Cool Science: Crowdsourcing Big Data

Anyone who knows me at all knows I really like data.  It’s a tremendously nerdy interest, but I find data really fascinating, I guess in part because I love the idea that there is some great knowledge that’s hidden in the numbers, just waiting for someone to come along and dig it out.  What’s very cool is that we live in an age when technology allows us to generate massive amounts of data.  For example, the Large Hadron Collider generates more than 25 petabytes a year in data, which is more than 70 terabytes a day.  A DAY.  Some data analysis can be done by computers, but some of it really has to be done by people.  Plus, some studies really rely on the ability to gather data from massive groups of people in order to get an adequate sample from various groups to prove what you’re trying to show.  To solve these and other “big data” problems, some very smart and cool research groups have jumped on the crowdsourcing bandwagon and are having people from around the world get online and help solve the problems of data gathering and analysis.  Here are some cool projects I’ve heard about.

Eyewire: a group of researchers working on retinal connectomes at MIT found a fascinating way to get people to help with their data analysis – turn it into a game.  They have a good wiki that explains the project in depth, but the gist of it is that these researchers have microscopic scans of neurons from the retina.  Neurons are a huge tangled mess, so their computers could figure out how some of them fit together, but it really takes an actual person to go in and figure out what’s connected and what’s not.  So this team turned it into this 3D puzzle/game thing that’s really hard to explain unless you try it.  You go through a tutorial to learn how to use the system, and then you’re turned loose to start mapping neurons!  It’s not like the most compelling game I’ve ever played or something I’d spend hours doing, but it is interesting, and it helps neuroscience, so that’s pretty cool.

Small World of Words: this study aims to better understand human speech and how we subconsciously create networks of associations among words.  To do so, they set up a game to gather word associations from native and non-native English speakers.  Again, I wouldn’t necessarily call this a game in the sense of “woohoo, we’re having so much fun!” but it is kind of interesting to see what your brain comes up with when you’re given a set of random words.  (Plus it’s perhaps a little telling of your own psychological state if you really think about the words you’re coming up with.)  It takes like 2 minutes to do, and again, it’s contributing to science!  Also, according to their website, they are making their dataset publicly available, which as a research informationist/data librarian I wholeheartedly endorse.

Foldit: I haven’t played this yet, so I can’t speak to how fun it is (or boring), but it sounds similar to Eyewire in the sense of being a puzzle in which the players are helping to map a structure – in this case proteins.  Proteins are long chains of amino acids, but they fold up in certain ways that determine their function.  Knowing more about this folding structure makes it possible to create better drugs and understand the pathology of diseases.  For example, one of the things this project is looking at is proteins that are crucial for HIV to replicate itself within the human body.  Better understanding of the structure of these proteins could help contribute to drugs to treat HIV and AIDS.

So I encourage you to go play some games for science!  Do it now!  And if you’re at work and someone tries to stop you, just politely explain that you’re not playing a game – you’re curing AIDS.  🙂

Holiday Traditions for the Librarian in the City

As most readers will know (or will probably have surmised from the many, many posts about my dog), the Librarian in the City is a solitary city dweller.  With the holidays approaching, I’ve been trying to get into the spirit, but it’s not the same when it’s just you and your dog.  Back in my early 20s, when I got my first solo apartment, I was very excited because I was going to get my very own, REAL Christmas tree.  As a child, we’d had real trees when I was young, and I just adored the smell of the Christmas tree in the house.  But later, we stopped having a real tree and switched to a realistic, but fake tree.  I know that’s probably better than cutting down trees, plus my brother had asthma, so he couldn’t take the real thing, but as a little girl I was so disappointed that we wouldn’t have that awesome pine tree scent ever again.  So from that time, I became bound and determined to have a real tree the first time I had my own apartment.

I did just that the first Christmas I had my own apartment when I was 20 years old, during my first year of grad school.  On a blusteringly cold evening when I didn’t have class, I went to the only place I knew to buy trees in that small college town.  It was starting to snow, and I got myself the tiniest, ugliest little tree.  It was probably about 6′ tall, but I didn’t have a very big apartment, and also, I was going to have to carry it up two flights of stairs by myself.  So I got the tree into my Honda Civic, carried it up the two flights of stairs, and put it in my apartment.  It smelled very pine-y and I was extremely happy with it.  I covered it with lights and ornaments in purple and silver.  For a couple weeks, things went well with the tree.  I didn’t have many guests, so it wasn’t like anyone really saw the tree but me, but I was so happy when I walked in the door coming from class, and there was my Christmas tree!

