioinformatics domain using different datasets present in the book. With the help of real-world examples, you’ll learn to put each independent recipe to use to tackle problems in the field of bioinformatics.

BookOct 2023396 pages
Build Your Own Metaverse with Unity

Build Your Own Metaverse with Unity

Build Your own Metaverse with Unity is a practical guide for developers to create their own metaverse - a virtual world with infinite possibilities. It empowers you to identify gaps in existing metaverses and improve upon them, enabling you to shape your virtual world.

BookSep 2023586 pages5