Monday, April 22, 2013

Do we need naming regulations for computer software?

Well, just saw this new paper: BMC Bioinformatics | Full text | Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data.  Seems potentially interesting.  But one part of it struck me as very awkward.  You see, there already is a Bellerophon software program used by many in my field: Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.  Seems like a very bad idea to have a new program with the same name as an existing (and still used) one in a similar general field (DNA sequence analysis).

This leads me to the following question - do we need some sort of naming guidelines or regulations for computer software?  We have all sorts of naming regulations and conventions for genes, for species, for other groups of taxa, and more.  Why not software tools?  But seriously, I don't think we need such a thing - we just need people to use Google and to do a little searching before they invent / publish a software package in case it's name is, well, already used.


  1. I presume that Lhaka and Gentleman never foresaw Google when they wrote a language named "R"

  2. The silliest name for a computer program I have seen is COMPUTE. So-named because it computes something.

  3. This isn't the first time this has happened. Do you think there was a deliberate attempt to confuse people? I see the advantage of a naming convention would be that it would keep corporations from naming products that already exist as free software written by researchers for researchers.

    Here's my proposal: common names will be used for discussions and so-called "scientific names" will be used in code and in publications ;)

  4. Personal opinion/rant:
    We don't need naming conventions, we need to find a way to reduce the need to publish or perish, so that we can stop re-building software that does the same thing over and over again, and just make new modules.

    Can someone please perform a coup at all of the funding agencies to make it possible to get funding without your publication record being a primary driver of rankings of the merits of the team?

    1. Count me in for the coup ... though not sure how to pull it off

  5. I'm not sure there is really such naming regulations for taxa either. There are lots of conflicts, particularly between different groups of organisms: Coxiella can be the bacterium or a mollusc, for example...