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Author Archives: halfawake

Toast of the Town

I went out of town for a long weekend, and while out there my peripheral Twitter psyche picked up on chatter about “avocado toast” and home mortgages.

I had to look up what they were talking about on the way home. The New York Times has a good rundown of why this was trending, but it doesn’t really explain what avocado toast really is. This recipe is the first I found online and I’m thinking of trying it.

Thankfully I already own a home.

 
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Posted by on May 16, 2017 in Uncategorized

 

Run Control

Between travel and illness, a half marathon I signed up for has snuck up on me. My first run in a few weeks today was an exhausting 2 miles. This is what I’m looking at between now and March 8th:

Feb 16, 2014 – 2.1 miles
Feb 22, 2014 – 7 miles
Mar 1, 2014 – 10 miles
Mar 8, 2014 – 13.1 miles (Half Marathon)

I’ll be filling in runs in between the long runs, but I think I need to hit these long-run goals to make the 13.1 feasible. Any advice on how to safely ramp up here would be appreciated.

 
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Posted by on February 16, 2014 in Uncategorized

 

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Am I Too Old to Run Cross-Country?

On Saturday I joined the Eastside Runners Club to compete in the Sundodger XC Invitational at Lincoln Park.  The men’s open race was an 8K (about 5 miles) with a lot of local community college runners.  The whole field went out fast and I threw some elbows to maintain my space and position.  Going through the first mile in 5:30 felt good… better than it should have.

Somewhere around 2.5 miles I stepped on something, or took a misstep, and sprained my ankle.  When it happened, I screamed and stopped, and quickly made the executive decision to drop out of the race.  Those of you who’ve read my blog for a while now might know that this is a recurring theme for me.  I hate it.

The answer to my titular question is, of course, no.  I know many strong XC runners who are decades older than me.  But I think I have to  come to terms with some subtle lessons about what I can sustain as a runner at this point in my life.  Important lessons from this sprain include, but are not limited to:

  • Listen to my body – For over two weeks, I’ve been complaining about foot pain.  It didn’t hurt while running, just while flexing it in particular ways (imagine doing calf raises), so I procrastinated every time I thought to call a PT about it. I’m sure that this was a portent about my more catastrophic injury in the race. I should have taken time off and fixed what was wrong before doing a hard race, particularly one that involved running 5 miles on trails with a crowd of (real) athletes a decade my junior.
  • Eat and sleep right – I’m embarrassed to admit the number of nights I ate a peanut butter sandwhich for dinner last week, and I’ve been staying up late to satisfy an eerie obsession with work. The days leading up to the race I felt sluggish, sickish, and generally broken.  Garbage in, garbage out.
  • If I’m not running, don’t race – I’ve been looking forward to XC for so long, and running this race was pretty important to me.  So when I ran out of time for regular running in the last two-weeks, having trouble fitting in runs of even a couple miles, I did not reconsider my race schedule, and I should have.  That 2.5 mile run the night before the race was not enough to get me back in the game for a hard 5-miler.
  • Take a holistic approach to fitness – I’ve always valued a well-rounded approach to exercise…  in principle.  But when I get busy, I prioritize my activities and make cuts.  Maintenance activities like ankle-strengthening drills are the first things to go (haven’t done them for at least a year).  Stretching, weight lifting, form drills, strides – they’re all gone the moment I get busy.  Usually, the actual running is the part I hold onto the longest.  And when the busy time is over, I don’t add the other activities back in.  So I’m left with a 100% running regimen, which is fun, but not sustainable.  I need to hold myself to not running if I don’t have time for proper warm-up and stretching at the minimum.  Even if it means I run less.
These lessons apply to athletes of any age…  I think I’m just too old, or too busy, to get away with skirting around what’s good for me anymore.

 

 
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Posted by on September 18, 2011 in Garbage In, Garbage Out, No Easy Days

 

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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Pot Of Gold

I somehow dragged myself out of bed at 6AM on Daylight Savings Day (today) to run the St. Patrick’s Day Dash in Seattle. It’s an odd distance (3.75 mi) but attracts a huge crowd (over 7K people) partially because of the party/beer garden at the finish line.

The weather was chilly – low 40s – with light Seattle rain. As far as long distance racing weather goes it was pretty great. Chilly temps are actually desirable for some races because you can warm up pretty quickly when you’re pushing the pace. I started near the front because I didn’t want to get caught up in the crowd too much, but I committed to going out conservatively. Adrenalin and the crowd make it easy to go out too fast in races like this. I often think “oh man this feels great I’m going to go for it!” and then sorely regret my enthusiasm in about 6 minutes. My conservative start really paid off. After the first mile I felt like I was racing rather than just trying to hang on for dear life. I spent the rest of the course just trying to pick off people one-by-one. My finish wasn’t that strong, but my overall pace seems to have been quicker than the last race I ran, even though this one was 3/4 of a mile longer.

