Re: [MLUG] coding languages used in genetics

[Mike Miller <EMAIL:PROTECTED>]

On Thu, 1 Apr 2004, Jonathan King wrote:

> On Thu, 1 Apr 2004, Mike Miller wrote:
>
> > Might as well post this.  I just did a search of the long list of
> > programs given here:  http://linkage.rockefeller.edu/soft/ Most
> > programs should be listed there.  They have a line for "source code
> > language" so I grepped that line to get a list of languages used in
> > coding these programs.  Then I grepped that list and came up with
> > these data:
>
> Interesting.  I think it's worth noting, though, that you would have
> gotten very different numbers if you'd looked into code that wasn't
> doing linkage analysis.  In the sequence world, stuff lke EMBOSS and the
> bioperl project are huge, and there ain't no FORTRAN or Pascal there.

That is very true.  One thing:  Many of the programs on the "linkage" list
don't do linkage analysis but do other kinds of things with marker data.
Some do pedigree drawings, some haplotyping, some association analyses.


> In any case, I think it's worth combining C and C++, Pascal and Delphi,
> S and R and re-tabulating:

One problem with that method:  Categories were overlapping, so when you
add the numbers that way, some programs are counted twice in the same
frequency count (e.g., nearly every R program was also an S-Plus program).


> So the languages on this list that most MLUGers are probably less
> familiar with are S-plus/R and SAS.  SAS is the language of big-time
> statistical data analysis.  I think most of you would think SAS
> was...pretty awful.

The most awful thing is the price.  I was just told that without an
academic discount, it costs $19,000 PER YEAR to run SAS under Linux.
Another source quoted it at $1,500 PER USER PER YEAR *with* an academic
discount!!!  No wonder the founder of SAS corp is the richest man in North
Carolina!


> R is an open-source implementation of S-plus, and is actually quite an
> interesting system. S(-plus) was written for stats geeks by computer
> geeks at Bell Labs, so it's actually a decently designed language, and
> then the open-source R people have been improving it even more.

Yes!  So we want to start trying to dump SAS and do as much as possible in
R.  Some people also like Stata, but it is not open source.

Mike
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