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New science/informatics interest area?

by bobf (Monsignor)
on Aug 16, 2004 at 04:38 UTC ( #383193=monkdiscuss: print w/replies, xml ) Need Help??

Hello monks,

I was wondering how much support there would be for an informatics-based interest area. I am a biologist turned quasi-bioinformaticist, and while I have found PM to be very helpful, I also think having a forum for science-related questions would be beneficial. Not only would it would aid scientists that currently use perl in their work, but it might also encourage non-programming scientists to take the leap into perldom if they knew such a resource existed (thereby expanding the PM community and spreading the glory of angelic chorus echos through the Monastery).

Discussion with BioGeek and SciDude convinced me that this idea was at least worth bringing up in a post. SciDude suggested expanding the focus of the area to include fields beyond biology: chemistry, physics, math, and all things science. In addition, for those that are interested, BioGeek has started compiling a list of monks that indicated a scientific interest on their home node.

Of course, arguments could be made both for and against creating an informatics area. For example, many questions can be boiled down to something that is application independent and therefore something that can be easily posted to existing areas of the Monastery (a problematic regex is still just a regex), but non-generalizable questions might be better organized into a separate area. I am sure there are many reasons to support or to discourage this idea - here is a partial list:


  • provide a place for specific Q&A for specific (and perhaps not widely-used) informatics modules
  • provide a forum for focused discussions about approaches to field-specific tasks
  • encourage members of the bioperl/etc communities to join PM
  • expertise from the broader PM community could be applied to informatics problems that are typically posted on more subject-specific lists
  • provide a central repository for informatics-related nodes currently in the Cool Uses for Perl section
  • provide a more specialized support area for these users of perl (a growing minority)
  • tutorials that illustrate common tasks may help attract currently non-programming scientists


  • many general questions are application-independent and do not require a specialized forum
  • some support for biologists already exists through
  • might impart an exclusionist feel to existing but non-science members
  • most posts containing informatics code examples could go to Cool Uses for Perl

    If interest is high enough, perhaps a small room in the Monastery could be cleaned out for an informatics area? I thought a dusty room in the basement, perhaps "The Laboratory", would be appropriate...

    Thanks - comments are welcome!

  • Replies are listed 'Best First'.
    Re: New science/informatics interest area?
    by davido (Cardinal) on Aug 16, 2004 at 05:09 UTC

      Adding major sections is something not done often. Think about how broad the sections are: SoPW is for all questions, Meditations is for all Perlish discussion that doesn't involve questions, PMD is for Monastery discussions, Obfuscation, CUfP, Code, etc... all but one (PMD) relating to Perl, the language. CuFP is essentially applied Perl, but it's still Perl.

      If we start adding topic-specific sections, we'll have to add CGI / Web, Science, Networking, System Administration, Software Development and Prototyping, Finance, Manufacturing, Accounting, and all the other things to which Perl is frequently applied.

      I get that science is cool (among us geeks), and that it has a certain sexiness to it among this kind of a group. But it's not a Perl-specific topic, IMHO.

      As for adding Q&A sections, recently we added a Testing section. I had high hopes that it would quickly be populated with all sorts of interesting FAQ-like Q's and A's. That hasn't happened, for the most part. I don't see Q&A as being a very good place to start a Science section either.

      I don't mean to just poo-poo any suggestion for new PerlMonks sections, or Q&A categories. I just think that we have to remember that this is a Perl site, and that in the interest of keeping it simple, we should keep it simple. ;)

      Update: Having said all that, and subsequently giving it a little more thought, Perl for Biologists could be a category of Perl type questions and answers. If there is enough support for it in response to this thread, I would not oppose the creation of such a category under 'Categorized Questions & Answers'.


    Re: New science/informatics interest area?
    by ysth (Canon) on Aug 16, 2004 at 07:33 UTC
      I don't quite see the point in separating off an area to hold SoPWs, Categorized questions, module reviews, tutorials, etc. that are specific to bioperl or informatics. It might be a good thing to create categories in module reviews, and a bioperl category in Categorized Q&A.

      Perhaps a node could be set up to contain links to the information that appears in those diverse places? If one person wants to set up and maintain such a node, there's nothing prevening it. I'd suggest Meditations, or perhaps a bioperl user. If there's desire to have more than one person with update rights, the gods could be petitioned to create a wiki page. (Wikis can have read and write permissions set to minimum monk level or to a specific order of monks.)

    Re: New science/informatics interest area?
    by bobf (Monsignor) on Aug 18, 2004 at 06:10 UTC

      Thank you for your responses. One of my biggest hesitations before posting this idea centered on the difference in classification systems between a new science/informatics area and the rest of PM. It was, in fact, one of my first arguments against myself before I posted: PM currently categorizes posts based on "type" (e.g., PM discussion, obfuscation, examples of code, etc), whereas an informatics area would involve categorizing by "content" (please excuse the weak verbage - I am not sure how else to describe it). In a sense, an informatics area would be a specialized cross-section of all existing areas in the Monastery.

      Therefore, I agree that creating a new area based on topic (whether it is for science, CGI/web, networking, etc) runs a bit counter to the current configuration of PM. My intention was not to try to reformat the Monastery, only to make an effort to concentrate subject-specific posts (and expertise) into a single area. After meditating on this a while, I think the suggestion by davido and ysth to add a bioperl (or similar) section to Categorized Q&A might represent the best solution. It would successfully maintain the feel of PM, while still providing an area for posts relating specifically to biology and bio-related tasks. Similarly, I would also support ysth's suggestion to add a section for module reviews.

      Thanks again for the comments. I look forward to further discussion.

        There is a section for module reviews; I was suggesting making it be sorted by category rather than alphabetically. Probably too much of a maintenance hassle, though.
          Whups - thanks for the link - I hadn't found that one yet!
    Re: New science/informatics interest area?
    by jdporter (Chancellor) on Aug 17, 2004 at 18:41 UTC
      PerlMonks isn't separated into application areas. Bioinformatics can be discussed in SoPW, or Meditations, or Q&A, or whatever, just as any other application domain.
    Re: New science/informatics interest area?
    by Prior Nacre V (Hermit) on Aug 19, 2004 at 12:15 UTC

      Registering definite interest in this idea.



    Re: New science/informatics interest area?
    by Solo (Deacon) on Aug 23, 2004 at 00:43 UTC
      An industrious monk could google mine for science releated nodes and use his/her home node as an index for them.

      This option has the benefits of

      • not being application domain specific (if we have a bioinformatics section, why not a cgi section? infinitum...)
      • being no work for pmdev since any user could do this today
      • providing a litmus test for what interest there is in the use of such an index (provided there's any way of measuring node hits, referrals, and such)
      • building and maintaining the index falls to those who would find it most interesting, with users /msg'ing maintainers not to miss an on-topic node, etc.

      A really industrious monk could mine the Newest Nodes XML feed to help maintain the index for well-titled nodes.


      You said you wanted to be around when I made a mistake; well, this could be it, sweetheart.
    Re: New science/informatics interest area?
    by chaserx (Initiate) on Aug 21, 2004 at 02:39 UTC
      Great idea! As another biologist who has been seduced by computers, I think that a science/bioinformatics/bioperl section would be quite helpful.

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