December 30th, 2016
|02:29 am - DreamWidth|
I have an account there, same username as here.
October 31st, 2016
October 29th, 2016
Today I approved the final page proofs for the paper I've been writing. It's my first first-authorship.
September 12th, 2016
February 10th, 2016
September 3rd, 2015
|10:30 pm - The pretty version of those papers.|
Life got dramatic enough that I didn't post them a month ago. So here they are now, with a bit of attached significance.
A few people had asked what these papers were about. My group did a complete
reannotation of the Drosophila melanogaster genome, using the sixth release of
the genome (the groups that do the sequencing filled in many of the release 5
gaps). We also used the RNA-Seq data from the modENCODE project, to fill
in additional transcripts and non-coding genes that it had previously not been
possible to annotate (previous gene model annotations were primarily protein-
based). This is interesting outside the fly research community for several reasons.
The D. melanogaster is the most thoroughly hand-annotated eukaryotic genome; one
could say it’s an artisanal genome. We’ve found, through the process, that there
are details that experienced manual annotators see that prediction algorithms
miss. However, hand-annotation is labor-intensive and expensive. The rules
than govern how genomes are organized are pretty similar between organisms,
so the hand-annotation of a model organism allows for much more powerful
prediction algorithms for other genomes; if the prediction gets you 90% there,
filling in the rest by hand is much less daunting.
The second interesting detail is the modENCODE data. modENCODE was
undertaken as a pilot project for ENCODE, which aims to identify all the transcripts
made by the human genome, as well as identifying regulatory sites that govern
when and where genes are transcribed. modENCODE was the proof of concept,
and allowed us to fill in a lot of details (distant upstream start sites, unexpectedly
long UTRs (untranslated terminal regions), previously unidentified intron/exon
junctions, lots of non-coding genes that were effectively invisible before this project,
lots of gene merges). Our experience has produced a robust dataset that will
inform the interpretation of the ENCODE data.
The RNA-Seq raw data is hard to understand; it takes a lot of staring before it
stops looking like messy noise. One of our developers, Victor Stretlets, wrote a
tool called TopoView, that translates that data into a robust topographic visualization
(it’s the multicolored track at the bottom of several figures. Each color indicates a
specific developmental stage and/or tissue, and the colored areas indicate genomic
regions that are being transcribed into RNA. That is, where the genes are). He’s
made this tool publicly available.
The second paper concerns what we call “rule-benders”. Most gene models
follow rather rigid rules as to what a gene looks like…but a few don’t. It turns
out that the ways in which rules are bent are well-conserved. For the most part,
if it looks weird in flies, it looks weird in us too. This paper describes those weirdnesses,
thus serving as a resource for people looking at other genomes; when they
see the same weirdnesses (for instance, every organism has exactly one example
of the wackiness involved in the gene Xbp1), they’ll know it’s not a mistake on
August 11th, 2015
|08:20 pm - RIP William Gelbart|
My boss, Bill Gelbart, passed away this morning. He was the head and heart of FlyBase, and one of the grand old men of Drosophila genetics.
I'm told that it was peaceful, and that he was among his family and close friends.
Memorium from the Genetics Society of America
and a essay from our other boss when he was awarded the Beadle medal
August 4th, 2015
|09:41 pm - that thing I've been working on|
I think the first bolus of it might be done.
July 7th, 2015
|12:15 am - airline disparities|
When I fly one of the two airlines I use most often, at security I'm directed to line where I don't have to take off my shoes.
When I fly the other one, I always get the complimentary pre-flight massage.
June 24th, 2015
March 8th, 2015
|12:53 pm - Home from flies|
I've been having an enjoyable and productive Fly Meeting, but I'm looking forward to being home with my housemates, my kitties, and my own bed.
August 11th, 2014
|08:11 pm - I've adopted these kitties|
Despite having my heart set on a big fluffy Maine Coon, I adopted these guys. They're a sibling pair, about 4 years old.( NatashaCollapse ) is the girl kitty; she seems to be permanently a kitten, and is less than half the size of her ( brotherCollapse ) . I adore ( Byron'sCollapse ) ridiculous face. Unlike his sister, who turns her face away when I point a camera at her, Byron ( posesCollapse ) for me.
December 15th, 2013
|09:44 pm - Delerium Rose Darling, returned to the earth|
Today we buried my cat.
pywaket and lyonesse dug the grave for me earlier in the week, before the ground had a chance to freeze; and pywaket covered it with a board before it snowed. lyonesse wrapped her body in silk scarves for me; I couldn't bear to see her body again.
