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Monthly Archives: April 2012

While the recent wedding I attended was spectacular, the days leading to it were not.

Having never been to a wedding before (or any other black-tie event), I was in a panic about what to wear. Once again the internet gave largely unhelpful advice. “An evening gown or a dressy cocktail dress,” it said.

What did that mean?!?!
Were sleeveless dresses appropriate? Or knee-length ones?

After consulting a few slightly more seasoned friends, I ordered a dress online: Arabelle in Jalapeno.
It was beautiful, chic, and many vanity sizes too large. It seemed I still haven’t learned my lesson about how strapless dresses will always fall on me.
Arabelle
Unfortunately, the Arabelle misfit happened the weekend before the wedding date. I ran around all weekend looking for an alternative. I eventually purchased a vintage Slyvia Cuur dress from a local consignment store. It was my first vintage dress, and I probably grossly overpaid it out of desperation, but finally, I had an outfit for the special day.
Sylvia Cuur
With a bit a self-tayloring, the Slyvia Cuur dress fit wonderfully. It featured a spiffy front zip and a faux tie. Oh how I loved ties.

I slept easy for the next few nights until my mom frantically called me after receiving pictures of my new dress. “It wasn’t formal enough!” she relayed the message in a panic-stricken voice.
The very next day, I once again dashed about the local stores. My mission was to purchase the first formal dress that fit, no matter how hideous. Off the racks at Macy’s, I grabbed a XSCAPE one-shouldered ombre dress with flowers.
XSCAPE
Much to my surprised, the dress fit quite well, and looked fabulous. I’d never gotten this lucky before!

In the end, I wore the Slyvia Cuur dress to the rehearsal dinner and the XSCAPE dress to the actual wedding. I got a lot of compliments on the dress, which was quite nice.

Here’s what I learned about what to wear to a black-tie wedding:

1. Strapless and knee-length are totally acceptable, unless it’s a ultra-conservative setting.

2. Dresses needn’t be fancier than the shiny one-colored dresses listed on J. Crew’s website, and certainly doesn’t need to cost as much

3. My lovely vintage dress with floral prints ARE formal enough. In fact, I saw some other lovely ladies sporting floral dresses. The strictness seemed to be much looser with women and their dresses than men. Most men I saw were in tuxedos or nice suits and jackets.

Hope this helps some future wedding guest neophyte!

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I attended a wedding this weekend at the Codman Estate.
It was beautiful.

The venue was a picturesque Italian garden centered around a long lily-filled reflecting pool.
The sun peered through trees and Greek columns, illuminating the altar.
columns

Songs of birds and violins welcomed the wedding party.
The groomsmen were in handsome tuxedos and the bridesmaids were in beautiful teal dresses.
bridesmaids

The bride and groom, Lis and Mike, were an incredibly lovely couple.
Lis and Mike

The entire ceremony was wonderful.

I was super delighted with the tiny details.
The wedding had a hint of ancient Greek theme. The centerpieces of the reception tables were statuettes of Greek gods and goddesses. The bride and groom sat with their families at the table of Hera. I sat at the table of Aphrodite, with other close friends of the family.

I absolutely loved the small Dionysus at the bar.

This was the first time I’d been a guest.
It was an amazing experience.
I shall judge all other weddings based on this one.
They have set the bar high.

1. Introduction

absee is a friendly ABIF reader in Ruby.

Three years ago, I desperately needed to analyze the trace values from DNA sequencing chromatograms (in the form of ABIF files). To my frustration, none of the available ABIF readers exported raw data. Even today, while lots of software are able to visualize ABIF files, very few allow for scripted inputs and custom manipulation of outputs. I want a ABIF reader that simply extracts the data and can be easily incorporated into other projects. Hence, I created absee.

absee is a Ruby gem. It has no GUI, no fluff. It simply reads the ABIF files and returns the values in six arrays, an array for each of the trace data for ACGT at discreet intervals, a called sequence, and an array of peak indexes corresponding to the called sequence.

% irb
>> require 'absee'
=> true
>> readAB("my_sequence.ab1")

With a simple Ruby script, it can be incorporated to rapidly read and process many ABIF files and pipe the data for further downstream processing. absee is a very nifty tool, one that I wish I had three years ago. The above code works for versions less than 0.1.0.0.

[update: new version as a Ruby Module]

2. Background

ABIF is a binary file format, usually with an .ab1 extension. It contains a trace value for A, C, G, and T at each point for a interval. Most ABIF viewing software will interpolate those values at the points to display sinusoidal lines.

