Bioinformatics Data Skills
Reproducible and Robust Research with Open Source Tools
Publisher: O'Reilly Media
Final Release Date: March 2014
Pages: 300

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This practical book teaches the skills that scientists need for turning large sequencing datasets into reproducible and robust biological findings. Many biologists begin their bioinformatics training by learning languages like Perl and R alongside the Unix command line. But there’s a huge gap between knowing a few programming languages and being prepared to analyze large amounts of biological data.

Rather than teach bioinformatics as a set of workflows that are likely to change with this rapidly evolving field, this book demsonstrates the practice of bioinformatics through data skills. Rigorous assessment of data quality and of the effectiveness of tools is the foundation of reproducible and robust bioinformatics analysis. Through open source and freely available tools, you’ll learn not only how to do bioinformatics, but how to approach problems as a bioinformatician.

  • Go from handling small problems with messy scripts to tackling large problems with clever methods and tools
  • Focus on high-throughput (or "next generation") sequencing data
  • Learn data analysis with modern methods, versus covering older theoretical concepts
  • Understand how to choose and implement the best tool for the job
  • Delve into methods that lead to easier, more reproducible, and robust bioinformatics analysis
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oreillyBioinformatics Data Skills
 
5.0

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100%

of respondents would recommend this to a friend.

Pros

  • Helpful examples (4)
  • Easy to understand (3)
  • Well-written (3)

Cons

    Best Uses

    • Intermediate (4)
    • Novice (4)
    • Student (3)

    Reviewed by 5 customers

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    (2 of 2 customers found this review helpful)

     
    5.0

    a very good read

    By crazyhottommy

    from Gainesville, FL

    About Me Phd Student, Student

    Verified Reviewer

    Pros

    • Helpful examples
    • Well-written

    Cons

      Best Uses

      • Intermediate
      • Novice
      • Student

      Comments about oreilly Bioinformatics Data Skills:

      It is a very good read for me. I am a wet biologist and I've been using linux commands for two years. but even so, I found some useful tricks. I really like the reproducible research part, the project organization part and documentation of your data and analysis part. To me, it is more important to learn these concepts. One good thing is that the author uses examples to illustrate the usage of the commands which is really helpful. Highly recommend for anyone who wants to do "good/reproducible" bioinformatics!
      There are some minor grammar mistakes. Since it is an early release, it is totally understandable.

      (2 of 2 customers found this review helpful)

       
      5.0

      Great collection of practical tips

      By Cosmin

      from Paris, FR

      About Me Bioinformatician, Scientist

      Verified Reviewer

      Pros

      • Accurate
      • Concise
      • Easy to understand
      • Helpful examples
      • Well-written

      Cons

        Best Uses

        • Intermediate

        Comments about oreilly Bioinformatics Data Skills:

        Many bioinformaticians are self-thaught and would definitely benefit a lot from a book like this one. It gathers together tons of practical advice, clearly explained. I especially liked the examples of how things can and will go wrong. The emphasis on reproducible data analysis is also welcome.

        (4 of 4 customers found this review helpful)

         
        5.0

        Excellent & Practical

        By Kaittenage

        from Seattle, WA

        About Me Statistical Analyst

        Verified Reviewer

        Pros

        • Covers Best Practices
        • Fundamental Principles

        Cons

        • Incomplete At This Time

        Best Uses

        • Intermediate
        • Novice
        • Student

        Comments about oreilly Bioinformatics Data Skills:

        Although still in early release, I've already used this book to solidify my understanding of some of the bioinformatics data skills covered, and learned some new things that can come in handy. There is an emphasis on certain tools (and rightly so), yet the author talks about principles that can be used to, in my opinion, create a strong foundational understanding of the importance of certain concepts in bioinformatics data work that could be applied to other tools (for example, although the author covers Linux shell scripting, the principles may be applicable to Windows PowerShell or similar tools).
        If I were to teach a single course in bioinformatics, I can already tell I would want to use this book to do it, because it is practical and goes over what seem to be current best practices for this type of work.
        I might even go for as to say this: the things taught in this book are probably more important for those trying to get a foundation in "data science" type skills-- I feel many other texts focused on "data science" may be trying to cash in on a fad or show very basic model fitting with toy data sets. Therefore, perhaps as an "odd" recommendation, I would actually suggest this book to folks who do not understand how to use the tools and principles reviewed in this book, because they seem very applicable to data handling, reproducible analyses, and some best practices for scientific computing.
        Looking forward to the finalized version!

        (3 of 3 customers found this review helpful)

         
        5.0

        Very good book

        By Luis Soares

        from Boston, MA

        Verified Reviewer

        Pros

        • Easy to understand
        • Helpful examples

        Cons

          Best Uses

          • Novice

          Comments about oreilly Bioinformatics Data Skills:

          Very good introduction to using UNIX for data analysis workflow in Bioinformatics. Well organized and good reading flow. Despite editorial mistakes (that certainly reflect early version status)I look forward to re-reading the final version.

          (4 of 4 customers found this review helpful)

           
          5.0

          Must read for Bioinformatics

          By bmpvieira

          from London

          About Me Bioinformatician, Web Developer

          Verified Reviewer

          Pros

          • Concise
          • Easy to understand
          • Helpful examples
          • Well-written

          Cons

          • Too basic

          Best Uses

          • Intermediate
          • Novice
          • Student

          Comments about oreilly Bioinformatics Data Skills:

          Everybody starting in Bioinformatics should read this book. It might be a bit too basic for more advanced users, but teaches things like Git, Tmux, Markdown, etc, that might be new for some.

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