I write a Rails server for each of my experiments. Rake tasks are GREAT for bioinformatics pipelines, and migrations and database backups make it incredibly easy to save old experiments.
Plus, various Ruby gems (starling, workling) enable me to farm out long-running experiments to a variety of lab machines. I can use Rice to write C++ Ruby extensions that are compiled individually on different machines.
And all of this is stored in a PostgreSQL database. (MySQL is slow for complex joins, which you sometimes have to write in bioinformatics.)
Oh, I'm also pretty new to it. What lab are you in?
I'm rotating in the brand new Sawyer Lab at UT Austin. During Dr. Sawyer's post-doc (at Hutchinson), she was doing a lot of work on both TRIM family and APOBEC family genes in the context of positive selection and ancient retroviral signatures in primates and even other mammals (cows, dogs, mouse). Basically, those proteins have been playing a role in defense against retrovirus for quite a while.
I was kind of annoyed that this story made it on Slashdot. What about that RNAi screen in Science back in February? That was way more interesting than the TRIM22 crap, which doesn't even appear to be peer-reviewed.
My PI (S. Sawyer) looked at that as a post-doc (and is still), but no one's been found (yet) who possesses the versions of the various TRIM genes which restrict HIV. Only in monkeys.
I've got TWC through Earthlink in Austin and it's been teh suck. First, they gave me the wrong AC adapter, which prevented DHCP from working properly. Basically only Windows machines could get IPs, and not, say, my router or iPhone or room mate's Mac. Sometimes my Linux box got lucky. Eventually, the adapter fried the cable modem, at which point they replaced it and it started working.
Speed was much better until last week. I had thought it was due to the rerouting of traffic due to the cables being cut in Eurasia, though that theory felt a bit strange; but lately, the ping to places other than Google has been just awful. iTunes was the least of my worries.
How would you immediately reduce military spending? It would put lots of people out of jobs. (Not that I think it shouldn't be done--I agree with you. But you can't really do it immediately.)
This tragedy has nothing to do with gun control. The incident last semester with William Morva could not have been prevented by either more or less gun control; nor can this one.
Please, please stop using this tragedy to support political agendas. No one could have seen it coming, and most students here wouldn't carry a gun to class even if it were permitted.
Virginia Tech is not really a high-pressure campus. Anyway, forcing people into counseling when they're really busy tends to make them more stressed out, not less...
Hidden Markov Models and the Viterbi Algorithm
on
A Useful Grammar Checker?
·
· Score: 2, Informative
Man, I wish I had better karma, because I've got useful things to say here.
You can check grammar using a well-trained Hidden Markov Model and the Viterbi Algorithm. If I were to design such a program, I would have the part-of-speech tagger have a go at a sentence, and if it came back with a confidence below, say, x, then the sentence's grammar is probably not good.
This is nice because it also helps sentences keep from being awkward.
I was the president of the computer club in my high school. It never went well. Of course, there weren't many people IN my high school. We never seemed to accomplish anything we intended to accomplish. It kind of sucked, but it was fun getting together and watching All Your Base or other such things.
Just wait till college, then you'll find yourself pleasantly satisfied.;-)
I could have sworn this movie was an Austin Powers parody. I kept expecting Shinzan or whatever his name was to demand one million space-bucks with his pinky. He even had the little scar.
Aside from that, I rather liked the movie. I have huge problems with plot holes, which Star Trek is generally full of no matter what you do. Ebert's right, Star Trek has problems--but that doesn't make this movie bad, in my opinion.
I was very impressed with Data's role in the movie. Including the sad ending. Nearly broke my heart.
Joe Barr is not the most reliable of sources. He gave very biased reviews to Xine and MPlayer. I won't say much more than that, except that you should read what they have to say about him at www.mplayerhq.hu.
Not trying to troll, just trying to point out that this guy isn't necessarily a reliable source.
Our time system is based on geometry, and geometry on our time system. When ancient peoples observed that there were about 360 days in a year they decided to make that the number of degrees in a circle. There are twelve months because it divides evenly into 360 and that's about the number of lunar cycles we see here on earth. The metric system would throw that off completely. Plus imagine all the trig we'd have to relearn.
