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Category Archives: Alchemy

Self Empathy

I have never been into meditation, but today I tried an experiment.

When I got into my car on the way to work, I sat for two full minutes with my eyes closed an the engine off. During these two minutes, I repeatedly gave voice to the feelings and sensations I was aware of. Each time I felt something I said “I am aware that I …”, where the blank was the sensation I was experiencing. I said things like:

“I am aware that I am hearing a plane fly overhead.”
“I am aware that I am stressed about a project I have to work on today.”
“I am aware of the feeling that I have to go to the bathroom.”
“I am aware that I enjoyed time with my friends this weekend.”
“I am aware that despite having a good weekend, I am judging myself for not accomplishing enough.”
“I am aware of the feeling of the sun shining through my car window.”

The goal was not to place judgments on any of these feelings or inner interpretations, but rather just to acknowledge them. I found myself wanting to follow “I am aware that I feel …” with “and that means I should…”. I tried hard to veer away from those thoughts.

At the end of two minutes I felt relaxed, but the real impact was more subtle, and over the course of the day. I acutually found myself more conscious of what I was thinking and feeling, and a bit less reactive in interpersonal situations. It wasn’t perfect, and quite often that awareness came only in retrospect, but it was somehow refreshing to hear the words “I am aware that I” going through my head spontaneously.

 
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Posted by on May 31, 2011 in Alchemy

 

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Using LaTeX with Microsoft Word

In grad school I wrote as much as I could in LaTeX, including my Ph.D. thesis. This offered several advantages, the largest being that it enabled me to script the generation of very large tables (50+ pages) automatically. If I made a change to my project that affected the output of said tables, all I had to do was rerun the script that generated those tables and my thesis would be updated.

The biggest drawback was that occasionally I have to submit manuscripts to publishers who either will not accept LaTeX submissions, or who seem to go out of their way to make submitting in LaTeX extremely difficult.  Similarly, sharing documents with collaborators in LaTeX can be frustrating.  Sure, you can send the PDF, or maybe they are even comfortable editing the LaTeX directly (rare in my experience), but I have yet to see an end-to-end procedure for tracking changes made by peers in a PDF or LaTeX document that makes it easy for me to accept or reject the changes.

There are a few tools available that can help make converting your LaTeX projects into Word format a few steps better than retyping your whole thesis (though it’s still pretty painful!):

  1. LaTeX2rtf will help you convert your LaTeX document to a Rich Text Format (RTF) file that can be opened in Word.  This will leave you with a lot of formatting fixes to implement, particularly for any tables, figures, equations, etc., but I find it’s better than having to start from scratch.
  2. Bibtex4Word can format your entire bibliography in Word using Bibtex bibliography files as the reference source.  This means you can use all those old .bib files you’ve created for LaTeX in word documents!  I find the particularly useful if I know I need to use Word for a project but I don’t want to have access to RefMan or EndNote.  I also recommend JabRef for managing BibTex files.

Recently I’ve been struggling to format a paper for Nature Molecular Systems Biology.  They accept LaTeX submissions, but for ease of sharing my manuscript with my collaborators I decided to write it in Word.  Unfortunately Nature does not provide a BibTex style file for Nature MSB, so in order to use Bibtex4Word I was forced to make my own using makebst.tex.  Luckily, the Endoplasmic Reticulum blog documented their struggle with making a BST file for Nature MSB and I was able to make a BST file without too much trouble.  Note, however, that to use this BST with Bibtex4Word you’ll need to make use of some style flags.

I should clarify that this is all a terribly convoluted process and there are definetely bugs you’ll encounter along the way.  If you want the simplest end to end solution, invest your time and resources in a solution that’s specific to Word, or specific to LaTeX.

 
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Posted by on March 20, 2011 in Alchemy

 

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Values in Science – How to Judge Scientific Posters

(apologies if this post isn’t super clear — I just wanted to get it out)

I haven’t posted in ages, but I am at a conference, I can’t sleep, and something is on my mind, so I figured I’d strike while the iron is hot.

I’m at the 2010 Computational Science Graduate Fellowship Fellows Conference in Washington D.C. This evening I had the pleasure of serving as a judge for a poster competition. The current fellows present posters on their graduate research. The poster topics shared the theme of “computational science”, but besides that they can be from any discipline. I’m not going to discuss the specifics of the posters here.

The basic criteria we judged posters on were visual, oral, and impact.

To me, there are fundamental rules governing effective poster design. For example, in the visual category, use no paragraphs of text, and large fonts (even in figures), and well balanced graphics. In the oral category, have a 3 minute speech prepared, and refer to the poster when delivering that speech. I was surprised, however, how other judges had vastly different values when evaluating the work submitted. Most specifically, some judges felt that work of high scientific quality could compensate for poor poster presentation.

Have you ever designed or seen a scientific poster? If so, what do you think are the most important criteria for evaluating this sort of work?

 
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Posted by on June 24, 2010 in Alchemy

 

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The Big Finish

Apparently the Diesel Wi-Fi terms-of-service requires users to blog.

So here I am.

