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Oct. 27th, 2009 @ 10:04 pm Matters of concern
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• Prices on airfare to NZ are climbing.  I picked the wrong week for the condo; have emailed the owner asking if the same days the previous week (when tix for our desired itinerary are a good $1000 cheaper for the two of us combined) are available.  Fingers crossed!

The SF Bay Bridge is broken.  Thank goodness nobody was seriously injured.  I wonder when it will be reopened?  Thank heavens I'm not trying to commute to the East Bay, but I'm really sorry for everyone who normally uses that bridge.

• Bah, silly minor cold-thing.  Not even really symptomatic, just tired and muzzy.  No fever, and scratchy throat.  NOT H1N1.  

• Bah, work stuff (contamination of cell cultures the last couple of times, failure to construct a couple of rather important vectors.  We'll get it, it's just taking too long.

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tazz
Oct. 12th, 2009 @ 10:32 pm Some random stuff
• Air New Zealand has one flight a day from Christchurch to Melbourne... and it's at 6 AM.  Hmm, rethinking order of New Zealand islands visitation.

• It's started sprinkling.  Go here to read a neat poem about the upcoming storm by my friend nezumiko.  Hope the kitty room in the garage doesn't flood.

• Work is busy but cool.  We will hopefully get a somewhat important result tomorrow.

• Scribblenauts is also cool  (Huz gave it me for my b-day.)  However, I do Not Approve of their opinion of Science (try it as an object, then interact with it!).  Also, it does not know the word terrarium.  Ribosome, I can understand and forgive it not knowing.  However, when it doesn't know the word I typed, it comes up with 2-3 suggestions, of which I often won't recognize one!

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tazz
Sep. 23rd, 2009 @ 05:23 pm News of the weird - Dead fish like humans!
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Ganked from [info]orichalcum , mostly for the benefit of the portion of my friendslist that doesn't overlap with hers:

Dead fish lights up when shown pictures of humans, a study that shows that neuroimaging experiments can give a lot of false positives.

----

In other work-related news:

• We've begun the Big Project that I've been making stuff for, like, a year for!  On a practical level, this means that I do pretty much the same physical actions day after day for probably about the next month and a half, doing a gazillion transfections.  It's tiring, believe me.

• It's nice to have a perfectly sensible explanation as to why a particular cloning didn't work.  It helps to have both enzymes functional in a double digest, just for example.

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tazz
Sep. 11th, 2009 @ 08:15 pm (no subject)
Like [info]ladybird97 , I haven't posted anything of substance in a while.  So, I post!

Work has been going along in a mixed-to-reasonable fashion.  We've got positive expression for enough of our genes to make it worthwhile to start on The Big Interactome Project.  One thing stands in our way: the ELISA that we're figuring on using to detect interactions isn't working.  Again.  We plan to work on the problem next week.  But meantime, just about everything else is ready for launch.

We had a fantastic time over the holiday weekend at the giant gaming party hosted by cerebralpaladin and orichalcum.  We saw a number of people that we hadn't seen in quite some time, and met some new - and of course cool - people.  I played two D&D games: one set in ancient Babylon, in which my thief character helped figure out why it was raining on the Jewish Quarter and nowhere else (everyone else in town was blaming the Jews for stealing their rain - turns out that basically, they were right!), and one in which all the PCs were members of a theatrical troupe.  The troupe put on plays of heroic adventures, and in this one-shot, we had to basically *become* adventurers to get our hands on a kidnapped playwright who'd promised he'd write us a play.  The last game that I played was in a system called "Dogs in the Vineyard," in which the PCs were essentially lawgivers of the One True Faith in something like mid-1800s Mormon Utah.  You can get a sense of the mechanics of conflict resolution from this Wikipedia article and the character creation and gameplay from this review.  It is significantly more freewheeling than any game system than I've ever played before (not that that's very many).  The traits and relationships that you use to define your character have essentially no limits on them in terms of their definitions: "sense truth", "skeptic", "healer", and "joyful celebration" were some of the traits in our group.  Having played a session, I can pretty definitely say that the more vague you can be in your traits and relationships, the better - it means that you can more easily bring the die values of those traits and relationships into conflicts.  It was fun, and I wouldn't at all mind playing in the system again.

We had our first choir rehearsal of the season a couple of nights ago.  We have two new people: a strong bass and a strong soprano.  Having two whole basses to our name makes a huge difference, as does having a soprano who can actually generate volume on Wednesday nights.  I'm really excited about choir this year - we're gonna be goooooooood...... :D

And next weekend we're going to see Spamalot and Yellow Face, both should be good pieces of theater.  I'll be interested in hearing what y'all think of the movie 9; it's on my 'hmm, could be interesting' list.
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tazz
Aug. 21st, 2009 @ 11:00 am If the tech ain't broke, don't fix it!
I've been spending an inordinate amount of time over the past few weeks throwing my ~120 IgSF proteins into Drosophila S2 cells, and running a whole lot of Western blots to figure out which ones are expressed and which ones aren't.

