Suggestions for Second Edition?

As Building Bioinformatics Solutions continues to be popular, we are considering producing a second edition. The first edition still is still current and will be around for some years yet but it’s not too early to be thinking about what we might add or change if we do a second edition.

We already have some ideas of our own but we think the best insights always come from readers, so we’d be grateful if some of you who’ve used the book could give us some pointers as to what we could add or change in the next edition.

You can send suggestions to us directly, make a comment via the link below, or make your thoughts known in the second edition forum thread.

8 responses to “Suggestions for Second Edition?”

  1. Philipp says:


    Thank you for your book, I am currently reading it and found it remarkable in many ways. Even if I’m not in the biotech sector, the problems I have to tackle are of similar nature, so it is very usefull and highly appreciated, to say it mildly 😀

    I don’t know in which extent it is relevant, however I think it could be worth considering including an Introduction to Python in a second edition of the book. that an introduction in Python could be a good idea. Indeed, you can seamlessly integrate all your R and MySQL programs directly in a Python framework, and it currently does it all. So, having seen that some books are being published on tackling biotech problems using python, it could be worth considering.

    Best regards,


  2. conrad says:

    A belated thanks for your comment, Philipp! We incorporated your feedback in our proposal for the next edition. It’s difficult to pick a single language for the book because Perl, Python, Ruby and Java are all common in bioinformatics. Perl still seems to be the most widely language used in the community, but we will definitely do more in the next edition to help people get started in the other languages too.

  3. xiaoyu Liu says:

    I happen to agree with Philipp on adding python into the second edition. for many biologists are new to bioinformatics. Python really lower the difficulty level for entering the new field for them. Perl is still the widest used language in field is not because its superiority but because it was established earlier. around me, people who started earlier in the field use perl, but more recent starters use Python than perl.

    YODA: Code! Yes. A programmer’s strength flows from code
    maintainability. But beware of Perl. Terse syntax… more
    than one way to do it… default variables. The dark side
    of code maintainability are they. Easily they flow, quick
    to join you when code you write. If once you start down the
    dark path, forever will it dominate your destiny, consume
    you it will.

  4. IS there any up date on this? did you add more python info. I do agree with Philip on the fact more python is need.

  5. daz says:


    So here’s what we’re currently planning for the second edition with regards to other languages… Please note the second edition of the book is still over a year away. 😉

    We’re going to stick with Perl as the primary language for the book – it’s still the dominant tool for bioinformatics programming, so if someone wants to work in bioinformatics they’re going to come across, and have to work with Perl sooner or later.

    Yes, Python has gained some traction in bioinformatics*, but if you can learn and become fluent with Perl, switching to Python (or any other programming language) is an easy transition once you have learnt the basic concepts of programming.

    To aid this we’re going to expand the Perl chapter to include object-oriented programming (this was one of the main programming concepts missing from the first edition) using modern Perl tools such as Moose (, and then once these concepts are clear we’re going to do an introduction to some other languages: Python, Ruby and Java. These introductions will not be exhaustive (there’s not enough room in the book to cover four languages in detail) but will show the differences/similarities between the languages and would be enough to get the reader going on migrating all of the Perl examples in the book to these other languages, and then point them where to go from there. 🙂

    I hope this answers your questions, but please let us know what you think of this proposal. 🙂



    * Python is not the only other language in use in bioinformatics (as Conrad mentioned above), from my experience Java is probably more prevalent, but I also know of groups using Ruby, C, C++, PHP and many other languages. Our main aim with the second book is to teach readers how to become a good bioinformatics programmer, by teaching them the concepts, problem solving and organisational skills that they will need to able to get things done – once someone is comfortable with these, transitioning between languages is a simple task of learning the differences of the syntax and the language ecosystem (libraries, frameworks etc).

  6. D says:

    Three cheers for expanding discussions of modern perl developments such as Moose. For those using Perl5, Moose is heaven on earth. Many concepts that Moose has brought to perl (such as roles, introspection, and metaclass programming.. huhh??) are very nice and in line with other OO languages… as far as I understand. So for readers able to “consume” OOP, design concepts for your second edition would be broadly useful to development in other languages.

  7. conrad says:

    Thanks to everyone for their input. We’ve started writing the second edition and it should be with you some time in 2013. Release dates will be posted right here on this site as soon as we know them.

  8. conrad says:

    I’m pleased to say that the manuscript for the second edition has now been submitted. Yes, it’s taken a while but a lot of work has gone into making sure everything is totally up-to-date and we’ve added a lot of new material, including everything discussed in the thread. The new edition will be 37% bigger than the original. We’ll post publication information here as soon as OUP have worked their magic.

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