5 Nov 2004 titus   » (Journeyer)

A few days ago, I needed to use my motif searching GUI to search a DNA sequence. Normally this would mean that I'd need to:

  • scp the sequence file to my Mac;
  • log into my Cartwheel account;
  • upload the sequence into Cartwheel;
  • create some analysis in Cartwheel using the sequence;
  • run FamilyRelationsII and load that analysis;
  • click on the sequence and selected 'motif search' from the menu.

Painful, ehh? Well, the system isn't exactly optimized for command-line use ;).

It turned out to be just as easy to write a separate command-line executable that loaded the sequence from the file and brought up the motif search view. (This required writing a new constructor for the motif search view & factoring out the common constructor functions into a _setup function, but heck, it was probably time to do that anyway.) 15 minutes later, & voila -- 'motif-search sequence.fa' lived!

So, naturally, I sent out an e-mail to my bioinformatics homies informing them of this mildly useful program. The response from one fella? "Hey, you know, it would be great if you could also search for this kind of motif, not just the simple kind that's easy to type in. Oh, and if you could maybe plot sequence conservation, too, then you'd have a pretty neat program."

Hmm.

First of all, there are a number of user-interface issues there that need to be worked out. Not difficult, but not easy. And making it useful for anyone but the five biologists at Caltech capable of using the command-line would be at least a week-long project. (That's why I wrote Cartwheel in the first place; biologists are not UNIX-savvy!)

Second of all -- dude, you're a programmer. It's open-source. I'd be happy to suggest a starting point. I'm willing to admit that GUI programming is trickier than many other kinds of programming, but I've got a working framework going and I'd even be willing to sketch out what you'd have to do. But I'm damned if I'm going to spend time working on something that's only useful to one person, unless that person is me ;).

O well. As a friend says, this is the Curse of the GUI -- the users always want that nifty extra feature, the one that's really only directly useful to them. Who knew that people would want to not only change the color of the elephant, but make him polka-dotted too?

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