[ETHANol]

If you like BIOinformatics then Perl.
If you like bioINFORMATICS then C++.

It's a personal choice and obviously both have their place. Pointless argument.

[rskr]

If you like BIOinformatics then Perl.
If you like bioINFORMATICS then C++.

It's a personal choice and obviously both have their place. Pointless argument.

However, BIOinformatics(as opposed to bioINFORMATICS) isn't an academic pursuit. More like a trade school endeavor. See reasons listed above.

[ETHANol]

However, BIOinformatics(as opposed to bioINFORMATICS) isn't an academic pursuit. More like a trade school endeavor. See reasons listed above.

Someone better tell the NIH and Cell press. Because anyone using quick and dirty perl scripts to solve complex biological problems is not an academic. I never realized that I would have been better off getting my training at a trade school rather then UCSC, Cold Spring Harbor and MIT. Cool, I learn new stuff every day.

Note: I'm only responding here because it's kind of funny. The argument is itself is obviously pointless. We can talk about the advantages of C++ and Perl for bioinformatics, which could be informative to some.

[rskr]

Someone better tell the NIH and Cell press. Because anyone using quick and dirty perl scripts to solve complex biological problems is not an academic. I never realized that I would have been better off getting my training at a trade school rather then UCSC, Cold Spring Harbor and MIT. Cool, I learn new stuff every day.

Note: I'm only responding here because it's kind of funny. The argument is itself is obviously pointless. We can talk about the advantages of C++ and Perl for bioinformatics, which could be informative to some.

And you have no point because all the good programs are written in C++, and your perl programs just call them. Academically speaking, quick and dirty perl programs usually aren't publishable. If you look at the programs that get published and actually cited.... C++(BLAST/Abyss/Velvet/Hmmer/ClustalW are all in C++)

As a utilitarian there is something beautiful about a script that uses these libraries, but really its nothing to write home about much less a paper about the source code. A trade skill like Cisco certification or something not an academic discipline.

[rskr]

Someone better tell the NIH and Cell press. Because anyone using quick and dirty perl scripts to solve complex biological problems is not an academic. I never realized that I would have been better off getting my training at a trade school rather then UCSC, Cold Spring Harbor and MIT. Cool, I learn new stuff every day.

Note: I'm only responding here because it's kind of funny. The argument is itself is obviously pointless. We can talk about the advantages of C++ and Perl for bioinformatics, which could be informative to some.

Another way to think about it is Perl is the software equivalent of duct tape. Sure you can rig up all kinds of Novel devices by taping them together or fix broken stuff with it, but not something that gets taught in your mechanical engineering course. You learn that on the job.

[ETHANol]

Another way to think about it is Perl is the software equivalent of duct tape. Sure you can rig up all kinds of Novel devices by taping them together or fix broken stuff with it, but not something that gets taught in your mechanical engineering course. You learn that on the job.

You want to make the perfect program. That's cool. I am glad there are people out there doing that. But some people are much more interested in biology and see computing as a tool. Higher level languages are very useful and save a lot of time. When you learn the intricacies of molecular biology, cell biology, biochemistry, immunology, developmental biology, cancer biology, etc., I'll say you have the right to come here and post about how people that use higher level languages are lazy and stupid. Until then.....

Most inane internet argument ever.

[lsbrath]

Perl was the glue for the Human Genome Project. If you need speed then yes you go with a compiled language. Other than that scripting has proven its worth.

[rskr]

I'll say you have the right to come here and post about how people that use higher level languages are lazy and stupid. Until then.....

Most inane internet argument ever.

I use interpreted languages like Perl, they have their place, just not in academia as a teaching language.

Maybe you could teach people to program Perl on Macs, because the bioperl libraries aren't cross platform.

Then again why are you using the biolperl libraries for a class, have you seen the code in there? Maybe you could answer all the kids questions about why X Y or Z libraries wasn't fully implemented or breaks, and just tell them Perl programmers are the most wonderful people in the world, they were on the Human Genome Project.

[lsbrath]

Do what makes you happy as long as it works. The saying goes that a poor rat has only one hole. There are many folks in the bioinformatics community that have been very successful using only Perl with BioPerl and increasingly R and Bioconductor.

[bpgoll]

Try Linux ^^

Yes

You should try linux