Comments on: Beginning Perl for Bioinformatics http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/ Enhance your site with CGi, PHP and ASP scripts Sun, 25 Jul 2010 18:52:22 +0000 hourly 1 By: John Knepper http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/comment-page-1/#comment-76 John Knepper Sat, 06 Feb 2010 12:45:48 +0000 http://bloghost.xaviermedia.net/blog/beginning-perl-for-bioinformatics/#comment-76 If you haven't programmed in perl before, this book is perfect for learning. It also teaches very low level bioinformatics skills that'd probably help an undergraduate get their next internship. I was clueless to perl, and programming for that matter, when I got this book a long time ago. I painfully flipped each page from front to back, because it 'is' a technical book, and absorbed everything as much as possible. This book set me off in a direction that I never imagined. Although we're on the brink of version six of the language, this book will do you right in any aspect of computer programming. For a 'beginner' looking to get into any language, this book is for you. It's painful, but try and take the time to really learn the information the book presents. It not only teaches you perl, but gives you a peek into the numerous databases and resources that exist as well as a terrific job of teaching you how to use regular expressions. <br /> <br /> In the end, you'll have the foundation to become whatever kind of perl programmer you desire. If you're looking into bioinformatics, or a bioinformatician looking to learn, I recommend this book as well as 'Programming Perl', 'Mastering Perl for Bioinformatics', and 'BLAST'. 'BLAST' is fairly easy to breeze through and does a good job of explaining everything you would need to know. 'Mastering Perl...' picks up where this book left off, and 'Programming Perl' is one of the best buys I ever made, in regards to perl. I know these are all O REILLY books, but they're probably the best source for perl books out there. I'm not pitching their books either. Lastly, if you have the time I recommend you crunch on through 'CGI Programming with Perl'. Although the book is a bit out of date, it's definitely another 'piece' of the puzzle for someone to become a LAMP programmer. Rating: 5 / 5 If you haven't programmed in perl before, this book is perfect for learning. It also teaches very low level bioinformatics skills that'd probably help an undergraduate get their next internship. I was clueless to perl, and programming for that matter, when I got this book a long time ago. I painfully flipped each page from front to back, because it 'is' a technical book, and absorbed everything as much as possible. This book set me off in a direction that I never imagined. Although we're on the brink of version six of the language, this book will do you right in any aspect of computer programming. For a 'beginner' looking to get into any language, this book is for you. It's painful, but try and take the time to really learn the information the book presents. It not only teaches you perl, but gives you a peek into the numerous databases and resources that exist as well as a terrific job of teaching you how to use regular expressions.

In the end, you'll have the foundation to become whatever kind of perl programmer you desire. If you're looking into bioinformatics, or a bioinformatician looking to learn, I recommend this book as well as 'Programming Perl', 'Mastering Perl for Bioinformatics', and 'BLAST'. 'BLAST' is fairly easy to breeze through and does a good job of explaining everything you would need to know. 'Mastering Perl…' picks up where this book left off, and 'Programming Perl' is one of the best buys I ever made, in regards to perl. I know these are all O REILLY books, but they're probably the best source for perl books out there. I'm not pitching their books either. Lastly, if you have the time I recommend you crunch on through 'CGI Programming with Perl'. Although the book is a bit out of date, it's definitely another 'piece' of the puzzle for someone to become a LAMP programmer.
Rating: 5 / 5

]]> By: Anonymous http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/comment-page-1/#comment-75 Anonymous Sat, 06 Feb 2010 11:13:34 +0000 http://bloghost.xaviermedia.net/blog/beginning-perl-for-bioinformatics/#comment-75 I have used this book in a beginning Perl programming course for biology majors. While it is good if you sift through it from start to the end, I often found it impossible to find things when I needed to go back to remind myself of something. The index does not help, and there is no concise language reference anywhere.<p>Also, I do not like the fact that it uses "quick and dirty" Perl (no "use strict" pragma). While it might be less confusing to skip it at the very beginning, very soon students start to waste too much precious class time trying to locate bugs that would make the program not compile with "use strict" in the first place (e.g. mistyped variable names). Rating: 3 / 5 I have used this book in a beginning Perl programming course for biology majors. While it is good if you sift through it from start to the end, I often found it impossible to find things when I needed to go back to remind myself of something. The index does not help, and there is no concise language reference anywhere.

Also, I do not like the fact that it uses "quick and dirty" Perl (no "use strict" pragma). While it might be less confusing to skip it at the very beginning, very soon students start to waste too much precious class time trying to locate bugs that would make the program not compile with "use strict" in the first place (e.g. mistyped variable names).
Rating: 3 / 5

]]> By: Mat T. http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/comment-page-1/#comment-74 Mat T. Sat, 06 Feb 2010 09:24:11 +0000 http://bloghost.xaviermedia.net/blog/beginning-perl-for-bioinformatics/#comment-74 I liked this book because I had very little background in programming (aside from a semester of C++ a long time ago) and it wasn't too overwhelming. The excercies were great and the programming was explained fairly well.<p>I did a lot of bio-informatic work (lineplots, blasts, etc). The book was great for teaching programming that would be useful for these applications, and not a lot of other miscellaneous programming, that i would never really need. Rating: 5 / 5 I liked this book because I had very little background in programming (aside from a semester of C++ a long time ago) and it wasn't too overwhelming. The excercies were great and the programming was explained fairly well.

I did a lot of bio-informatic work (lineplots, blasts, etc). The book was great for teaching programming that would be useful for these applications, and not a lot of other miscellaneous programming, that i would never really need.
Rating: 5 / 5

]]> By: Anonymous http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/comment-page-1/#comment-73 Anonymous Sat, 06 Feb 2010 08:07:23 +0000 http://bloghost.xaviermedia.net/blog/beginning-perl-for-bioinformatics/#comment-73 One can enjoyably learn some Perl and genomics from Tisdall, but a more thorough approach is first using a dedicated Perl primer, like Pierce's ,Teach Yourself Perl in 24 Hours, or Schwartz & Chistiansen's, Learning Perl, and then studying the professional toolkit in Dwyer's Genomic Perl which is accompanied by 65 intuitively derived programs and modules. Rating: 3 / 5 One can enjoyably learn some Perl and genomics from Tisdall, but a more thorough approach is first using a dedicated Perl primer, like Pierce's ,Teach Yourself Perl in 24 Hours, or Schwartz & Chistiansen's, Learning Perl, and then studying the professional toolkit in Dwyer's Genomic Perl which is accompanied by 65 intuitively derived programs and modules.
Rating: 3 / 5

]]> By: Peter J. Neame http://www.cgiphp.com/blog/beginning-perl-for-bioinformatics/comment-page-1/#comment-72 Peter J. Neame Sat, 06 Feb 2010 07:05:41 +0000 http://bloghost.xaviermedia.net/blog/beginning-perl-for-bioinformatics/#comment-72 This book manages to be an astounding introduction to actually using Perl in general as well as a good introduction to its use in bioinformatics. It's also very readable. Needs more than 5 stars! Rating: 5 / 5 This book manages to be an astounding introduction to actually using Perl in general as well as a good introduction to its use in bioinformatics. It's also very readable. Needs more than 5 stars!
Rating: 5 / 5

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