There were several mistakes that I noticed. For one thing, detectives and cops are practically conditioned to never pick anything investigation-related up without those plastic evidence gloves. The worst one, though, was that at the end Robin Williams sinks when he's dead. But dead people don't sink, they float. Little inconstencies like that which could easily be fixed bugged the shit out of me.
Also, I was hoping Williams would actually be evil, not just a stupid guy trying to escape his guilt. I wanted pinky and the brain evil from him.
Funny that this should come up. I met Senator Landrieu yesterday with my AP Government class (her husband and my teacher coach baseball together). She was a very nice woman, and a brilliant public speaker. She also kept her political perspectives separate from her personal ones. I'm usually very suspicious of politicians but I think she's one people can count on.
I do happen to disagree with relegating EVERYTHING bad to.prn. Too easy to abuse.
Landrieu is one of the good guys (or girls). My guess is she may secure the nomination for democratic vice president in the next election.
Actually, we learned in family life (sex-ed) today that gender can actually fall somewhere between male and female ("intersexed" persons). See also Jamie Lee Curtis.
Maybe I misunderstood the article, but I thought it said that Microsoft prewrote the letters and sent them to people to sign. Now, I couldn't tell from the article, but were any of these letters exactly the same? All I know is several times I've been asked to protest things like the DMCA and UCITA, and have even been given a prewritten letter to sign and send in. This sounds like exactly like what Microsoft is doing in at least a few states. Granted, it's not good for them to be making the letters appear to be written by the individuals who are signing them...but what is really going on here?
Slashdot Mirror
I write a Rails server for each of my experiments. Rake tasks are GREAT for bioinformatics pipelines, and migrations and database backups make it incredibly easy to save old experiments.
Plus, various Ruby gems (starling, workling) enable me to farm out long-running experiments to a variety of lab machines. I can use Rice to write C++ Ruby extensions that are compiled individually on different machines.
And all of this is stored in a PostgreSQL database. (MySQL is slow for complex joins, which you sometimes have to write in bioinformatics.)
Guess what; you can't compile Linux without a computer either.
Well, you could, but it might take a pretty long while to do it by hand. And it wouldn't do you much good, either.
Oh, I'm also pretty new to it. What lab are you in?
I'm rotating in the brand new Sawyer Lab at UT Austin. During Dr. Sawyer's post-doc (at Hutchinson), she was doing a lot of work on both TRIM family and APOBEC family genes in the context of positive selection and ancient retroviral signatures in primates and even other mammals (cows, dogs, mouse). Basically, those proteins have been playing a role in defense against retrovirus for quite a while.
I was kind of annoyed that this story made it on Slashdot. What about that RNAi screen in Science back in February? That was way more interesting than the TRIM22 crap, which doesn't even appear to be peer-reviewed.
Nice to meet you.
My PI (S. Sawyer) looked at that as a post-doc (and is still), but no one's been found (yet) who possesses the versions of the various TRIM genes which restrict HIV. Only in monkeys.
Actually, TRIM5alpha is an isoform of the TRIM5 gene. No one knows much about the other two isoforms.
TRIM22 is related to TRIM5alpha, but it's not homologous--the term you're looking for, I think, is paralogous (but I get them all mixed up).
TRIM55 and TRIM58 probably also play a role in HIV infection, according to a recent study published in Science (February, I think).
APOBEC3G is another interesting one in that vein; it attempts to mutate HIV, but HIV's vif protein adapts to block it.
I've got TWC through Earthlink in Austin and it's been teh suck. First, they gave me the wrong AC adapter, which prevented DHCP from working properly. Basically only Windows machines could get IPs, and not, say, my router or iPhone or room mate's Mac. Sometimes my Linux box got lucky. Eventually, the adapter fried the cable modem, at which point they replaced it and it started working.
Speed was much better until last week. I had thought it was due to the rerouting of traffic due to the cables being cut in Eurasia, though that theory felt a bit strange; but lately, the ping to places other than Google has been just awful. iTunes was the least of my worries.
Time Warner Austin? NO DON'T WANT.
How would you immediately reduce military spending? It would put lots of people out of jobs. (Not that I think it shouldn't be done--I agree with you. But you can't really do it immediately.)
This tragedy has nothing to do with gun control. The incident last semester with William Morva could not have been prevented by either more or less gun control; nor can this one.
Please, please stop using this tragedy to support political agendas. No one could have seen it coming, and most students here wouldn't carry a gun to class even if it were permitted.
