full stop.

Hey, I’m back! Didja miss me? In case the long gap without updates has caused you to forget, I took last week off from the blog to concentrate on BOP, my nascent blog manager/CMS thing. Didn’t get as much done on that front as I wanted to, but I did get some stuff done, and I may have gained a co-developer (more later as that develops), so maybe the rate of progress will start to pick up.

One reason I didn’t get as much done as I wanted to was because I woke up Monday with hives. I’m still not sure why I got them; there doesn’t seem to be a good causal event that Lor or I can identify. Appropriately, it was the day of my seventh wedding anniversary. I never realized that seven-year itch thing was supposed to be taken so literally. Anyway, between the itching (which rendered rational thought pretty much impossible) and the heavy dosing with Benedryl (which stopping the itching but damn near rendered me unconscious), I didn’t get much coding done.

The only other personal event of note during the week off: Lor gave me a cell phone as an anniversary present. (Apparently the pet store was out of leashes in my size. 8^) Just kidding honey!) I don’t think I’m going to broadcast the number, but if there’s some reason you need it, drop me a line.

I did manage to bookmark a few things during the break, however, so let’s see if I still remember how to do this…

CipherSabre looks like an interesting example of grass-roots crypto activism. I haven’t forged one (yet), but I did finally get Mailcrypt and Gnus to play nice with each other. So, in the future I’m going to be GPG signing all my mail and news postings, and using encrypted mail where possible. Just seems like the prudent thing to do.

One of the reasons it seems prudent, of course, is Echelon. For those of you not familiar with this, here’s an overview.

Oh, and my key is over here, or on the public key servers.

Speaking of crypto stuff, cryptome.org has been silent since shortly after the names of two FBI agents were posted there in defiance of a FBI demand to keep them secret. Anybody know what’s up over there?

I’ve been playing around with Galeon a little bit. It’s nice, but the lack of cookies is a real killer, and it’s been on the unstable side. Encompass is another alternative Gnome-based browser. I haven’t built it yet, but I’m going to give it a go later tonight, assuming I don’t just blog until all hours.

Third edition of the Camel is out; anybody had a chance to check out the changes relative to the second edition yet? I know I’ll be buying it, the question is more how long I’m going to put it off.

Hey, all you Visor users out there – anybody upgraded yet? Thumbs up or down?

Odd and/or disturbing search engine queries that hit Genehack last week:

It’s not just that these searches are going on; I’m actually okay with that. My confusion and amazement stems from the fact that in order for me to even know about these things, the searchers are clicking through to Genehack – presumably because they think they’re going to find what they’re looking for here. I just don’t get it.

The release of Debian 2.2 has been dedicated to Joel Klecker.

Here’s another ‘do-good via clickage’ project: Race for the Big Cats. (via Dave, who is web-page-less.)

Hey, speaking of Dave, (seriously belated) thanks to the people who sent him birthday emails. He did indeed freak out. 8^)

Some useful bioinformatics Perl one-liners. I keep meaning to polish up my one-liner skills, but never seem to have the time to do it. It’s usually quicker for me to do a multi-line script that will work the first time, rather than mess around with getting the one-liner right.

Lots of Perl stuff from the indomitable Abigail.

The closure of K5 really sucks. When the guilty party is found, I hope they kick 'im once for me.

So, last week I mentioned writing a letter to Richard Grant about his ‘UNIX versus Linux for Bioinformatics’ article. Apparently my letter and his response are going to be in The Biochemist at some point, but you can read them now. The exchange also ended up sparking a somewhat lengthy thread over in bionet.software, which has veered into a discussion of source code access and peer review, with numerous side forays into related topics. One of the better Usenet exchanges I’ve been involved in in quite some time.

Some tips on avoiding bad software design. I think I’ve made about half these mistakes, and I’m probably working on making the rest. Maybe I’ll manage to miss one or two of them now.

Jessamyn is trying to take back Vermont – .com guerrilla style, baby! (See this for the explanation.) Good on Jessamyn.

I’m listening to a mp3 of a bootleg of the Get Up Kids doing ‘Better Half’. At one point, before a chorus, the singer shouts out “Sing it with me, Seattle!”, followed by about three bars of no vocals and no audience participation. Cracks me up, every time.

Another legal link from Jay Baylink’ Ashworth: PTO to rein in gene patents. I think the new guidelines still sound a bit looser than I’d like. Here’s a quote:

Companies like Incyte Genomics have isolated, purified, sequenced, and discovered a commercial utility for genes and put them into commercially useful formats for development of drugs and diagnostic tests," [Randal Scott of Palo Alto, Calif.-based Incyte Genomics Inc.] testified.

Okay, but why should they be allowed to patent the genes? The therapeutically useful drugs and what not aren’t the genes – they might be the proteins encoded in the genes, or they might be other molecules that interact with the genes, or the protein encoded in the genes, but in most of the cases I’m aware of, the actual DNA is not the therapeutic. So why not patent the actual drug, be it protein or molecule, or whatever? Answer: Because it’s more difficult to get to the point where the drug has been developed, or the protein has been purified, or whatever. It’s difficult to see the attempts to patent gene sequences as anything other than premptive land grabs, designed to prevent competition from other companies.

Cool! Gimp for Newbies. I just turned a co-worker onto the Gimp. (Builds just fine on our Solaris workstations, once you get all the libraries built too.)

Okay, I think that’s it for today. Hopefully I’ll be back tomorrow with more. If you’ve got a spare minute, shoot me some email (jacobs@genehack.org) and stroke my ego by telling me how much you missed me.