Cut for shop talk )
But now I am at home, on another required vacation day, waiting for the tree guys to finish their work so I can go do stuff. My right arm is pleasantly sore from having played FFT A2 for too long. Opened up the Fusilier jobline!
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ig-fold
Aug. 12th, 2009 @ 08:42 pm Update and vacations
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I haven't posted much lately.  Mostly that's because there's not a lot to post about.  We're around and alive, hosted local Storyreading this past weekend, and might actually get to see HP:HBP this weekend.  I have stupid amounts of vacation to get rid of before the end of August.  As a result, I have not-full weeks of work for like 5 or 6 weeks in a row:

Week of July 26: full day off Friday to watch ice skating
Week of August 2: half day off Friday to get useful things done in the AM
Week of August 9: full day off Friday to spend vacation time
Week of August 16: full day off Friday to spend vacation time; be home while tree work gets done
Week of August 23: half day off Friday
Week of August 30: full day off Friday, 'cuz that's September and my department is forcing me to take it off
Week of September 6: full day off Monday, 'cuz that's Labor Day

Wow.  7 weeks in a row.  I'm going to be very spoiled once September really hits.
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tazz
Jul. 31st, 2009 @ 09:19 am Take that!
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I've spent the week all by my onesies at work, so to speak, as my coworker is on vacation in his homeland of Turkey.  While I can claim to have accomplished certain things (taking care of tissue culture and counting cells, getting genomic-based PCR to work to the point I'll be able to clone stuff next week), I am peeved enough by the various results I got yesterday that I am REALLY GLAD that I get to take today off to go watch people skate.  Ha!  So there!  Work, I shall deal with you next week.
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tazz
Jul. 8th, 2009 @ 01:09 pm Ok, the advertising guys can cool it now.
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Spotted on an Eppendorf product page:

"Eppendorf Research® pro with its unmistakable button nose and merry switch eyes has shown its happy face in many laboratories and so brightened up the tedious daily routine."

Gah.  They'll be selling talking doors next.  Or maybe paying the talking doors to write product descriptions.

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ig-fold
Jun. 16th, 2009 @ 12:15 pm Somewhere out there, someone is wondering...
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...why their sequencing data lines up with Drosophila robo3 instead of whatever they submitted. I'm guessing they're working with (A)H1N1 (the swine flu virus), which is the data I have in my hot little hands.

(Update: I do have to give our sequencing company credit - I informed them of the mixup, and within 15 minutes they'd resolved the problem and gotten my actual data back to me.)
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ig-fold
May. 21st, 2009 @ 05:56 pm Can you count to 97?
Current Mood: accomplished
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I just submitted 97 samples to our local processor for sequencing.  It took quite some time to first draw up the sample sheet then fill in the actual plate!  And it means that I'll have a helluvalotta data to deal with when I get back from vacation.  But that's a good thing - these will tell me if the several clones that I did Gateway transformation of worked.  :)  I'll continue plugging along on this part of the project till all my guys are in the two expression vectors we're using... then it'll be off to the races with actually expressing the guys!

This post also gives me the opportunity to show off my new icon.  (I got it off this page at Wikipedia if anyone's curious.)  It's a so-called cartoon of the structure of an immunoglobulin domain.  This is the common element of all the genes/proteins that I'm playing with - all of them have at least one of these.  If you're curious, I can generally recommend this other page at Wikipedia to find out more about the superfamily of proteins that share this structural motif. 

Now, off to vacation!

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ig-fold
May. 3rd, 2009 @ 02:20 pm Good days
Current Mood: accomplished
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Yesterday was quite productive.  We:

• got taught the steps to our first true ice dance, the Dutch Waltz

• got work done on my car
    This took longer than it was supposed to and I failed to bring anything to entertain myself with while waiting.  So I hung out in the customer lounge and watched a bit of Game Seven of the Boston/Chicago basketball game.  It's the first time I've watched pro basketball in literally decades, and the main thing that struck me was, wow those guys are beefy!  Muscles on muscles in their torsos and arms.  Way back when (in my kiddie memory of Larry Bird and his ilk) I remember that the typical basketball-player phenotype was tall and skinny.  When did that change to tall and burly?

• performed in the voice studio's recital
    Which went quite well, really.  Laurie's Song went at least as well as it's ever gone in practice, ditto the Doll Song.  The Green Dog was fine till the very end when I flubbed the timing.  Pretty much everyone was an active pleasure to listen to - it was really nice!

• had a fence between us and a neighbor built after the old one blew down a couple of weeks ago

And today, I've already done church and we've gone skating.  We need to go over to Stanford so I can pack up some supplies I'll need, take care of the neighbor's cats, and go grocery shopping.  Yes, busy.  But good.
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tazz
Apr. 13th, 2009 @ 01:47 pm Well, that explains a couple of things.
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When you have lots of trouble getting PCRs to work off a supposedly known template.... it's a good idea to double-check the template!
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tazz
Mar. 17th, 2009 @ 01:00 pm Work: progressing!
Current Mood: kinda astonished
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I finally finished trawling through my miles of sequencing data today and started figuring out exactly where I stand with regards to the clones I'm after.  Turns out I'm much closer than I thought I was to having around a hundred of these buggers.  Here's my update, for anyone interested.