At the finish line I saw a friend from high school who was meeting up with her husband and their running club to do a 6 mile cool down. They invited me to come along. 6 miles! It’s been a decade since I ran a cooldown that was actually longer than my race, let alone hit 11 miles in a single day. I had to try though. We ran around Lake Union, and by the end my whole body was seizing up with the overuse and cold weather. I’m feeling it now, everywhere, but so glad that I went for it. I needed a win this week, and I think I got one.

 
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Posted by on March 13, 2011 in No Easy Days

 

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What Do You Do With the Mad You Feel?

Been having a rough time recently, and heard an excerpt of Mr. Rodgers reading his song “What do you do with the mad you feel” before a U.S. Senate committee in 1969. It really hit home.

(the song/poem starts at 4:45)

 
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Posted by on March 11, 2011 in Garbage In, Garbage Out

 

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Sugar Boost Before Running

A couple weeks ago, something strange happened on one of my runs.

I stopped running.

Choice in the matter was seemingly stripped from my grasp. One moment I was running, and the next I was limping along feeling devoid of all energy and motivation to go on.

There’s nothing inherently wrong with this. I got tired and stopped, so what? The strange part, to me, is that this has never happened before, to my memory. I’ve stopped on runs for various reasons — digestive problems, seeing someone I know on the route, or even for a quick snack at a bread shop. But I cannot remember a time where I had to stop because I was utterly sapped of remaining energy.

Since then I’ve made it through each run successfully, but not without a good deal of wanting to stop.

A few friends suggested the same hypothetical explanations… Diet, sleep, and age. I haven’t had any recent major dietary or sleep changes, and I’m remiss to think that it’s age related (although it’s possible).

I asked a trainer at the gym for some suggestions and she suggested trying to have a ~100 calorie snack before my runs, something like a few pieces of dried fruit. I followed her advice this morning, wolfing down a few pieces of dried apricot before I hit the road, and the difference was immediately noticeable. The run was still hard but I didn’t feel as drained. I finished after 5+ miles with the feeling that I could keep going!

I don’t know if this was the fruit talking, a placebo effect, or something else unrelated, but whatever it is I’ll take it!

Yours In Running,

–Me

 
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Posted by on March 6, 2011 in No Easy Days

 

Considering Blogging again

Trying out the Choco theme on WordPress.

If you still actually read this blog (via RSS or some other such monitoring system), toss me a comment or an IM to let me know. Knowing that people are watching might motivate me to publish some old drafts I have lying around and get the ball rolling again.

 
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Posted by on March 6, 2011 in Garbage In, Garbage Out

 

The Miracle of Flight / Confidence Week

I’m such a nerd/internet addict I can’t resist pressing a WP post using my in-flight internet!

I’ll also take the opportunity to remind everyone that it’s Confidence Week. Take a moment to think about how today you can avoid being passive or aggressive (or both), and instead take steps to be assertive.

 
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Posted by on November 24, 2010 in Garbage In, Garbage Out

 

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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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Resemblance

Normally I’d tweet something this short, but I wanted a chance to give a SPOILER WARNING for season 1 of Dexter.  More after the “more” thing.

Read the rest of this entry »

 
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Posted by on October 23, 2009 in Entertainment

 

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Seeking Advice on Exercise Logs

For about 8 years, I’ve kept track of my running mileage in an Excel workbook.  Before that, I was logging things in a Claris Works Spreadsheet for a couple years, and before that I had a couple years of paper logs.

The Excel workbook has worked well because it’s functionality has evolved as far as I have been willing to push it.  But for a while I’ve felt that its development has stagnated and it has grown unwieldy.

running log winter spring 09

running log graphical summary

Now that I’ve been benched from running for 4 months (more on that later), I’d like to explore other exercise tracking options that are more amenable to cross training.

Features I’d like:

  • Accessible anywhere (i.e. on the web).
  • Can accommodate different sorts of workouts (running, biking, weight lifting, pickup frisbee, etc.).
  • Exportable to spreadsheets or database files.
  • Nice graphical data and meta-data summaries with easily adjustable parameters.
  • Easy to track peripheral data such as gear (e.g. shoe mileage) and routes (possibly with maps).
  • It would be awesome if there were some kind of API or other method that allowed me to import my running logs from the last 8 years into the system, but I think that may be asking too much.
  • Social networking would be nice, but not necessary.

A couple friends (thanks Z and G) suggested Daily Mile.  I’m happy with that but it would be nice if it could track strength training as well.  Does anyone have other suggestions?

 
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Posted by on September 13, 2009 in No Easy Days

 

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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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