Comments on: A holiday, Ruby and Scala http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/ Computational Biology, Epidemiology, Infectious diseases, Open Science Mon, 02 Nov 2009 14:07:57 +0000 http://wordpress.org/?v=2.8.5 hourly 1 By: Bioinformatics Zen » February 2008 edition of Bio::Blogs http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/comment-page-1/#comment-3439 Bioinformatics Zen » February 2008 edition of Bio::Blogs Fri, 01 Feb 2008 18:18:37 +0000 http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/#comment-3439 [...] So that’s the open science part done, but there were plenty of other things going on in the bioinformatics blog community. Neil Saunders mentioned the Gene Wiki project, the aim to give every human gene a page on Wikipedia, some kind of online encyclopedia. He also gave an interesting perspective on the history of nodalpoint.org, the original bioinformatics blog. Researcherid.com, a site to give every researcher a unique id, received attention from Pierre, Neil, and Deepak. A recent paper on the uncertainty in aligning sequences took the interest of Blind.Scientist, Thirst for Science, and Computational Biology News. SNPs are hot at Open Helix and the Spittoon. Gopubmed.org is even hotter at Medical 2.0, Konrad’s Konsiderations, Peanut Butter, What You’re Doing, and BBGM. Pawel Szczesny became a Freelance Scientist, and posted a novel method for visualising repeats in sequences. Stew showed how to increase MySQL speed, and Biocurious had a biohumorous article about the anatomy of a seminar. Last, but not least Perfect Storm compared Ruby with the new programming language Scala. [...] [...] So that’s the open science part done, but there were plenty of other things going on in the bioinformatics blog community. Neil Saunders mentioned the Gene Wiki project, the aim to give every human gene a page on Wikipedia, some kind of online encyclopedia. He also gave an interesting perspective on the history of nodalpoint.org, the original bioinformatics blog. Researcherid.com, a site to give every researcher a unique id, received attention from Pierre, Neil, and Deepak. A recent paper on the uncertainty in aligning sequences took the interest of Blind.Scientist, Thirst for Science, and Computational Biology News. SNPs are hot at Open Helix and the Spittoon. Gopubmed.org is even hotter at Medical 2.0, Konrad’s Konsiderations, Peanut Butter, What You’re Doing, and BBGM. Pawel Szczesny became a Freelance Scientist, and posted a novel method for visualising repeats in sequences. Stew showed how to increase MySQL speed, and Biocurious had a biohumorous article about the anatomy of a seminar. Last, but not least Perfect Storm compared Ruby with the new programming language Scala. [...]

]]> By: tiago http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/comment-page-1/#comment-3230 tiago Thu, 24 Jan 2008 23:40:36 +0000 http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/#comment-3230 Just a final comment: Being a DSL fanboy, makes Python a bit out too... Actually that is probably the biggest reason Just a final comment: Being a DSL fanboy, makes Python a bit out too… Actually that is probably the biggest reason

]]> By: tiago http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/comment-page-1/#comment-3229 tiago Thu, 24 Jan 2008 23:35:47 +0000 http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/#comment-3229 Erik: I need a language that works under JVM. You might say that Python is an, option... I use Python a lot: I am the author of the Biopython Population Genetics module, and my most recent work (I am a PhD student) is Python on Java. But Python on Java still lags a bit. I am actually a Prolog/Caml (probably LISP) fan, but there are no options, JVMwise, other than Scala. Don't get me started on C++ ;) Raphaël: I think I agree 100% with your points... Erik: I need a language that works under JVM. You might say that Python is an, option… I use Python a lot: I am the author of the Biopython Population Genetics module, and my most recent work (I am a PhD student) is Python on Java. But Python on Java still lags a bit. I am actually a Prolog/Caml (probably LISP) fan, but there are no options, JVMwise, other than Scala. Don’t get me started on C++ ;)

Raphaël: I think I agree 100% with your points…

]]> By: Raphaël Valyi http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/comment-page-1/#comment-3193 Raphaël Valyi Wed, 23 Jan 2008 23:28:17 +0000 http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/#comment-3193 Hi, well, I should say I woudn't go for a pure dynamic language either. Type sefety is just too good sometimes. Actually I found JRuby was a good mix. Yes Ruby doesn't have types, but then you can externalize code parts you find risky without types to typed Java code. Granted Java isn't very expressive, neither very good at meta-programming. But I find that associated to JRuby it's just good enough. Other are even talking about using JRuby+Scala combine sharing the same bytecode. Well if Java really doesn't fit, may be. Also, a JRuby to Java language (not just bytecode) compiler is being actively developed. That means that you'll soon be able to meta program in JRuby and get complex generated object injected into your inexpressive but type safe Java language. I personally think that's better that anything else available. Regards, Raphaël Valyi. Hi,

well, I should say I woudn’t go for a pure dynamic language either. Type sefety is just too good sometimes.

Actually I found JRuby was a good mix. Yes Ruby doesn’t have types, but then you can externalize code parts you find risky without types to typed Java code. Granted Java isn’t very expressive, neither very good at meta-programming. But I find that associated to JRuby it’s just good enough. Other are even talking about using JRuby+Scala combine sharing the same bytecode. Well if Java really doesn’t fit, may be.

Also, a JRuby to Java language (not just bytecode) compiler is being actively developed. That means that you’ll soon be able to meta program in JRuby and get complex generated object injected into your inexpressive but type safe Java language. I personally think that’s better that anything else available.

Regards,

Raphaël Valyi.

]]> By: Erik Engbrecht http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/comment-page-1/#comment-3184 Erik Engbrecht Wed, 23 Jan 2008 15:17:35 +0000 http://tiago.org/ps/2008/01/23/a-holiday-ruby-and-scala/#comment-3184 Why have you chosen Ruby over Python or Lisp? In Common Lisp you can add type information and the compiler will perform both safety checks and optimizations using them. I don't think metaprogramming conflicts with static typing. C++ is statically typed, and has fairly powerful compile-time metaprogramming capabilities (although they are almost impossible to comprehend). Why have you chosen Ruby over Python or Lisp?

In Common Lisp you can add type information and the compiler will perform both safety checks and optimizations using them.

I don’t think metaprogramming conflicts with static typing. C++ is statically typed, and has fairly powerful compile-time metaprogramming capabilities (although they are almost impossible to comprehend).

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