However, I watered it dutifully, but within a week or two it had started to drop needles.  I vacuumed.  I vacuumed some more. Finally Christmas came and went and it was time to get rid of the tree.  I’d purchased a huge bag that went under the tree, so in theory, when it was time to dispose of the tree, all I had to do was take all the ornaments off and then just pull this bag up around it.  Well, that didn’t go so well.  Needles ended up everywhere.  There were so many needles on the floor that I don’t even know how any were even left on the tree.  I swear, I was still vacuuming up pine needles in May.

So needless to say, I didn’t get a Christmas tree again after that.  However, I do want to feel like I’m in the holiday spirit!  It’s especially difficult living in Southern California, where the average temperature in December is 68 degrees F.  Not exactly the kind of weather that makes me think “holiday” for a girl who grew up in Dallas, where I even once had snow on Christmas!  I don’t really watch TV, so I’m not seeing all the holiday commercials, and I don’t really go out shopping, so I don’t see all the holiday stuff in stores.  It would be easy to overlook the fact that it’s the holidays up until the moment that I get to my parents’ house for Christmas.  So, in the absence of the usual holiday rituals – group celebrations, meaningful decorations like trees or menorahs, and what have you – here are some of the holiday rituals of this nerdy little librarian:

  •  “holiday” movie marathons.  I put “holiday” in quotation marks because the movies I associate with the holidays are probably not even remotely like what most people would consider holiday movies.  Some of them include:
    • The Lord of the Ring trilogy: because these came out around Christmas, I’ll always think of these as holiday movies, even though there is nothing remotely holiday about them
    • The Harry Potter….hepatology?  series? ouevre?  Whatever.  Same reason as the above, at least for the first couple movies.
    • The Girl with the Dragon Tattoo: yup, same reason.  Saw it last year at the holidays.
    • Kiss Kiss, Bang Bang: this does take place not only around Christmas, but also in LA!  It’s a totally demented dark comedy, but I love it.
  • painting my fingernails with extremely glittery nail polish.  I used to work at Crate and Barrel, and like 90% of the Christmas ornaments we stocked had glitter, so I spent the months of November – December perpetually covered in glitter for the 5 years I worked there.  So when I think holidays, I think glitter!  Plus, December means the end of the quarter at work, and thus not much interaction with students, faculty, or anyone that I need to think of me as a Highly Professional Research Librarian Type, so I feel like glitter nail polish is more acceptable. 🙂
  • burning my Evergreen candle from Bath and Body Works.  This is a $10 candle that smells even better than any real tree ever did, and it can be carried into the apartment in my purse, rather than having to be hauled up the stairs like a dead body as I did with a real tree.
  • listen to holiday music, but I’m picky.  Since I’ve worked in retail for a total of almost 10 years, and in restaurants for 2, I’ve heard enough traditional holiday music that I would rather strangle someone with my bare hands than listen to some of that stuff again voluntarily.  For that reason, last year I devised a holiday music playlist on Spotify that I called “Holiday music that doesn’t make me want to kill someone.”  It’s a lot of really cool indie artists doing some decent Christmas/holiday music, if you’re into that kind of thing.
  • drink eggnog!  I usually just have it straight out of the carton.  That is to say, straight without any alcohol added – I am putting it in a glass and not drinking it straight from the carton.  I like it in coffee.  And every once in awhile, I do add a little bit of alcohol to it, usually in the form of 44.  I’ve not had any yet this year, so I must get some next time I go shopping.
  • buy my dog Christmas-themed toys that she will disdain and totally ignore.  This is because she disdains every toy that she is ever given, with the exception of this exact squirrel.  It is first toy I had for her when I got her, and it’s the only toy she will recognize.  I call it Squirrelly, and after just over a year, we’re on Squirrelly Number 6, with Number 7 waiting in my closet (yes, I buy more than one at a time now).  She plays HARD with Squirrelly.  So if you ever feel inclined to get Ophelia a gift, I advise that it either be a.) made of meat or b.) Squirrelly.

This is how rough Squirrelly looks when you buy him, right off the shelf. Imagine how he looks after three months with Ophelia.


So those are my holiday traditions!  How about you, my dear readers?  What kind of nonsense are you getting up to this holiday season?


On Singing, Showers, and the Politics of Neighborly Relations (Plus Music and Movies!)

