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Category: science

07/10/08 05:51 - 75ºF - ID#44920

Linkage Disequilibrium Blocks/Triangles

I just had a zen moment in the interpretation of Linkage Disequilibrium Maps. (Also called LD maps, LD blocks, LD triangles - take your pick.) Turns out I was actually sweating 1st grade stuff!

I found that NO ONE explains this EXTRAORDINARILY SIMPLE thing in their umpteen papers, reviews, tutorials and what-nots. I just want to post this here so that when people google this simple little question, they find an equally simple and straight-forward answer!

This is an example of what a very small section of a Linkage Disequilibrium Map or an LD Map looks like.

Concentrate on the upper part of the map.

The thick blue line represents a strand of a chromosome. The white bars on the blue line of the chromosome are SNPs (Single Nucleotide Polymorphisms) that have been identified and sequenced. This means that we know what initial Nucleotide base has morphed into what final Nucleotide base. (Thus making it a polymorphic locus - or a position on the chromosome that exists in more than one form. The two forms are the intial nucleotide base and the final nucleotide base.)

These SNP locations or loci are labeled in this picture as 1, 2, 3, ... and so on. Each of these SNPs has a name that starts with rsXXXXX where XXXXX is some numeric code. Each SNP is represented by a labeled grey triangle below the thick blue line (the chromosome).

The purpose of an LD map is to tell us whether any two given SNPs are INHERITED TOGETHER in an offspring. In other words, we want to know if any two given SNPs are in Linkage Disequilibrium.

An example: Are say, SNP #5 and SNP #9 in linkage disequilibrium? You trace down the column leading from grey triangle #5 or SNP#5 (Name: rs2299433) going toward SNP #9 (rs2237717). Do the same for SNP #9 going toward SNP #5.

The square in which the columns leading from SNP #5 and SNP #9 intersect is the one you should focus on. I have encircled it above. As you can see its a LIGHT RED and has a number, 75. Thus SNP#5 and SNP #9 have a correlation of 0.75 and are in fairly high linkage disequilibrium with each other.

In simple terms, if your square of focus is a deep red, then the two SNPs you are interested in have the highest correlation with each other and have a highest Linkage Disequilibrium. Thus, one of them can easily act as a proxy for another. The lighter the shade of red, the lesser is the correlation between the two SNPs. For example, SNP #5 and SNP #7 have a low correlation (0.32) with each other. Thus, you cannot reliably take SNP #5 and say that it could possibly act as a proxy for SNP #7.

LD Maps also tell us about HAPLOTYPE blocks. See the blocks labeled, "Block 1 (49kb)", "Block 2 (23kb)", "Block 3 (93kb)" ... and so on.

These triangles or the blocks of dark red represent SNPs that are all in high linkage disequilibrium with each other and thus are all inherited together. They are also on the same section of the chromosome. These SNPs form a HAPLOTYPE. Every big red triangle or block in the LD map indicates a HAPLOTYPE on the corresponding stretch of the chromosome above. You only need to look at one or maximum a couple SNPs in a haplotype to know about the fate of the entire section of the chromosome that forms a Haplotype. It saves money and time.

The HapMap Consortium project has painstakingly constructed such an LD map for each and every known SNP in the entire human genome. Their LD maps look somewhat like this (using the haploview software: )

Though it is complicated, if you followed the simple tutorial above, you should be able to make sense of even complicated maps such as these. You are most welcome to leave a comment or drop me an email if you need further clarification!

I don't care who is laughing at this ridiculously detailed explanation of a kindergarten concept in genetics and genomics. Personally, I am just EXTREMELY relieved to finally know it well enough to be able to explain it. :)

Permalink: Linkage_Disequilibrium_Blocks_Triangles.html
Words: 714
Location: Buffalo, NY
Last Modified: 08/28/14 06:01

Category: i-tech

07/09/08 08:40 - 74ºF - ID#44915

Nifty Research Tools and Software

I found a host of nifty and useful research tools out there that are totally worth sharing multiple times. These might be just the life-savers, organizers and new-idea germinators that graduate students and serious researchers are looking for. Can't guarantee that they would make your life easier though...