In the next six months, my three major activities are:

  1. TA a “drug delivery” class (provides current income).
  2. Finish and defend my thesis.
  3. Find a job (provides future income and intellectual fulfillment).

TAing isn’t so hard to fit in because it’s scheduled into the academic year.  I go to class twice a week.  Immediately after class, I review the notes for the class using a codified note-taking system.  Once a week, I hold office hours.  Three times this semester, I’ll have to grade about 90 exams.  These activities fit themselves into my schedule.

It can be harder to make time for dissertation work and job searching.  Essentially, these are both full-time jobs being fit into a single set of full-time man-hours.  Overscheduling seems to be the hot business strategy in this economic downturn, however, so I’m trying to view this over-commitment as my way of cutting back (“I had to let the guy who normally applies for my jobs go — we just couldn’t justify his salary to corporate in this climate.”)

I’ll let you know how it goes.

 
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Posted by on September 8, 2009 in Alchemy, Garbage In, Garbage Out

 

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A Million Little Files

My office desktop’s Windows partition fills up on a weekly basis (I usually notice first when CNN news videos start to quit unexpectedly), so I’m always looking for some way to search for and destroy large files or folders on Windows XP and free up disk space. Usually this involves clever guesses and manual breadth-first searches on my computer.

Enter WinDirStat. This program combs the hard drive for you and helps get detailed information about where larger files are hiding. This is not a review of the program, nor it is an endorsement, but I’m a fan of pretty pictures, so when I saw this I couldn’t help but say something.

WinDirStat output

The graphical output at the bottom visualizes all the files on your drive, as well as their relative size. With a few clicks, I cleared ~3 GB of space.  The main culprits were the “sharing folders” in MSN Messenger (a program I no longer use) and various cached installer files.

 
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Posted by on August 24, 2009 in Alchemy

 

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Newton Fractal Visualization with Python

I felt like trying something new, so I wrote a Python script to plot Newton’s fractal.

Newton's Fractal (30 iterations, 1500 x 1500 resolution, 1e-6 convergence)

This graphic shows the time to convergence for solving z^4+1 = 0 using Newton’s Method.  The solution to this equation is one of four possibilities, which are represented using the colors red, blue, green, and yellow.  The solution that Newton’s Method returns depends on the initial guess.  I plotted the final solution for initial guesses in the range 0-1 (real, horizontal axis) and 0j-0j (imaginary, vertical axis).  Color depth represents faster convergence to a particular soltion (i.e., brighter pixels represent initial guesses that converge to a solution faster).

The script is based heavily on Listing 7-1 from “Beginning Python Visualization” by Shai Vaingast. It’s a good book with other fun examples, but my code for this problem is here.

 
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Posted by on August 13, 2009 in Alchemy

 

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Pearl Harborer

Last year at Zandperl’s Halloween party we were playing “The Coachride to the Devil’s Castle” (aka Die Kutschfahrt zur Teufelsburg), and we spontaneously came up with the following definition of “Pearl Harborer”:

Pearl Harborer

In the Card Game “Die Kutschfahrt zur Teufelsburg” (“The Coachride to the Devil’s Castle”), a Pearl Harborer is someone who is surreptitiously hiding the “Schwarze Perle” (a.k.a. “Black Pearl”) card.

Brian’s going to declare victory this turn, unless he’s a pearl harborer…

I submitted this definition to Urban Dictionary.

It was rejected.  Superficially, that’s not a big surprise, nor do I care.

coachride_small

What surprised me, initially, was that it took so long for them to get back to me.  I submitted the entry on October 27, 2008, and received my “entry not published” email three days ago.

Peer review is known to take ages, but still I could not imagine why the rejection would be so slow (compared to Wikipedia rejections, which can happen within minutes).  But the real surprise here is that Urban Dictionary has standards at all. The rejection letter came with a link to Urban Dictionary’s publishing guidelines (you may need to sign up to see the link):

As an editor, you decide what gets published. Use these guidelines while you make your decisions.

1. Publish celebrity names but reject friends’ names.
2. Publish racial and sexual slurs but reject racist and sexist entries. 
3. Publish opinions.
4. Publish place names.
5. Publish non-slang words. Ignore misspellings and swearing.
6. Publish jokes.
7. Reject sexual violence.
8. Reject nonsense. Be consistent on duplicates.
9. Reject ads for web sites.
10. Publish if it looks plausible.

So anybody can sign up to be an editor, and some consensus of arbitary/random editors decides which entries get accepted and which get rejected.  According to these guidelines, my entry should have been published.  However, whichever editors saw it disagreed, probably because they didn’t “get” the definition, so now it’s lost to the world forever.

The sad part is that this isn’t so far off from academic peer review.  Sometimes you discover or create knowledge that you know is right, and you try to put it out there but the people reading it don’t think it should be seen, and they reject it, often with little or no explanation why.  If it’s this hard to publish in the haphazard, anything goes environment of Urban Dictionary, imagine how hard it must be to publish in a journal, where entries theoretically have consequences.

 
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Posted by on January 27, 2009 in Alchemy, Entertainment

 

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