Weighting Nucleosome Modifications

The more modifications a nucleosome carries on its eight histones, the less likely it should be to occlude DNA from binding.  

Our modification data is given as a ratio of modified / non-modified histones.

i can think of three template weighting schema: additive, multiplicative, or exponential:

• weight \alpha 1/(average mod/non modified ratio)
• weight \alpha 1/(product of mod/non modified ratio)
• weight \alpha exp(-(sum of mod/non mod ratio)
• weight \alpha exp(-(prod of mod/non mod ratio)

What is the null hypothesis??

A nucleosome which is consistently unmodified at a site s will have a modified/unmodified ratio of 0 at s.

A nucleosome which is consistently modified will have a modified/unmodified ratio of infinity at s.

We want to weight a nucleosome with weight 1 if it is unmodified, so we need a weighting function that maps 0 to 1. 

We want to weight a nucleosome with weight 0 if it is always modified, so we need a weighting function that maps infinity to zero. 

1/weighting score works for that one, but not for the first one.  1/o gives infinity, not one. This means that unmodified nucleosomes are going to get artifically high weighting scores

I think exponential would work?

e^0 = 1 

e^(-inf) = 0

For those who fly alone, hopping from family to family and friend to friend:  there is a strange and pervasive sentiment in the air post-airport-security: that sinking knowledge that “goodbye” has just happened and that “hello” will not for at least a few more hours, and whether the goodbye was hard or the hello will be harder, each of us finds ourselves prisoner to a magical space and time which isolates us in that in-between place that those who do not “hop” as such will never quite understand.  

Here we are left alone and uncomfortably close to that truest essence of ourselves: that we want to be everywhere, and that as a consequence, we will always be in a sort of nowhere.  This “nowhere” is a privilege as well as a cost.  It is a beautiful place, where we find our roots not in a home or a family here or there, but in the knowledge that wherever we go, we can create a home and we can find and nourish a family - and supporting that knowledge from the other side, it seems so trivially clear that in any part of this world there will be those searching for the same: a family where they haven’t had one, a home away from what they are used to calling home. 

Yet as we load our liquids and laptops back into our bags, hurriedly slip on shoes and check to make sure we have all our belongings,  there is something deeply unsettling about the whole business- a notion of guilt lurking not-so-far beneath the surface, a twinge for leaving who we’ve left behind and, equal and opposite-ly, one for not having stayed with those towards whom we are headed.  

Proof that sugar makes me have awesome/crazy dreams

So this is a hypothesis I’ve been working on for some time now, but the theory was that if I eat a lot of sugar before I go to bed, I have funky dreams, whereas normally my dream life is nil.  Confirmed last night: being back in the land of dairy queen and having run a long run in prep for my half marathon, I did something I’ve never done before and forced my mom to pull over so I could buy ice cream (have to take advantage of being 24).  I got a blizzard which I worked on gradually from about 7 pm to 9 pm or so.  

So this is the dream: I’m staying in a hotel with the MIT sailing team in San Diego.  We wake up hearing that there is a tsunami coming and that there was a major East Coast disaster where essentially a quarter of the country folded down into a “subduction zone” running roughly along the Appalachians.  I look out and see that indeed, big waves are lining up.  So, in my first test of skill and stamina, I race inland, up a large set of stairs (Thank goodness for all that stadium running!)  and into another hotel, where I pilfer sugar packets from the room service guy as I run through the top floor and get onto the roof, which allows me to exit to higher ground as the hotel is built into a hill.  I now am watching waves pummel the place where I was minutes ago, but I am safe.  A few others have made it this far too, and we can see that the waves are growing, so we keep running.  I get to the top of another building, and the base of the building is hit by a wave, causing it to tumble.  Super-Mario style, I scuttle around to the side which will be the top as soon as it hits ground, and bounce off onto the next highest building as soon as it does so. 

This is my last stop as somehow when I come out of the roof of this building, I am in a dark, dreary, silent neighborhood with a few stealthy survivors creaking around.  I try to hide my blond hair. I look at one of the street signs and read that it was Cesar Chavez, a road I used to frequent when biking in downtown LA.  I keep sneaking around and somehow run into friends.  We find an empty house to live in.  It turns out, we are able to deduce, that the house belongs to a gay couple that caters, and the freezer is full of giant carrot cakes.  (The stuff dreams are made of.)  We hold base here for a bit, everybody charges their cell phones (um, this one clearly comes from standing in line at starbucks to charge things after Irene) then try to move on and get / give more news from the outside world.  We end up in another empty house for the night. The last thing I remember is this homeowner coming in to wake us up and make sure we were ok. He was probably 65 and grey, a veteran and a professor.  

Anyways I was a total badass and survived, thanks mainly to all the time in my life I have spent running up stairs.  Now I feel much more prepared to live my day.