05 March 2010

Names on Nodes: Cutting Out the Fat

While pondering the headaches of homonymy recently, I started to ask myself, What am I doing with my life? Why am I worrying about this?

Seriously, though. I've been working on Names on Nodes on and off for about three years, and I still haven't launched it. And it's because I've been so focused on getting things like this right. (Well, that and having a day job.)

But things like this aren't part of the core functionality. The core functionality is the automated evaluation of phylogenetic definitions (encoded as MathML) within the context of phylogenetic hypotheses (modeled as directed, acyclic graphs). That part of it's been done for quite a while. So why am I wasting time on the rest?

By cutting out the entire database portion of the project, I could actually have something launched this year. Sure, it'd be nice to have a repository of taxonomic names, definitions, authorities, etc. But it's not necessary. It's phase II, not phase I. In fact, by the time I'm ready for a phase II, there will almost certainly be other services out there that already perform those things.

So, here on out, I'm going to be focusing on getting a lean, mean version of Names on Nodes up. Here's a quick summary of what you'll be able to do with it:
  1. Open bioinformatics files (NEXUS to start with, other formats like nexml going forward).
  2. View the phylogenies in a pretty graphical interface.
  3. Merge phylogenies.
  4. Tweak phylogenies (adding or removing parent-child relations, adding or removing taxonomic units, equating taxonomic units, etc.).
  5. Formulate phylogenetic definitions using a spiffy interface.
  6. Apply these definitions to the phylogeny.
  7. Save your work as MathML files.
And that should be manageable (although there is still much work to be done, especially for the user interface). Once that's launched and working, then I'll look into connecting to other services and/or launching an associated database.

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