The title of this blog is of course Librarian in the City, so tonight I’m going to deal more with the “city” aspect of that moniker. 🙂  Since 2009, I’ve lived in LA.  I’ve been in three different apartments, but each has always meant living in very close proximity to people.  Often loud people.  Frequently drunk people.  I think several mentally ill people.  At least it was always interesting.  But my frustration with my neighbors has perhaps made me hypersensitive to being loud in my own apartment.  Apartments in LA are very close together, and since most of us lack air conditioning, and the weather is perfect nearly year-round, windows are always open.  So sometimes it feels like your neighbors’ party is happening in your bedroom.  Or your neighbor’s awkwardly personal conversations is right at your kitchen table.  So I assume if I can hear them so easily, they can probably hear me, too.

One of the things I would totally do if I didn’t have to worry about neighbors overhearing: sing in the shower.  I’m thinking of this after watching the latest Woody Allen film, To Rome with Love on my last flight from Dallas to LA.  I’m sorry to say that even in such a captive situation, it didn’t hold my interest and I didn’t watch to the end.  It may well be that Allen can never do anything that will surpass Midnight in Paris for me, because it is honestly one of my favorite films of all time, about my favorite city, and I would SO love to have the plot of that movie happen to me. 🙂  However, one part of To Rome that I did really like – the character who is a fantastically talented opera singer, but only when he’s in the shower.  As Woody Allen’s character points out in the film, it’s true that we all do seem to sound better in the shower.

I do love to sing – I used to sing in the Women’s Chorus of Dallas before moving to LA, but never found something like that in LA.  If I didn’t have to worry about it, I’d sing in the shower all day long, but in an apartment, I don’t feel like that would be very polite.  I had some crazy neighbors at my old apartment who would sing a lot – well, sing is putting it very politely.  It was more like…moderately tonal screaming, I guess?  I would hate to be that neighbor, so I have thus far refrained from singing in the shower (especially since I think I am one of the earliest up in this whole building).  However, sometimes you need to sing a little, so I have been doing it (quietly) while I work on stuff tonight.  In case you’d like to hear some good music and sing along with me, here’s my (in progress) Spotify playlist.  Some of it might surprise you, and it’s not all very good quality music artistically speaking, but it’s all stuff I like to sing along with.

So what’s your take on neighborly relations, my dear readers?  Would you sing in the shower with neighbors in close quarters?

A Book Review: The Confidant

I read a lot (as you may have surmised from last night’s post), and I’m also trying to blog more, so perhaps now I will inflict a book review upon you, my dear readers!  After all, I’m a librarian, so I’m supposed to talk about books, right? 🙂 My latest read was a novel called The Confidant by Helene Gremillon, which I guess I might describe as a sort of insane World War II-era romance set in France.  I bought this book at the Tattered Cover, a very cool bookstore in downtown Denver, when I was in town for the Digital Library Federation conference.  I wandered in with no particular book or even genre in mind and just looked around at what was new and recommended.  This book was one of the four I walked out with.

The story itself does veer perhaps a bit into soap opera territory in its drama, but I liked the mystery it built.  For toting around when you’re running from one flight to the next, it’s quite nice.  It starts when Camille, a French woman whose mother has just died, starts receiving strange letters addressed to her from a man she’s never heard of.  The letters tell the story of a young couple right before World War II and all the really crazy stuff that happens to them, and Camille has to figure out who these people are,  why this guy is sending her letters, and how she’s connected to all of this.  At a certain point it becomes a little predictable, but it’s a well-told, and interesting, story.

The main reason this book won my heart is that it’s got unreliable narrators all over the place.  I wrote my master’s thesis on unreliable narrators, so I always love when I stumble upon a piece that manages to use them well.  If you’ve never heard this term before, it refers to first-person narrators whose story cannot be trusted for some reason – mental illness, youth or age, drug or alcohol impairment, or just the fact that they’re lying.  I wouldn’t call this particular book serious literature, but at least in the sense of making the story surprising, I find the author’s use of her various narrators to be very well done.  Each of them tells their different stories, and every one sounds true and sincere, though in the end the narrators are all revealed to be bending the story for their own reasons.  What I love about unreliable narrators is that I think that life really is like that – you could take two people and ask them the story of their relationship, and they would probably say very different things.  Even without meaning to, people just notice different things and have a different viewpoint, so no two people would tell the same story.

So there you go!  The Confidant gets the librarian’s endorsement!

The Librarian’s Strange Bedfellows

Strange bedfellows

When it comes to books, I’m afraid I must confess to be non-monogamous.  I usually like to be reading some combination of a variety of types of books: fiction, non-fiction, some sort of self-improvement (yoga or philosophy or something), and some sort of textbook.  And now that I have a nice queen size bed as a result of a very nice Christmas gift from my parents last year, the side I don’t sleep on is often full of books (and dog!)  Especially since I’d been sick recently and spent essentially two days in bed, a lot of books piled up there.  So in case you’ve ever wondered who a librarian shares her bed with, they are:

1. Sex on the Moon by Ben Mezrich: despite its salacious title, this is actually the true tale of the theft of moon rocks, evidently “the most audacious heist in history.”  Haven’t started this one yet.

