Comments for Programming for Scientists http://www.programming4scientists.com Software development wisdom and common-sense for the scientist-programmer Wed, 07 Jan 2009 13:40:43 +0000 http://wordpress.org/?v=2.6.5 Comment on The basics of…R by List of programming languages used by programmer scientists | Programming for Scientists http://www.programming4scientists.com/2008/12/the-basics-ofr/#comment-111 List of programming languages used by programmer scientists | Programming for Scientists Tue, 23 Dec 2008 04:45:52 +0000 http://www.programming4scientists.com/?p=364#comment-111 [...] R. A statistical programming language.  It has loads of statistical libraries that are either built-in or downloadable.  R is open source and has a community that develops new code for it; for example, the Bioconductor toolbox for analysing gene expression data is very widely used.  It can be slow to run big jobs, unless you use the built-in functions (written in C and hence v. fast) or attach your own C or C++ code to speed up the critical bottlenecks.  Interfacing C/C++ to R in this way take a bit of care, but can be very powerful (See Basics of … R). [...] [...] R. A statistical programming language.  It has loads of statistical libraries that are either built-in or downloadable.  R is open source and has a community that develops new code for it; for example, the Bioconductor toolbox for analysing gene expression data is very widely used.  It can be slow to run big jobs, unless you use the built-in functions (written in C and hence v. fast) or attach your own C or C++ code to speed up the critical bottlenecks.  Interfacing C/C++ to R in this way take a bit of care, but can be very powerful (See Basics of … R). [...]

]]> Comment on The basics of … C\C++ by List of programming languages used by programmer scientists | Programming for Scientists http://www.programming4scientists.com/2008/12/the-basics-of-cc/#comment-110 List of programming languages used by programmer scientists | Programming for Scientists Tue, 23 Dec 2008 04:45:37 +0000 http://www.programming4scientists.com/?p=368#comment-110 [...] C++. The object-oriented version of C.  This makes is both fast and able to benefit from all the nice (from the developers’ perspective) qualities of an object-oriented language.  It needs the developer to handle things like memory allocation, which can be a headache, but the skilled programmer can use this to their advantage (See Basics of … CC++). [...] [...] C++. The object-oriented version of C.  This makes is both fast and able to benefit from all the nice (from the developers’ perspective) qualities of an object-oriented language.  It needs the developer to handle things like memory allocation, which can be a headache, but the skilled programmer can use this to their advantage (See Basics of … CC++). [...]

]]> Comment on Seven ways to test your number-crunching code by Rich http://www.programming4scientists.com/2008/12/seven-ways-to-test-your-number-crunching-code/#comment-109 Rich Mon, 22 Dec 2008 13:58:49 +0000 http://www.programming4scientists.com/?p=376#comment-109 I completely agree! Other people can be very creative when it comes to breaking your code and this is a Very Good Thing, because it's a form of testing :-) I completely agree! Other people can be very creative when it comes to breaking your code and this is a Very Good Thing, because it’s a form of testing :-)

]]> Comment on Seven ways to test your number-crunching code by nico http://www.programming4scientists.com/2008/12/seven-ways-to-test-your-number-crunching-code/#comment-108 nico Mon, 22 Dec 2008 13:49:53 +0000 http://www.programming4scientists.com/?p=376#comment-108 I would add: if someone else is going to use your code, have them testing it! Let them misuse the program as worst as they can... and bugs will come out! It happened to me that I wrote some routines for the analysis of a time series. Well, it worked perfectly on all my data, but when someone else in the lab tried to use it it didn't work anymore, giving weird results. Well, the problem was I was assuming (never do that!) that the time series was starting from time 0. This was always the case with my data, but not with my colleague's... I would add: if someone else is going to use your code, have them testing it! Let them misuse the program as worst as they can… and bugs will come out!

It happened to me that I wrote some routines for the analysis of a time series. Well, it worked perfectly on all my data, but when someone else in the lab tried to use it it didn’t work anymore, giving weird results. Well, the problem was I was assuming (never do that!) that the time series was starting from time 0. This was always the case with my data, but not with my colleague’s…

]]> Comment on The basics of…R by Rich http://www.programming4scientists.com/2008/12/the-basics-ofr/#comment-106 Rich Tue, 16 Dec 2008 17:33:05 +0000 http://www.programming4scientists.com/?p=364#comment-106 There may well be, but I've not come across any (please let us know if you find some!). The FOR loops issue can be a real killer, but can be worked around (sometimes thinking in vector operations is a bit...challenging :-) ). I know from experience that Matlab and IDL suffer from exactly the same issue, which is why they also provide vectorised operations. That said, I have found all three languages extremely useful! There may well be, but I’ve not come across any (please let us know if you find some!).

The FOR loops issue can be a real killer, but can be worked around (sometimes thinking in vector operations is a bit…challenging :-) ). I know from experience that Matlab and IDL suffer from exactly the same issue, which is why they also provide vectorised operations. That said, I have found all three languages extremely useful!

]]> Comment on The basics of…R by gioby http://www.programming4scientists.com/2008/12/the-basics-ofr/#comment-105 gioby Tue, 16 Dec 2008 17:21:30 +0000 http://www.programming4scientists.com/?p=364#comment-105 Thank you for the article. I am also a newbie to R and I should start studying it already. I didn't know of this 'for' loops problem. Are there any testing frameworks for R programs? Thank you for the article.
I am also a newbie to R and I should start studying it already.
I didn’t know of this ‘for’ loops problem. Are there any testing frameworks for R programs?

]]> Comment on The basics of…R by Ben http://www.programming4scientists.com/2008/12/the-basics-ofr/#comment-104 Ben Thu, 11 Dec 2008 22:40:34 +0000 http://www.programming4scientists.com/?p=364#comment-104 Glad you found it useful. Please get back to us on how you get along and what you think we should add to the article. Glad you found it useful. Please get back to us on how you get along and what you think we should add to the article.

]]> Comment on The basics of…R by James P. http://www.programming4scientists.com/2008/12/the-basics-ofr/#comment-103 James P. Thu, 11 Dec 2008 22:35:08 +0000 http://www.programming4scientists.com/?p=364#comment-103 Thanks for this, I am about to dive into R as a new graduate student, this provided some good perspective. Thanks for this, I am about to dive into R as a new graduate student, this provided some good perspective.

]]> Comment on The basics of…Matlab by Will Dwinnell http://www.programming4scientists.com/2008/11/the-basics-ofmatlab/#comment-102 Will Dwinnell Thu, 11 Dec 2008 12:11:52 +0000 http://www.programming4scientists.com/?p=342#comment-102 Though MATLAB has a reputation for slowness, I find it speedy enough for use with re-coding in other languages. It'd be interesting to see an examination of execution times for tasks typically performed in MATLAB, implemented in MAATLAB and other langauges. Though MATLAB has a reputation for slowness, I find it speedy enough for use with re-coding in other languages. It’d be interesting to see an examination of execution times for tasks typically performed in MATLAB, implemented in MAATLAB and other langauges.

]]> Comment on Book review of … Facts and Fallacies of Software Engineering by Ben http://www.programming4scientists.com/2008/12/book-review-of-facts-and-fallacies-of-software-engineering/#comment-99 Ben Tue, 02 Dec 2008 00:31:51 +0000 http://www.programming4scientists.com/?p=354#comment-99 Thanks for suggesting our blog for the nature blog network! It's nice to know that people like what we're doing here. Thanks for suggesting our blog for the nature blog network! It’s nice to know that people like what we’re doing here.

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