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.

 

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?

 

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.

 

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?

 

Bill Nye Photos

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

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.

 

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.

 

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.

 

Ancient Blogging Wisdom

A little less than a year and a half ago, I decided to start a blog so that people I know could have a small window looking out over the events of my life, and so that people I don’t know could have the chance to cut me down for expressing my thoughts on the internet.  Really, I started it on a whim.  I thought that writing about nothing and everything might help me feel better about the parts of my life with which I wasn’t totally happy.  And I think it did partially serve that purpose.  Expressing my thoughts in a place outside my head seems to engage a different, underused, part of my brain, and that’s been cathartic.  I still blog for those reasons, but the focus and applicability has been expanded.

Today’s topic in the Science Communication Workshop that I’m taking was “Web Media and Making Your Research Homepage/Blog”. Most of the discussion revolved around blogs, why one might be interested in reading blogs, and how/why one might write a blog.  Bruce, the instructor, gave us a primer on blogging, and we were also treated to a blog design presentation from Molly, Tyler, and Casey of Ancient Wisdom Productions.  I came away with a renewed enthusiasm for blogging, and a list of useful tips from the AWP reps:

• “Design matters” – This was definitely the focus of the AWP talk, but probably the part I will think about the least.  What font we should use.  What line spacing we should use.  How the colors we choose should contrast.  Information hierarchy. It’s a lot, and I really do truly believe that it matters. However, I’m probably going to ignore anything that WordPress takes care of for me (for now, anyways). Someday I hope to be able to pay someone lots of money to make my ideas look pretty.
• “It’s All About Content”– They recommended blogging a lot, at least once post per day if you want to keep people reading.  This makes sense – I know I am much more likely to come back to blogs that update regularly.  Some blogs seem to update too frequently (this is an arbitrary descriptor, and depends on mood, interest, and attention span).  For example, I (personally) couldn’t keep up with the frequency and length of posts at Dooce, so I had to remove it from my RSS feed (I still browse over there manually though). 
• “Don’t Be Afraid to Swear”– This one reminds me of a post I’ve been meaning to write about swearing, but I think the take home point is that blogs do well when they have some character. 
• “Blog for the Moment”– They explained that most people judge a blog by what’s in the most recent posts, and that digging through the archives is relatively rare.  This may be true, but I also know that most traffic that comes to this blog is via keywords that have only appeared in single posts in the archives.  I wish I had a better idea if that traffic ends up visiting the “home” link.
• “Tag the F out of your posts”– After the presentation I asked what their recommendation for tagging and categories was.  They said they liked to have a limited list of post categories, with no more than one category per post.  At the same time, they recommended adding as many one-word tags as you can think of.  Now that WordPress has actually separated tags and categories, this is doable and also sort of fun. 

One of the most interesting impressions I gleaned from the session was that a significant portion of the class is quite anti-blogging.  They think that most blogs are junk, and that the comments are even worse.  They might be right, but I disagree with their (apparent) conclusion that the junk makes blogging less worthwhile. 

First and foremost, our goal in this course is to communicate science to everyone (or at least, to as many people as possible).  That includes the people writing, reading, and commenting on junk blogs.  Communicators of science will almost certainly have to explain ideas to people who don’t get it, don’t care, or just aren’t nice, but whose opinions still matter.  I think blogging is good practice for this.

Secondly, the junk can be amusing.  Read stupid comments.  Respond to peoples’ nonsense.  Get in an argument with someone you don’t know and will never meet.  But, to quote Wil Wheaton, “Don’t be a dick!”.

 

Ethice ex Machina

“Ethics is important when goods collide. It’s no problem deciding between something bad and something good – where ethics really comes is when you have two good things two decide with and you must decide between them because it has consequences.” – Roald Hoffman, 2006

Do ethics arise naturally out of the pursuit of science? What, if anything, about the scientific process inherently forces scientists to confront ethical issues in their work? Last July, Professor of Chemistry and Nobel Laureate Roald Hoffman gave a talk (update: search for ‘ethics’ at the talk link) on this subject at the Annual Meeting of Nobel Laureates in Lindau, Germany.

There’s been an increasing spotlight on scandalous acts of fraud in the scientific community. Hoffman gives an elloquent overview of how the peer review process and the scientific method force scienctists to come to terms with their work, themselves, and eachother in such a way that ethical conduct arises natually, and in doing so marginallizes sensational scandals. Communication forces researchers to confront ethical quandries that must be faced, evaded, or navigated, and it is this negotiation that promotes ethical conduct.

The upshot of this is that while scientists may not necessarily be ethical, science itself acts as a set of rails for behavior in the scientific community. Having such a self-correcting system is important, because otherwise it may seem like the only reason for ethical behavior amongst scientists is the fear of being caught.

Hoffman’s talk raises some excellent questions about the motivation for ethical behavior, the critical importance (to ethics) of publishing experimental methods, and how our ethics need to be excercised so that they do not wither and atrophy. The talk is long, but if you can make it to the last 5 minutes he closes with a cool interpretation of the story of The Garden of Eden and how Original Sin was our first foray into the world of experimental ethics.