1. Keep tabs on what's happening in the peer-reviewed research world. From the website:
Discussing and Creating Peer-Reviewed Research: Research Blogging

Do you like to read about new developments in science and other fields? Are you tired of "science by press release"? Research Blogging is your place. Research Blogging allows readers to easily find blog posts about serious peer-reviewed research, instead of just news reports and press releases.

The RSS feed is here:

The real question is however, just how many RSS feeds can one read before it turns into an unmanageable information overload and just becomes toxic??

2. Making a Checklist and sticking to it: The Tada list

It has a very simple interface that I use to make a checklist of things I need to do everyday. Finishing the tasks on the list actually is very satisfying. I find that the more I use it, the more disciplined I want to be in my reading and work goals. I know I can very well make lists on paper. But if I use an online interface (a) I don't have to worry about losing my lists, (b) I can access and tick off my list from anywhere (Well, almost. Any place that has net access). (c) Save paper! (d) copy out the list if I need to be in a really remote location, or maybe a conference.

3. An excellent comparison of Reference Managers: This is an exhaustive wiki about all the reference managers out there. Some of them are free, web-based and help you access your references anywhere and anytime. The next time that dreaded hard-disk crash happens or worse, your laptop or USB drive gets stolen, you don't have to worry about your dissertation references anymore. I currently use RefWorks - that is free via my University and via Roswell. However, I am actively exploring other free and open-source alternatives such as:
-- Connotea from the Nature Publishing Group ->
-- Zotero - a Firefox Extension for Reference Management ->

4. Synchronizing Notes, PDF Annotations, Anywhere, Anytime: Note-Taking Software Comparison: If you print out PDFs just because you can't mark them up online/on-screen, there is help! By using some of these FREE note-taking software you can mark and highlight those PDFs on-screen, avoid all that paper clutter and save all those reams of paper (and trees). I currently use Jarnal - a platform-independent, open-source, free Java-based note-taking software ->

Options. Options. So many Options.

Permalink: Nifty_Research_Tools_and_Software.html
Words: 477
Location: Buffalo, NY

Category: heroes

07/07/08 08:15 - 85ºF - ID#44897

Three Cheers to E:boxerboi

My current inspirational summer hero is (e:boxerboi). He is taking on the formidable MUSSELMAN TRIATHLON CHALLENGE!!! this weekend!

You could walk by his office and not notice the absolutely cool bloke who works there. But beneath his calm and almost zen-like efficiency lies the makings of a genuine hero! While lesser souls on the third floor show varying degrees of wimpiness and run around in circles, (e:boxerboi) quietly comes by and conquers the world! Like a true hero, he has a magically unceasing and very much hidden stash of some very lethal weapons.

1. Chuckles

2. Blueberries

Don't underestimate the power of these weapons of choice. They are jam-packed with massive undercurrents of overwhelming charm. Needless to say, I have been totally swept away and I hereby appoint him the

Hero of the Extreme 3rd Realm of Planet K

Join me in wishing him all the very best of luck in his mission to conquer the Musselman World not once, not twice but a WHOLE THREE TIMES!!

THREE CHEERS to you, (e:boxerboi)!!! You ROCK!!!

Permalink: Three_Cheers_to_E_boxerboi.html
Words: 184
Location: Buffalo, NY

Category: eating out

07/04/08 12:05 - 69ºF - ID#44858

Subway. Finger-licking Freedom.

I know I am mixing up punch lines and writing a blasphemously laudatory post about a fast-food place, but Subway deserves my respect in so many ways! I am not being paid an obscene amount of money for an ad campaign or miraculously losing bucketloads of adipose tissue by eating here but this chain has rescued me from many a day of hypoglycemia and certainly prevented me from turning cannibalistic. In due recognition of its consistent and gastronomically positive contributions to my life, I am going to do a (e:Drew)-style 10 things I like about Subway here:

1. It's the most healthful food you could eat if you are without access to your kitchen or in a tearing hurry or just poor.

2. If you wisely pick your sandwich (and yes, I do mean the veggie sandwich. I don't care what all you carnivores out there think. The veggie sub rocks your socks off!) you get a very balanced meal.