Virginia Tech is not really a high-pressure campus. Anyway, forcing people into counseling when they're really busy tends to make them more stressed out, not less...
Is that like Space Taxi?
Man, I wish I had better karma, because I've got useful things to say here.
You can check grammar using a well-trained Hidden Markov Model and the Viterbi Algorithm. If I were to design such a program, I would have the part-of-speech tagger have a go at a sentence, and if it came back with a confidence below, say, x, then the sentence's grammar is probably not good.
This is nice because it also helps sentences keep from being awkward.
Perhaps the Viterbi Algorithm would be appropriate for this?
http://en.wikipedia.org/wiki/Viterbi_algorithm
It's used in grammar checkers and part of speech taggers to determine what parts of speech can validly follow others.
I was the president of the computer club in my high school. It never went well. Of course, there weren't many people IN my high school. We never seemed to accomplish anything we intended to accomplish. It kind of sucked, but it was fun getting together and watching All Your Base or other such things.
;-)
Just wait till college, then you'll find yourself pleasantly satisfied.
Yeah, my boxed set has that on the first DVD. I noticed it when I was watching last night.
I could have sworn this movie was an Austin Powers parody. I kept expecting Shinzan or whatever his name was to demand one million space-bucks with his pinky. He even had the little scar.
Aside from that, I rather liked the movie. I have huge problems with plot holes, which Star Trek is generally full of no matter what you do. Ebert's right, Star Trek has problems--but that doesn't make this movie bad, in my opinion.
I was very impressed with Data's role in the movie. Including the sad ending. Nearly broke my heart.
pation.
CircleMUD runs on *nix. http://www.circlemud.org
Joe Barr is not the most reliable of sources. He gave very biased reviews to Xine and MPlayer. I won't say much more than that, except that you should read what they have to say about him at www.mplayerhq.hu.
Not trying to troll, just trying to point out that this guy isn't necessarily a reliable source.
The Four Horsemen of the Apocalypse:
War, Death, Famine, and MICROSOFT.
Our time system is based on geometry, and geometry on our time system. When ancient peoples observed that there were about 360 days in a year they decided to make that the number of degrees in a circle. There are twelve months because it divides evenly into 360 and that's about the number of lunar cycles we see here on earth. The metric system would throw that off completely. Plus imagine all the trig we'd have to relearn.
I've thought about this before.
There were several mistakes that I noticed. For one thing, detectives and cops are practically conditioned to never pick anything investigation-related up without those plastic evidence gloves. The worst one, though, was that at the end Robin Williams sinks when he's dead. But dead people don't sink, they float. Little inconstencies like that which could easily be fixed bugged the shit out of me.
Also, I was hoping Williams would actually be evil, not just a stupid guy trying to escape his guilt. I wanted pinky and the brain evil from him.
Funny that this should come up. I met Senator Landrieu yesterday with my AP Government class (her husband and my teacher coach baseball together). She was a very nice woman, and a brilliant public speaker. She also kept her political perspectives separate from her personal ones. I'm usually very suspicious of politicians but I think she's one people can count on.
.prn. Too easy to abuse.
I do happen to disagree with relegating EVERYTHING bad to
Landrieu is one of the good guys (or girls). My guess is she may secure the nomination for democratic vice president in the next election.
Actually, we learned in family life (sex-ed) today that gender can actually fall somewhere between male and female ("intersexed" persons). See also Jamie Lee Curtis.
What, I'm serious!
Maybe I misunderstood the article, but I thought it said that Microsoft prewrote the letters and sent them to people to sign. Now, I couldn't tell from the article, but were any of these letters exactly the same? All I know is several times I've been asked to protest things like the DMCA and UCITA, and have even been given a prewritten letter to sign and send in. This sounds like exactly like what Microsoft is doing in at least a few states. Granted, it's not good for them to be making the letters appear to be written by the individuals who are signing them...but what is really going on here?
Aciel
aciel@speakeasy.net
Darkchapter.net Free Speech Message Board
I haven't had a problem with Speakeasy. And I've asked--I am allowed to run a server, and I do (the Darkchapter.net Free Speech Message Board). Of course, I'm located in DC.
But from what I know, Speakeasy also has a backup plan even though they're on Covad to keep their users online even if Covad fails. I love Speakeasy.