Bioinformatics Data Skills
Reproducible and Robust Research with Open Source Tools
Publisher: O'Reilly Media
Final Release Date: March 2014
Pages: 504

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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
 
4.8

(based on 12 reviews)

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    (10)

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100%

of respondents would recommend this to a friend.

Pros

  • Helpful examples (10)
  • Easy to understand (9)
  • Well-written (8)
  • Concise (6)
  • Accurate (4)

Cons

No Cons

Best Uses

  • Intermediate (9)
  • Novice (9)
  • Student (6)
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    • Student (3)

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(2 of 2 customers found this review helpful)

 
5.0

Clear and concise

By sam

from Lyon, FRANCE

About Me Student

Verified Reviewer

Pros

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

Cons

    Best Uses

    • Intermediate
    • Novice

    Comments about oreilly Bioinformatics Data Skills:

    It gives you a basic overview of some of the most useful tools to study biological data. Without going into avoidable details, it goes straight to the point, and introduce you to the tools, so that you know they exist, how to use them, and how to know more about them.
    With an emphasize on reproducibility and good practices, the author does a great job at explaining common mistakes and how to avoid them.
    A must read for someone —not utterly— new to the field !

    (2 of 12 customers found this review helpful)

     
    3.0

    Many basic English errors

    By zerotimer

    from Wisconsin

    Comments about oreilly Bioinformatics Data Skills:

    I am reading the book at safari books online and noticing many grammatical as well as some missing English words. Some editor to clean this book up!

    Since I haven't finished it(no way close to it), I can't say anything about the usefulness yet. The choice of topics is excellent and I am looking forward to eventually buying it.

    (3 of 4 customers found this review helpful)

     
    4.0

    Fantastic DIY course textbook

    By Simon B

    from UK

    About Me Student

    Verified Buyer

    Pros

    • Easy to understand
    • Helpful examples
    • Well-written

    Cons

      Best Uses

      • Novice
      • Student

      Comments about oreilly Bioinformatics Data Skills:

      Superb book for those looking to develop bioinformatics skills. Covers loads of the supporting skills that are generally learnt through years of experience and aren't obvious in other textx/courses.

      Should be required reading for any PhD students or lab scientist working with data.

      (3 of 3 customers found this review helpful)

       
      5.0

      Best Bioinformatics Book

      By Mgollery

      from Lake Tahoe

      About Me Bioinformaticist

      Verified Buyer

      Pros

      • Concise
      • Easy to understand
      • Helpful examples

      Cons

        Best Uses

        • Expert
        • Intermediate
        • Novice
        • Student

        Comments about oreilly Bioinformatics Data Skills:

        This is the best bioinformatics book that I have seen. It gives you an introduction to the most necessary tools in the arsenal of the practicing Bioinformaticist. UNIX, R, Git, shell scripting, sequence files, alignment files.

        Of course, it doesn't have everything. But it gives you the essential skills to get things done. Not a lot of wasted space on theory or history.

        If you want to do Bioinformatics, you want to get this book.

        (4 of 4 customers found this review helpful)

         
        5.0

        Real-life bioinformatics

        By Gur

        from Israel

        Verified Reviewer

        Pros

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

        Cons

          Best Uses

          • Intermediate
          • Novice
          • Student

          Comments about oreilly Bioinformatics Data Skills:

          Reading halfway through (so far), I can best describe this book as a roadmap with stepping stones and practical tips to how *any biologist* can use computational power and bioinformatics for every day research tasks.
          From learning bioinformatics from scratch, I found most books I read to be focused on a specific topic or language, but lacking a bigger view of "real-life" bioinformatic projects with start, middle and end, including many other aspects that one should consider.
          This book is the first one I came across that does just that. It lays the framework of how to approach a project, covers important topics for managing a complete project, and refer to further resources if one needs to dig deeper into a specific aspect.
          I wish this book was available two years ago when I first started my graduate studies - It literally could have saved me a year.

          (3 of 3 customers found this review helpful)

           
          5.0

          Recommended to PhDs and post-docs alike

          By Peter

          from UK

          About Me Developer

          Verified Buyer

          Pros

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

          Cons

            Best Uses

            • Intermediate
            • Novice

            Comments about oreilly Bioinformatics Data Skills:

            I've not read all the book yet (the early release isn't even finished yet), but Vince has done a great job with this.

            I will be recommending it to future PhD students and early post-docs, as well as colleagues who like myself may have learnt much of this material the hard way, but are bound to find some little gems they've not seen before.

            I've mostly looked at the PDF edition, which with full page layout as expected in the printed version, looks very good. However, my initial inspection of some of the eBook formats show many of the code and data samples will struggle with narrow page layouts forcing line wrapping. That is incredible difficult to deal with through.

            (4 of 4 customers found this review helpful)

             
            5.0

            Full of great programmatic tricks

            By KATS

            from Minneapolis, MN

            About Me Developer, Educator

            Verified Buyer

            Pros

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

            Cons

              Best Uses

              • Expert
              • Intermediate

              Comments about oreilly Bioinformatics Data Skills:

              I have been programming in a UNIX environment for 26 years, and a leader in bioinformatics since I entered the field in 1998, and was surprised to find that I was able to learn useful tips and tricks in nearly every Chapter. We selected this book as the basis of a discussion group at our University and it is perfect. Very glad this book exists so I didn't have to write it myself!

              (3 of 3 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.

                (4 of 4 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.

                  (5 of 5 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!

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