ABIF files also contain estimated bases and peak indexes. The way DNA sequencing extracts a sequence from from trace data is to use a base-calling algorithm. The base-calling algorithm will estimate a peak in the trace data and determine a called-base for the peak. If peaks from more than one trace overlap and their values are sufficiently close, the algorithm may use N to denote uncertainty of the base for that peak, and lower the quality score. The sequence of called-bases is the estimated DNA sequence corresponding to a chromatogram.

3.  Details

Converting from the ABIF binary files to readable values was no small feat. Even with its file format architecture ready, I still needed a little guidance. I found an open-source ABIF viewer years ago (now no longer available) and translated absee from its ABIF reader.

The primary method to call is readAB. It opens the ABIF file, checking the filetype and version. Major ABIF versions greater than 1 are not supported, due to possible different encodings. If the check fails, readAB will return six empty arrays.

readAB(filename)

  • parameters:
      filename: a string containing the filename (including the path and extensions)
  • returns:
      six arrays, which are trace data for A, C, G, T, called sequence, and peak indexes

There’s more documentation in absee‘s yardoc / RDoc, as well as the source code on github.

4. Source Code

The source code for version 0.0.2.3 can be found at the absee github repository.

I’m a sucker for candy, especially sour candy.

My favorite is Sour Punch Straws.
They’re the perfect combination of sour and sweet.

Unfortunately, Sour Punch Straws is on the endangered candies list.
Once prevalent at local grocery stores and gas station stands, this rarity now exists only in Amazon specialty shops.

Last Christmas, I got a large box of Sour Punch Straws in Green Apple.
I enjoyed their mouth-puckering deliciousness everyday, for weeks.
It was paradise!
Nom Nom Sour Punch

I hope these will come back someday!

.

*In the process of writing this, I’ve developed serious cravings for Sour Punch Straws. Must order more!

Lost Crates is definitely an adventure! Tossed about the seas of designery goodness, Lost Crates deliver a small box of curated goods to your doorsteps.
Lost Crates
The crates come in many different flavors, one of which is stationery.

I love stationery! I love mail, and I certainly love surprises.
Why didn’t I jump on this in the first place? Oh right, the price.

Shelling out $38 every month for stationery is a bit much.
Fortunately, last week, they announced their Petite Stationery box for half the price!

I seized the opportunity. I’m not a pen-and-paper writer, so I signed up for the quarterly subscription. I’ll surely forget about it months from now, and doubly surprise myself.

Today, my first Lost Crate came in the mail.

Initially, I was a bit disappointed. From the reviews I’ve seen, the goods came in a
box, which played into the mystique of the Lost Crates. Sadly, my Petite Stationery came in a far less charming padded envelope.
envelope
Tearing into the envelope revealed April’s offerings: a seven-year pen, a small notebook, and a packet of wine-themed letterpress tags. I must confess, I spoiled my surprise by peaking inside the crate on the website. However, what I received is very different from what I imagined.

I got the following:

French Shirt Notebook by Pocket Dept.
It’s featured a sturdy cover and unlined pages. It was surprising tiny, yet surprisingly useful. I don’t fancy unlined pages, but having something small and portable to jot notes in is very pleasant. I’ve come to like this pocket pal.
Dept De Poche
Seven Year Pen – Ciao by Seltzer Goods
I like my pens rollerball tipped with nice grippy sides. This pen was definitely not my usual.
Ciao had a novel twist mechanism, and wrote pretty smoothly.
Unfortunately, it was a little too thick for my tiny hands to grip comfortably.
Though, I did love the concept of reducing the number of discarded pens.
Very eco-friendly!
Ciao
Wine Tags by OrangeBeautiful
When I saw this online, I thought to myself, “What am I going to do with wine tags?”
I didn’t have a collection of Merlot aging on some shelf.
However, when my crate arrived, these tags became my favorite of this bunch!
They were tiny, greeting cards, exquisitely pressed on beautiful paper.
I liked them a lot!
Wine Tags
Surprise would be a good one-word summary to my first Lost Crate experience. Even though I’m not head-over-heels with the products (except the wine tags), I’m glad I discovered unbeknown brands. I’m looking forward to my next Lost Crate, and no peaking this time.

Repo! The Genetic Opera is a must-see film!
It came to mind while I was reminiscencing about my recent discoveries: The Donkey Show, Evelyn Evelyn, and Sleep No More.

A friend and I watched it a few years ago, and absolutely loved it.
Repo
Repo is a rock opera, set in a dystopian future where organ repossessions have been legalized.
It has amazing music and gripping characters.
Repo Man

*Spoilers below*

This is my favorite scene/song.