Genes that I want: 125

Clones that are picture-perfect (or close enough for my purposes) 79
Clones that are very close (reverse orientation, 1-2 errors to fix) 14

Those groups alone add up to 93.  (7 of the second group are straight fixits and should be very easy; the others are reverse orientation, sometimes with additional errors.)  A standard plate format is 96 wells. 

There's an additional 15 which require additional sequencing, most of which should fall neatly into one of the two above piles.  At which point, we're up above 100 successfully cloned genes - a target which somehow just kept feeling really really far away.  (The remaining genes have issues of various sorts - cloned the wrong thing when I did RT-PCR, don't see a band when I do RT-PCR (or sometimes standard PCR off a known template, etc.)
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tazz
Mar. 16th, 2009 @ 09:52 pm Mostly several varieties of argh
Current Mood: tired and somewhat headachey
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• One of the hymns we sang yesterday is "What a Friend We Have in Jesus." I am less than fond of the words; suffice it to say that they are very Baptist, and I am quite definitely not a Baptist. I was therefore slightly put off to have it running through my head for chunks of yesterday afternoon and large parts of today. (It's a very chirpy, catchy tune. I suppose I could try using "Oh My Darling Clementine" words instead; I realized that these fit the tune equally well.)

• HHMI informed me today that they're really not s'posed to pay for lunches on day trips, and that after this most recent trip to Berkeley, they will cease to do so. Hmph.

• Much of the sequencing data I stared at today was useless: crap data (lots of overlapping squiggly lines for my traces), or inserts going in the wrong bloody way, or annoying errors all over the place.

• Life is made somewhat better by [info]digitalemur 's post of the following animation to Jonathan Coulter's song "Mandelbrot Set," of which I'd never heard before. Enjoy! (NSFW; uses the F-word to describe the coolness of a fractal)

</lj>
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tazz
Feb. 27th, 2009 @ 03:40 pm All ready!
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I spent today organizing little tubes and making lists.

I've spent large portions of the last couple of months doing PCR mutagenesis and subcloning (and in the last couple of weeks, some RT-PCR too).  I now have 40 different tubes of DNA to bring up to Berkeley to do sequencing.  Once I get there and start doing transformations, they'll turn into 90 transformation tubes - that's, um, kind of a lot. 

Those will turn into 40 agar plates with colonies, which will then turn into 4 96-well culture blocks, which will become 8 sequencing plates.  I will be very busy while I'm there.

*sigh* Well, I did want to be really productive while there, so that I wouldn't have to go up too often.

And now it turns out that I may have to make up some antibiotic here to bring up as well.  Maybe I should do that now so that I have it on hand if it turns out I need it. I can always store it in the freezer long-term if I end up not having to bring it to Berkeley.

Oh, and [info]nezumiko , I'll be free Friday afternoon 3/6.  You?

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tazz
Feb. 10th, 2009 @ 09:57 pm Good things
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• I got back DNA sequence data that confirmed that I have FINALLY finished making a particular expression vector that we've been working on for what feels like ages, and which will allow us to forge ahead on our experiments.  (That's what the bizarre "5mer-Gateway-AP" message in my Gmail chat profile was referring to, for anyone who wondered.)

• There was a box with See's chocolates in the lunchroom.  Not only that, but I picked out what was either a raspberry or a blueberry-filled chocolate.  Yummy!

• After clearing out a lot of the trees in my first two attempts on Inner Yoshpet to the Spirit Gate, Huz was kind enough to finish the run for me.  Thank you, Huz!!!!!! (I could probably have done it in another trial or two, but I needed a break.)

• Bedtime now!  Hope we sleep well, while it rains.  Yay rain!
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tazz
Jan. 28th, 2009 @ 08:34 pm But I read icanhascheezburger today...
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and I discovered this, which I think I need to print out and post at work:

funny pictures of cats with captions
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tazz
Dec. 11th, 2008 @ 10:07 pm Happy thing
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I am DONE with going to Berkeley on a daily/near-daily basis!  DONE DONE DONE I tell you!!!!

(Will still hafta go up for a day every so often.  But hey.)
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tazz
Nov. 19th, 2008 @ 10:02 pm Gmail themes
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Wow, Gmail has *so* taken a page out of LiveJournal with all these new themes they've got going.

Also, if one tries to do *everything* in the PCR cloning protocol in one day, you're at lab for a good solid 9 hours. 

.. In Berkeley.
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tazz
Oct. 30th, 2008 @ 07:08 pm Still not dead, despite appearances
Current Location: home!
Current Mood: exhausted
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Note to self:

Do not bother leaving Berkeley for the peninsula anytime between probably around 4:30 and 6 PM.  That is rush hour, and traffic will be iggy.

Door-to-door time this evening: just over 2 hours.  Ick.

My apologies to everyone who's had interesting/pleasant/need-help entries in the last while.  I feel like I do little beyond drive, work (with minimal computer/net access), and sleep these days. 
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sleepy tazz

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