Response to "Scientific papers and softwares"

Recently leprevost posted a comment on requiring better software in science. Its a good plea, read it! In response I started a comment, which got a bit too long, here it is:

A few of us have been talking about how to increase the use of Perl in the scientific community. While our efforts are in their infancy, we hope to fight this very problem. Some new sites are

  • Perl4Science, my stub site/org, to be expanded
  • The Quantified Onion, Joe Kline’s brand new Google Group, not sure if it’s been announced, guess it has now :-)

In the meantime, all I can do is contribute that good code, and put it on GitHub and CPAN for people to see and use.

There are many more projects, both written by me and others for this purpose. PDL, BioPerl etc. I really would like to reclaim some of the scientific computing that has been going to Python by default. It makes me very sad to read that when someone does choose Perl, that they would use that opportunity not to show off new modern Perl, but that old Perl that scares people away.

If you are a Scientist, you are more than welcome to contact me, David Mertens and others about how to interact with the scientific community in Perl. Even if you don’t want to do this, however, please, write Perl code that shows off the language we love.


I imagine that the Perl test framework would be a very big attraction to scientists. Perl makes it possible to very quickly code up tests. Science work relies on a precarious chain of assumptions, and writing testing code in Fortran or C is a nightmare compared to doing it in Perl.

How about showing how you wrote checking code for your electron microscope code? I would emphasize how easy it is to do this in Perl, how you can save time, because I think most scientists wouldn’t be attracted by the idea of learning Perl ins and outs, but would rather want to find a way to save their time, or save themselves from making a mistake.

Hi Joel, thanks for your reply. I already joined the quantified onion. Its nice to see others dedicating their times to help people work better with science and software development. I totally agree with you, we have probably the largest software database from the Internet (CPAN) and loads of material to help anyone in their development process, I think everyone involved with science and software creation should be aware of the importance of releasing a code that will be used for scientific purposes. As Bullock said above, people should be more careful when doing science and Perl really makes it easy when tests are needed.

This is great to hear! I am the author of Math::GSL, Math::ODE, Math::Primality and a few other math-related CPAN modules, as well as the now mostly defunct “Scientific Computing with Perl” google group.

I have been trying to foster the use of Perl in math+physics since 2000, but I thought I mostly alone. Seems like that is no longer true! Keep up the good work, and I also submit my name in the hat of “people to contact” if you want to know how to “do science” with Perl.

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About Joel Berger

user-pic As I delve into the deeper Perl magic I like to share what I can.