This morning I shoveled the snow from gravesite. My ex-housemates John and Robbie, John's girlfriend Karen, and our friend Katrien came. John and Karen cleared the snow covering the dirt around the grave. lyonesse acted as pallbearer, and also took Delerium out of the box she was in, when it was clear that the sides of the grave had collapsed just enough for it to not fit. I was really glad I'd thought to have her wrapped in silk. I said "She was a good cat, and I miss her" and shoveled in some dirt. John and Robbie finished filling the grave.
We went to my room, and listened to a video I took of Delerium snoring. I'm so happy I caught that, just a couple of weeks before she got sick.
She was a good cat. I miss her.
November 24th, 2013
|03:33 pm - Thank you for all the kind words|
I appreciate the sympathy and support you have all shown me.
|01:33 am - She is gone|
Delerium just died in my arms a few minutes ago.
November 23rd, 2013
|07:36 pm - I think it isn't long now|
She's alert, but not moving, or eating. She doesn't seem to be in pain. I can only be here for her.
November 18th, 2013
|07:33 pm - Delerium update|
For those following the kitty drama...Delerium had a decompensation of her kidney function last week. She was in the ICU of the Massachusetts Veterinary Referral Hospital for two days, receiving IV fluids and antibiotics, and a more thorough kidney workup. Her case is complicated because in addition to kidney disease, for which the treatment is pushing fluid as fast as possible, she also has an enlarged heart, for which rapid fluid pushing is contraindicated. That said, she is over the immediate hump, and is eating, drinking, and peeing again (none of which she was doing late last week). We're going for some more bloodwork tomorrow, and probably an echocardiogram to determine if (1) she'll be helped by subcutaneous fluids and (2) if it's safe to do that.
The vet I talked to when I visited Friday evening says she has a 50/50 chance of making it another year, virtually none of making it two years, and that we're probably looking at 6-9 months. My inclination is to treat her at a level that gives her better quality of life, rather than keeping her going as long as possible.
November 15th, 2013
|10:02 am - Delerium update|
She made it through the night. The overnight vet says she's stabilized somewhat, ate some food, and was a bit "sassy" at being handled.
I'm feeling more confident that I'll be bringing her home at the end of this.
November 14th, 2013
|05:56 pm - Back to vet hospital|
Kidney values bad; vet recommends inpatient treatment.
November 12th, 2013
|12:19 am - Tonight I'm grateful for excellent housemates|
Around 9:00 this evening, my cat developed an Alarming Symptom. Huge thanks to Vicka for excellent guidance in deciding what do, contacting the emergency vet, and coordinating transport, Andy for providing the car, Daniel for driving me and hanging out at the emergency vet for hours, and Pywaket for stopping by the emergency vet to check on us.
(Looks to be a UTI. First dose of antibiotics successfully administered. Ms D completely charmed the emergency vet staff; her discharge letter specifically mentions that "she's a very sweet cat").
October 16th, 2013
|03:31 pm - Seeing Janelle Monae tonight!|
I'm so crazy excited!
Current Mood: bouncy
October 4th, 2013
|01:12 pm - In search of small driving favor|
I need to make a quick run to my vet in the next few days to pick up 3 cases of prescription cat food. If one of my vehicularly-enabled friends has a bit of time in the near future, I'd be very grateful.
-sian & Ms D
September 30th, 2013
|07:02 pm - That root canal I dodged?|
I didn't dodge hard enough.
September 27th, 2013
|10:00 am - I got to snuggle a tiny kitten yesterday!|
Harvard has started having Baaaaby Animal Thursdays at the Science Center Plaza (12:00-2:00); I was having a really bad pain day yesterday, and being able to stop and snuggle a tiny kitten was just what I needed!
There were also a small sheep, some goats, a couple of potbelly pigs, duckings, chicks, and fluffy fluffy bunnies. Really, if you're in need of baaaaby animal therapy, Science Center Plaza, Thursdays 12:00-2:00 will hook you up!
September 6th, 2013
|07:53 pm - adventures in commuting|
I took a nasty fall on my way to work (Somerville has failed to cooperate in putting the uneven parts of the sidewalk in the same places Cambridge does). I landed with my right arm between my ribs and the sidewalk, and have badly bruised (but not broken) a few ribs. By some great good fortune, I had decided to take a couple of bags of plastic bags to recycle at CVS, and at least part of me landed on them.
|05:30 pm - Seeking help with a short errand that would be much easier by car|
I need to take Ms D (my kitty) to my vet (Fresh Pond Animal Hospital) on Saturday Sept 14 at 11:30, for just a blood draw. It should be a very brief appointment. I haven't yet worked out logistics for getting there by public transit from Davis Square, and it would be much easier with a ride.
