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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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1280 x 960

In 2008, I resolved to run 1000 miles.  This was a good resolution because it was quantitative, yet long-term, and challenging, yet achievable.  This year I want to resolve to do something that also meets these criteria, but I don’t want to just repeat my 2008 resolution.

I liked the running resolution in particular because I got something tangible out of it.  I’m in the best running shape of my adult life.  I feel good when I run.  I’ve improved my health and fitness.  Now I want to do something similar for my brain.

Recently, I realized that I’ve been learning more at the local trivia night than I have been working on my Ph.D. research topic.  This troubles me.  School is for learning, right?  So what am I doing wrong?  Part of the problem is that graduate research can have little tangible gratification along the way.  There are no grades.  We never feel the sweet release of final exams.  There isn’t always a clear measure of progress.

With that in mind, I wanted to make 2009 a year for learning new skills.  I made a list of goals for things to learn/practice over the course of the year.  It had everything from picking up a new instrument to doing 100 consecutive push-ups. This was a fun list to make, so I’m going to save it in a draft on my blog even though I eventually decided not to make it a part of my 2009 resolution.

Instead, I decided to take the practical route:

In 2009, I will finish my Ph.D. project, write my dissertation, and defend my thesis.

From my current vantage, this seems about as likely as a herd of cats carrying me to school tomorrow on their backs.  From your perspective, on the other hand, it may seem like a cop out to resolve to do something that I am pretty-much on track to do anyways.

But I assure you, this is not going to be easy.  I’ve been working on…  stuff…  for five years now, and I feel I have very little to show for it. Making this thesis happen is going to require discipline, planning, and maybe if I’m lucky, some learning. My running resolution was a success largely because of the logging and reporting I did throughout the course of the year. Completing my thesis will require a similar attention to progress.  I could record pages over time, or just blog more frequently about research, but I’m open to hearing any suggestions for reaching this goal.

What are your resolutions for 2009?

 
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Posted by on January 7, 2009 in Alchemy

 

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Bill Nye Photos

Here are a couple of the photos from the breakfast I mentioned.

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More recently, our class had a media training workshop where we practiced constructing clear messages, using sound bites, and performing camera interviews. It’s sort of terrifying to be on camera speaking as an ‘expert’ about something that in reality you don’t feel that confident about.

We watched a number of examples of good and bad interviews. One excellent example of what not to do came from an interview of Bob Dole by Katie Couric during the 1996 presidential election (sorry, I can’t find a video of it). Dole was downright combative rather than focusing on the issues that were important to him. But it’s tough. I’d probably blow up at a reporter who accused me of anything, too.

I think I could do a good job as the journalist too, though. I like asking questions and being critical of the responses (in a constructive way, of course). I like listening. Maybe there’s a career in sci-comm or policy for me after all.

 
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Posted by on April 4, 2008 in Alchemy, Photos

 

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The Science Guy

This morning my science communication class had breakfast with Mr. William Nye. We sat in a small classroom and for the most part, he spent the time asking us questions about what we do and why we’re in the class. When he got to me, and I explained my research on the minimal gene set (the smallest possible set of genes that can still support bacterial life), he asked me how large such a set would be. I said something like “well, we know there are bacterial species that have around 400 genes, so the smallest set is obviously smaller than that.” Bill called me out for that, firing back “it’s not obvious!!” He was just kidding around, but it was a good reminder that I shouldn’t use presumptive language when describing science.

It was impressive how kind and engaged Bill Nye is. As soon as he got to breakfast, he immediately hugged the instructor of our class, and another student in the class who he recognized. He really strikes me as a genuinely caring individual, who got into his business because he wanted to talk to people about important problems. Definitely an inspiration for how I’d like to behave as a scientist.

Note: I was holding off on this post because I wanted to post some pictures from the breakfast, but I haven’t gotten them yet. I’ll try to get them up in the next couple days.

 
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Posted by on March 28, 2008 in Alchemy

 

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Blogging as a Way to Think

A few days ago I wrote about some blogging tips I had gleaned from a talk by Ancient Wisdom Productions. I alluded to what some of my reasons for blogging have been, though that wasn’t exactly the reason for the post.

Today I saw a video of Clive Thompson talking about why he blogs (link via Baxt), and I think I have a lot in common with his motivation. As Clive explains:

I do it to sort of record stuff that I’m interested in, that I see, what I think about it. It helps me like literally think ideas out… I know [a concept] intrigues me, I don’t know why. As I write the blog entry, I literally develop the thoughts. So it’s a way of developing my thoughts, and recording them, so that you know, months later, I can look back and remember, and re-experience the stuff that I was interested in.

The focus of the interview was science and technology blogging, but I think the same reasons are broadly applicable. He also touches on the important aspect of user feedback, and reminds us that if you don’t want to blog, you don’t have to.

 
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Posted by on February 22, 2008 in Alchemy

 

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