3. They have a superlative item on their menu that I can easily zone in on (the creatively but wrongly spelled Veggie Delite Sandwich, what else??!!). This eliminates my aimless-vacillation-time (AVT). AVT is the eternity that I spend making food decisions while people's heads around me explode with pent-up frustration at my indecision.

4. You get UNLIMITED veggies for a fraction of the money that you might spend for a similarly loaded meal elsewhere in the whole city. I regularly test out if the "unlimited" part of the veggie deal is true and almost invariably the place passes my exacting standards of veggie greed with flying colours. The Chippewa Subway also has BABY SPINACH! 'Nuff said.

5. The bread choices are delicious. And most of them are super healthful. The honey-oat bread is a gustatory dream with its chewy delicious texture and is an awesome boost to your daily fibre intake.

6. If you say the magic (and secret no more) word "double toast", you can get your bread of choice toasted *twice* to a glorious rich golden brown delicious scrunchy heavenly colour. I am running out of elaborate adjectives to describe how perfect the double toasted bread is. Everything tastes about a million times better with a double toast!

7. You could get cheese on your sandwich and not only benefit from all the amazing proteins and calcium, but also make your sub 10x tastier.

8. The wait time between your order and the first morsel reaching your mouth is ridiculously low. Since you can watch your sub being built, it's even shorter and livelier. It's almost sandwich-making-by-proxy; calming and fun! You don't have to sit at a table and wonder whether the kitchen ran out of tomatoes and are as a result raising them from the ground or direct a contemplative and lifeless stare at at your companion's hand with the eminent possibility of chewing it off in a demented fit of hunger.

8. The sub arrives and it's time to pay the bill. The price is so reasonable that it blows your mind. After aeons of being overcharged at every single place that is half as comparable to the Subway, you cannot believe that the fabulous piece of divine contentment you hold in your hands only costs \$2.49 for a six incher and \$5 for a footlong! If you have foupons, the cost is cut by a further \$0.50 to \$1.

9. There is no presumption or discrimination at a subway. It's the only place you feel equally at ease chatting up the stressed businessman who has dropped by for a quick bite or the bag-lady from the greyhound station who wants to stretch her last dollar for a substantial lunch. The subway is an oasis of socialism even within a capitalistic framework.

10. You could ask that your sub be loaded up with a truckload of Jalapenos and not have the person serving you give you the look of death or a disgusted stare.

On July 04, 2008, to me, the subway chain represents one of the many facets of freedom that this country lavishes on its residents - citizens or not.

Permalink: Subway_Finger_licking_Freedom_.html
Words: 669
Location: Buffalo, NY

Category: art

07/03/08 01:20 - 76ºF - ID#44844

Yesterday

I had a splendid time at the concert yesterday and I am more than convinced that sighting 5 (e:peeps) in one day is the secret recipe to that day's quota of perfect happiness. If the (e:peep) sighting number (EPSN) shoots up to more than 5, the levels of euphoria increase exponentially. I often experience it after (e:) strip parties. I catch myself unconsciously grinning ear to ear for more than 24 hours at a stretch.

The weather was so perfect that the popular song by the Carpenters got stuck in my head. I had to listen to some angry flamenco rough and raw music to erase that ridiculous song. The first (e:peep) sighting was of course (e:imk2) at work. I thought it was weird that she was tip-toeing it into the printer/mail room. I actually checked to see if she was wearing new shoes and had a shoe-bite or something. I learned later that she had been risking her life and limb by going in there. Apparently, a huge wasp was hiding in that room somewhere and the chair of the department had been trying to swat it dead. I am super glad I didn't see it. Who knows what I might have done to (e:imk2) with my tendency to throw extreme drama freak-outs. I saw (e:boxerboi) on the way home and we had a very soul-purging talk about how high-school has an annoying tendency to persist sometimes. :)

I persuaded a couple of my friends to walk to the concert but I omitted to tell them that it was a good half an hour's brisk walk from downtown to Bidwell. We were somewhat dehydrated by the time we reached the concert venue and dashed into Cafe Aroma to get something to drink. A bloke dressed as a huge Target dog entered and in a proper touristy fashion, we got all excited about being clicked with **the target dog**. However, before we could shoot, the target dog made a beeline for the bathroom and was decapitated by his target-mates. It was probably the most disappointing moment of the evening.