If someone could drive me & the cat next Saturday, I'd be very grateful (Ms D not so much). Bonus: there's a Pepperidge Farm outlet store next door!
July 12th, 2013
|10:38 am - Do you know of a good mover (Boston area)?|
I've used Gentle Giant, who are excellent but pricey. Does anyone have recommendations for movers they've been happy with?
June 26th, 2013
|10:09 am - committing stupid|
I was halfway to work (on foot) when I realized I hadn't voted. So I turned around to go vote. Giving me just enough extra exertion (for someone both heat sensitive and with low blood pressure) to make me faint as I set back out.
Fortunately, with enough warning to get to the ground voluntarily, but I did have to call in "poorly planned" to work.
April 15th, 2013
|03:59 pm - checking in|
I'm ok and at work, as are my roomies.
January 29th, 2013
|01:38 am - Things my housemate does|
My housemate and his friend designed and baked this Penrose tile mosaic:
November 6th, 2012
|01:03 pm - voted!|
That was longest line I've been in in years that didn't have a special-effects-laden blockbuster on the other end of it.
Anybody want to join me for returns-watching tonight?
October 29th, 2012
|11:58 am - MBTA will shut down at 2PM|
Massachusetts folks who aren't already home, and are T dependent: get home before then!
September 30th, 2012
|07:28 am - Question for the younger ladies|
Younger than me, anyway.
I'm no longer in personal need of menstrual supplies, but I like to have a supply on hand for visitors in need. I'm stocked on everything but pads.
If you were visiting me, and had sudden need of a pad, what would you like to find in my bathroom? I was partial to Always with wings back in the day.
July 4th, 2012
July 1st, 2012
|11:52 pm - I love my city|
As I was coming home from a movie this afternoon, there was a busker on the subway platform, a middle aged butch Asian woman singing Take Me Home, Country Roads, heartbreakingly beautifully.
June 12th, 2012
|12:07 am - Under influence|
Yesterday I saw Prometheus, and also re-watched Remedial Chaos Theory. I've been doing huge amounts of genome reannotation for weeks.
Which made for some thematically interesting nightmares last night.
April 27th, 2012
|12:48 am - Is there anything more adorable...|
Than a snoring cat?
Current Music: kitty snores
November 23rd, 2011
September 11th, 2011
|06:20 pm - We are now with housemate|
Robbie arrived yesterday, and the St. Ellery Home is now fully inhabited.
September 1st, 2011
|10:50 am - Awesome|
I appear to have been located by the anonymous stalkers of a friend.
Anonymous commenting is now OFF in this journal.
August 27th, 2011
|11:19 pm - Boston area peeps: the MBTA is closed as of 8 AM on Sunday|
The T is suspending all service with the exception of The RIDE (and that only for medical emergencies) as of 8:00 AM, due to the impending arrival of Hurricane Irene. Details at http://www.mbta.com
August 18th, 2011
August 9th, 2011
August 5th, 2011
|12:09 am - Mutant and annoyed|
It would be awesome if my mutant ability was reading minds or mastering magnetism.
But no, it's spontaneously dislocating a fucking RIB. And it fucking HURTS.
Current Mood: annoyed
August 4th, 2011
|11:38 pm - car-needing favor|
If any of my car-enabled friends near Cambridge have time, I need a car related favor on Friday August 26.
I'm taking Ms D to have her teeth cleaned at the Fresh Pond Animal Hospital in Belmont. I need to get her there by 7:00 AM, which is daunting via bus. That would be just picking us up at my place and dropping her off. Sometime that evening, I need to retrieve her (time uncertain; FPAH will call when she's ready to leave). I'd also like to not do that by bus, as she'll have been under anesthesia earlier in the day. I don't need to have the same driver at both ends of the day.
If you could be available for either end of the trip, I'd be deeply appreciative (Delerium likely not so much...)
July 28th, 2011
|07:45 pm - My kittie|
Makes the most mournful little meows when I dislodge her from my lap before the lap-sitting part of the morning is over.
July 7th, 2011
|07:33 pm - good hair day|
On my way home from work I was stopped by a young man who went on and on about how beautifully colored my hair it. He's a professional hair colorist from NYC.
I feel validated.
July 5th, 2011
|07:35 pm - Seeking a housemate in Cambridge MA|
Our lovely housemate Anna has successfully defended her dissertation and is outta here. Thus, we are looking for a new housemate.
( Our housemate adCollapse )