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Monthly Archives: March 2011

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