We ran into (e:James) at the Bidwell crossing. I was all worked up about missing the photo-op of a lifetime with **the target dog** and all I could remember was (e:James) had been recently promoted to a power position as a deputy commander of something political. That title stuck and I had to struggle not to introduce him as "The deputy commander!". A second title of "James, the terrible (multi-translation poet)!" suggested itself, but I choked that one down as well. Instead, I introduced him to my friends as a "very powerful politician". I could see (e:James) through my peripheral vision looking at me as if I were from planet loony but it was too late! I admit that it was a desperate and poverty-stricken moment for my brain and those are the times I say the weirdest things. So, you all better tell me in advance what you would like to be introduced as! Your profession choices range from God of the Mountains to Ruler of the Land of the Dead. Take your pick.

We finally made it to the frontlines and plonked down on the grass. The Buffalo Philharmonic played some very popular tunes in full regalia.

However, this charming young couple stole a huge chunk of BPO's limelight by waltzing away in abandon in front of the stage. Their dance became more elaborate with every song and my friend and I were half expecting them to break into some crazy whirls and rock and roll dancing...

That didn't happen. At the intermission, I was somewhat bothered by the fact that I could probably never play this cello because it was taller than I was.

A thousand kids invaded the space in front of the stage. The concert was triple the fun just because of these little dancers. :)

However, some stuffed up people were bothered and the primary conductor tried to rein in their exhuberance for a couple songs.

But thankfully, was not very successful. :)

This pretty young artist from Williamsville High School played as part of a scholarship to the BPO. Her oboe solo was pitch perfect and wonderful. I think her whole family was in the audience to cheer her on. It was very sweet.

They had a raffle for this HUGE (and somewhat scary looking) stuffed dog sponsored by Target. No one claimed it for a very long time after the announcement.

I was sorely tempted to go up and lie my way into getting it. It might have made a fabulous chair and totally made up for the missed photo-op with **the target dog***. Much to my disgust, I found that I did have a sneaky little conscience that prompted me not to pull off the smooth con act.

I don't know if kids were losing their balloons or someone was intentionally releasing them every 15 minutes or so. They were so cool to watch in the cloud streaked sky.

The band struck up the chords of the most covered and yet the most perfect song ever recorded in the history of pop - Yesterday. Here's a choir version to give you an idea of how heavenly it sounded.

::DOWNLOAD SOUND::

The sunset was gorgeous.

On our way back, just as I was telling my friends that it would be so cool if they got to meet (e:drew) and (e:janelle), I walked almost right into (e:drew)! He and (e:Jason) were folding up the chairs. We walked halfway home with them. Enroute, I heard about the heroic story of Roberto Clemente Walker I was told that my lurid suspicion that his plane might have been sabotaged was not really true. Oh well. I guess real life imitates inspiring tragedies rather than spiffy spy movies. The excellent alliterative phrase "mediocre medium" was mentioned in relation to a video game called "Guitar Hero" - I think by (e:Drew).

After (e:Drew) and (e:Jason) turned into Lexington, we ran into none other than (e:fellyconnelly) and the king of (e:) strip, (e:RRRAAALLPPPHII)E! The excitement of finally seeing Ralphie was a like a shot of a crazy drug and my already fried brain could not recall (e:fellyconnelly)'s real name. If you thought (e:James) got a raw deal, hear this. I introduced her as Raphael. Raphael! Holy crackers, I couldn't even think of a modern name. I had to pick something from the 1600s. Don't ask me why!

All of (e:fellyconnelly)'s recent blogging was enacted in real life. My friend and I went down on our knees and cooed all over the little guy. (e:fellyconnelly) rules Ralphie's world. She held out some magic potion and Ralphie stood still for a photograph!

Special thanks to my friends who tolerated my non-stop brainless jabbering and came out with me to enjoy the evening and to all the (e:peeps) who made it even better! It was an awesome official grade 5-EPSN yesterday. :)

Permalink: Yesterday.html
Words: 1208
Location: Buffalo, NY

Category: art

06/28/08 11:07 - 71ºF - ID#44815

The Genome-Wide Global Dance

Dances bring people together.
So do LD blocks and HapMaps.