2.  When She Woke by Hillary Jordan: only just started this one too, but it takes place in a dystopian future in which people’s skin is dyed a color to match the crime they’ve committed.  Bought this one at the Tattered Cover when I was in Denver – love that place!

3.  The third book in the stack is actually my journal, but it was in the bed so I tossed it in the stack so it wouldn’t feel left out. 😉

4.  Thus Spoke Zarathustra by Friedrich Nietzsche: a good friend is always quoting Nietzsche to me so I decided to give it a try, and so far I love it.  Going all former-English major and highlighting my favorite passages.  This is why I can’t generally check out library books!

5.  Neurogastronomy: How the Brain Creates Flavor and Why It Matters by Gordon M. Shepherd: this is very science-y and probably wouldn’t appeal to your average foodie, but for the nerdiest of foodies, it is quite fascinating.  It’s very complicated, but the way I’d very briefly summarize it is to say that flavor is actually mostly neurologically occurring in the nose, though we perceive taste as being in the mouth.  It’s complicated but very interesting.

6.  Basic Neurochemistry by Siegel et al: well, you know, a girl needs a little light reading too. 🙂  In my work as a medical librarian I’ve become very interested in neurotransmitters and am learning all sorts of interesting things about research going on in this area, so I figured why not see what I can find out for myself.  So far some of it is over my head and I skip it, but I’ve learned some interesting things about how neurotransmitters work.

So that’s what I’m reading!  What are you Internet folks enjoying these days?  I’m always looking for a good book to add to the list!

Who Rescued Who: Bad Grammar, True Sentiment

A little more than a year ago, I met the girl of my dreams. That’s her in the picture above, my very sweet dog Ophelia.  In this picture, she’d been in this spot for almost two days straight while I was sick in bed, just staying by my side.  The last year of my life has been pretty big, with lots of things going on at work and in other aspects of my life, but I think the most significant thing to happen to me was the journey that Ophelia and I went on together.

I’ll start by saying I’m partly writing this post to encourage people to get rescue dogs, when it’s feasible.  Having a rescue dog is not always easy.  There’s a lot of unpredictable behavior, some apologizing to people, many hours spent training.  All the dogs in my family right now (3 in total) are rescues, each with their own crazy little quirks, and I’m pretty sure all of us have wondered at times if we had made a mistake in adopting these dogs.  But I think we would all agree that these three little beasties, as troublesome as they can be at times, are really the best things that have happened to us.

When I was looking for a dog, I really wanted a hard case.  I started my search looking for a black dog, because I knew of “Black Dog Syndrome” – for various reasons, black dogs are way less likely to be adopted (plus I wear mostly black, so hey, black fur works! ;)) .  I knew I had found a very interesting dog when I stumbled on Ophelia’s listing on Petfinder.  I watched her videos and I could immediately tell she was super smart, cute, and playful.  The first time I met her in person was when her very awesome foster mom brought her to my apartment.  Ophelia jumped up on the counter to check out my kitchen reference books (yes, I’m a librarian, so I do have a reference section in my kitchen).  Then she rolled over for a belly rub.  Then she chomped at me!  I was in love.

I saw the pictures of her injuries later – the metal plate in her femur, the way she stood looking at the camera in the utmost despair, pain, and fear.  I cried when I saw that picture.  I’m still not quite clear on exactly Ophelia’s past is, but I know it was very awful, so I’ve tried my hardest to give her the best life I can. And I’ve been rewarded with the most cuddly, adorable, sweet little dog anyone could ever ask for.  What makes me feel even more honored is that she rarely shows this side to people.  There are many people who’ve known her for a long time who are still even afraid of her.  She didn’t trust me at first either, but now, she sleeps with her body stretched along my legs, or her chin resting over my ankles.  Right now we’re in the chin-over-ankle position.  And to think, two years ago at this time she was living on the street with no one to love her.  I can’t think of a better way to have spent the last year of my life than on Ophelia.

It wasn’t always easy to come this far with her, but every challenge has been worth it.  So again, I urge you, if you can, to get a rescue dog!  There is nothing like the love you will get from such a dog.  I’ve had many dogs, so I can say this with authority – you will never feel love more truly or deeply than from a rescue dog once you earn its trust.