An inspirational cross-continent dance video with a number of analogies in genetics that I won't bore you with. :)

Permalink: The_Genome_Wide_Global_Dance.html
Words: 75
Location: Buffalo, NY
Last Modified: 11/09/11 08:14

Category: art

06/25/08 10:51 - 68ºF - ID#44781

The TinyPliny Avatarolution

Almost everyone has a story about their avatars - those 125 X 150 pixels of online identification that stay with your readers through the thick and thin of your posts. Since my posts have dropped to the extreme triviality level of picking arguments about comic book fonts and posting pie-charts from arcane web-gadgets that nobody uses, I am under some pressure here. The immediate challenge is to achieve the nadir of triviality and set the bar even lower for the most trivial post on (e:strip). This entry to the "Who-wants-to-be-most-trivial?-I-DO!"-contest is the nausea, triumph, obsession, and nitpickiness-filled story of the evolution of my 18750 pixels. Start holding your breath, the lower boundaries of a tonload of totally unnecessary fluff are about to waft your way.

Anyone who has walked through the Cancer Cell Center (CCC) at Roswell, and has even a fractionally functional olfactory apparatus, can recall the all-pervasive sickly and somewhat homely smell that hangs about in that building. I have heard people make all sort of wild guesses about the source of this smell, ranging from imported transatlantic ducks being slaughtered alive in the building to cell-culture media rotting away to yuck-tastic glory. When your imagination is not up-to-creative-snuff with the almost-hallucinogenic peak of glory that your companions seem to have, you usually have three choices: a) Accept the most entertaining conjecture and hurry away from CCC, b) Make a mental note to not recall the smell while you are eating your lunch and hurry away from CCC and c) Decide in an unhinged moment that you will find out the source of that yucky smell and thrust your already unimaginative mind into the deeper doldrums of absolute, annoying and certain knowledge.

Needless to say, I took the third route. (Now, don't tell me you didn't see this coming!!) Though the exact source of the CCC smell still remains elusive, I do have a fair idea... and also my very own avatar. If you cannot see the relationship between between the last assertion and the rest of the sentence, then I guess you can safely assume that you are sane. (Yeah, breathe slow. You can cancel that shrink appointment today.)

Late last year I took the "Working with the Laboratory Mouse" course in the Animal Lab Facility in the CCC/Library building. It was then that the sickly smell hit me full force. It invaded my senses and took over whatever grey matter I had left, when I got out of the stairwell and headed toward the Animal Lab Facility. At this point, countless crime novelists over centuries might have hastily scribbled, "The realization dawned on her." Since these cool novelists were not around to make their erudite observations, I took on the responsibility of playing up EUREKA moment by shouting, not the eponymous "EUREKA!" but the painfully obvious, "IT'S THE MICE!!!". I quite understand why the veterinarian of the facility smiles in sympathy at me even after all these days. I earned the smile in extreme style.

I spent the better part of the practical training sniffing around the facility in what I thought was a discreet and sophisticated manner. But unfortunately, my discreetness was mis-interpreted as an incipient cold and a precautionary mask was thrust into my hands. Being masked put a damper on my detection capabilities and thus the mystery of the exact source of the omnipresent smell remains thus.

I came home, and did what any disappointed graduate student would do - wikisurf. I discovered fascinating details about the life and times of numerous members of the rodent family, hit the wikimedia commons road and fell in love with this magnificent image of the wood mouse.

I resized it and adopted it as my 18-odd-k pixels of online fame. Days passed, and at a party someone remarked that seeing a mouse reminded them of me (actually, they didn't really say this, but my brain came to this euphoric interpretation). My avatar had finally arrived! It was thus time to embellish it with idiosyncratic accessories. I chose a starred neck-tie. As any movie enthusiast would agree, drawing montages are always rolled out to the background of music. My music of choice for the nitpicky tale of avatarolution is the genre better known to the mainstream listeners as rap and to the classicist snobs as poetry.

With ball-point ink and felt-tip pen, I fell to sketching
But captured with a flash, it didn't look so fetching

Under lamplight the eyes were perfectly beady and filled with vice ((e:libertad,41910))
But I had an issue with brightness and I said, "No Dice!"

Tweaked brightness and contrast in PAINT.NET
A software so free that it is not a financial threat

At this point it lacked a certain punch
The oil paint and ink filters gave it the furry scrunch.

But alas, it didn't gel well with (e:strip) so I tinted it red.
However, in the comments background it looked rather dead.

The magic wand and colour inversion came to my rescue
OH NO! I had neglected the neck-tie with the stars askew

Added the sparklies and lightened it up a bit
Behold the 18750 pixels of the TinyPliny image-split.

But those 18750 pixels make it so hard to see
The eye on the right, won't you agree?

Looking out my window I found the perfect antidote
The rich blue of summer skies with a hint of creosote.

'Twas too much of colour and one too many alteration
Got sick of 'em all and opted for a modified third iteration.

Permalink: The_TinyPliny_Avatarolution.html
Words: 975
Location: Buffalo, NY

Category: music

06/23/08 11:48 - 65ºF - ID#44764

The Chaotic Red Musical Pie

Not surprisingly, my daily airplay breaks down into quite a heavy dose of metal of various flavours along with a smattering of other genres:

My "open mind index" that apparently measures how open-minded I am when it comes to music is 102.

To get this silly graph, you need to:

a) have a last.fm profile
b) have played and scrobbled a sizeable chunk of music
c) Go here: and enter your profile name, type in the security code and choose your preferred colour craziness.

And Voila, your musical tastes are neatly broken down into a pie-chart in eleven different colour schemes ranging from tame to frank-epileptic-fit inducing. The epidemiologist in me cannot help but plot a population musical-taste study with such detailed statistics...

Happing Musickuming! :)

Permalink: The_Chaotic_Red_Musical_Pie.html
Words: 132
Location: Buffalo, NY

Category: art

06/21/08 10:22 - 73ºF - ID#44737

Oh, how I missed this...

I need to sketch graffiti.

Does Buffalo have an official free-to-all-artists graffiti wall?

Permalink: Oh_how_I_missed_this_.html
Words: 15
Location: Buffalo, NY

Category: whine

06/19/08 04:03 - 62ºF - ID#44721

The Comic Sans Font.

This question is for the designers and the typographers among you. Why is it that you hate the comic sans font so much? It is the only font that is extremely legible at small sizes, is pleasant to look at and can be read without giving one a headache, and yet there seems to be this almost virulent bunch of people who are hell-bent on eliminating this happy font from the web. Why is that?

I don't find any logic in several of their arguments:
1. It is ugly: How can such a legible font be "ugly". The word "ugly" implies loathsomeness and annoyance - both of which, are far away from your mind when you read text typed in comic sans. It's so darn easy to read it. No effort is required to make out what the alphabets are. It's so eye-friendly.

2. It's inappropriately used in varied contexts: How do you define inappropriate? Who defined what is formal and what is informal? Fonts are not equivalent to clothes, that analogy never works. Is eye-friendliness and ease of reading only meant for kids? What happens to us as adults? Do we intentionally want to ruin our moods and eyesights by being forced to read fonts that don't even have breathing whitespace?

3. It's ill-designed: Again, which font is the "best-designed" according to you? Why is it that only the designers complain ad-nauseum about this beautiful down-to-earth font and the general "lay-public" uniformly love it? Why can't typography be user-friendly instead of being snob-friendly?

I ask you, all you people heading to the Typography convention next month, here in Buffalo. Give me some logical arguments and not snob statements as to why I should not use this font. I sent out two international reports to the scientific community using this font and none of them had any problems with it. I even found a LaTeX version of the comic sans font! Why do you view it as a fly in the typographic ointment? I swear I shall be sneering at you if you say its a "kid font" because being an adult does not mean you punish your eyes!

Permalink: The_Comic_Sans_Font_.html
Words: 356
Location: Buffalo, NY

tinypliny

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mike said to mike
John Stamos is mentioned in a suprising amount of my journal entries. Who knew he was so impactful o...

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