Reading the literature

Since January, I have been making a stronger effort to keep up with the literature. Since joining the TT, I've had less and less time to just sit and think about research. One of the easiest things to do is to let reading new publications slide, since there are no deadlines and no immediate rewards. In the past, I've used emailed Table of Content, which I would skim over when they came in. I now find that email is way too easy to ignore these days, especially in the volumes I now receive.

I have three proposals in preparation right now, and I am starting to plan a fourth. I've noticed that it is harder for me to think of new and interesting projects lately, but not all the time. After attending a meeting, I am bursting with ideas. I just need that exposure to new ideas and new experiments to get my own creativity flowing. I know some people rely on their students and seminar attendance to keep themselves current, but that just hasn't been working for me. I clearly needed to make a change, and I think I found a solution (for now).

Using an RSS reader to read journals has been a revelation. It is much, much easier to skim through and click on what I want to look at in small time blocks, since I don't need to get through the whole contents in one sitting. Now that I am "caught up" in the feeds, I mostly see the ASAPs, which come in a few at a time instead of with a firehose of new stuff all at once. To anyone else who is struggling with this problem and hasn't tried RSS yet, I highly recommend it.

Quickie Mendeley review update

For anyone following my Mendeley experiences, I just updated to the latest version, and the integration with MS Word is much, much nicer. There is now a hotkey to use (instead of just the toolbar), you can search in a toolbar that pops up within Word, and it is even easier to add multiple citations at once. I am revising a paper this week, and I am much happier with this new version.

Choosing a journal when writing a paper

We are about to start writing a manuscript in an area that represents a change in direction from all of my prior work. My usual journals are not really a good fit for this work, so I am thinking hard about where to send it. Even in the age of Google Scholar and Web of Science, I think journal selection is important (especially for those who are TT and earlier in their careers).

At National Lab, where bean counting was becoming more and more important, the impact factor trumped all. All raises and promotions had to be justified to non-scientists and/or former researchers in a wide array of fields. To make things easy, they would rank papers by impact factor, regardless of field. This is hugely distorting, since a great specialty journal in physics can have a smaller impact factor than a decent specialty journal in biomedical research (just due to the number of researchers in the sub-field). To get ahead, many people would find the journal with the highest impact factor that would publish the research.

My preferred style is to find a journal where my target audience is likely to read it. So if I am doing physics-type measurements on a protein, I would prefer to put it in a physics-type journal (where others might pick up on it and find it useful) rather than a protein-type journal where most readers could care less about this physics-type measurement, even if the impact factor is lower. Even though my bean-counting impact might be lower, I am counting on the actual impact being higher. What is the point of a high-impact publication if no one reads it? That said, when DrugMonkeyasked people about their citation practices, many commenters said they prefer to cite papers from higher impact journals, so clearly impact factor must be balanced with target audience.

This type of selection is much easier when I am intimately familiar with the sub-field. In that case, I know well which journals I read and cite, and can select accordingly. In this particular case, I don't have any knowledgeable colleagues or collaborators I can talk to, but that is generally my first stop in deciding where. How do you all pick where to submit your work (especially work in a new area for you)?

Long delayed Mendeley review

Way back in August, I started playing around with Mendeley after getting annoyed with Endnote. I said that I would write up a review after I had been using it a while, and I think I have enough experience with it to compare it to Endnote.

There are many things I really like about Mendeley. I really like reading papers in it, since I can save notes about the paper that I can search and share if so desired. Searching inside pdf files also works very well, and it is much, much easier for me to use Mendeley than to try to remember which paper I was thinking of and then open it in Adobe Reader. I never really got into Endnote's pdf features--the pdf search and import features were buggy and irritating when first introduced, so I never got into the habit of using them.

The pdf import feature in Mendeley works very well for me. I was able to convert over most of my library directly from my pdf files. This also works well with my new literature review system. Now that I am trying to use RSS to keep up, it is very easy for me to download pdfs into a directory that Mendeley watches. I also use Web of Science for searches and download pdfs through there. This is a huge improvement from my old system of exporting Endnote data, then importing the reference, since bibliographic imports happen automagically. Correcting errors in imported files is really easy, and can be done manually or via Google Scholar search. I spent a bunch of time initially correcting entries, but now I don't really have to. There is a pretty decent time investment in importing hundreds of pdf files at once, especially if you want to be able to properly search by author (since the author names MUST be imported properly for this to work). I did not try importing my Endnote library, but that is another option.

There are a few downsides I've found to Mendeley. I find the cite while you write interface a little clunky. It is not unusably so, and it is really easy to find the paper I want to cite using Mendeley's search functions. I thought the same about Endnote's interface, so this wasn't a major downgrade for me. One minor quibble--it is not possible to do unrestricted edits in the bibliography generated by Mendeley. This is something I have only just started playing with, so I am not sure what exactly I did to cause Mendeley to complain about it.

One big issue I discovered is that Mendeley and Endnote DID NOT play well together in one document I was working with. The references got corrupted and I had to strip out all the references and redo it all using just Endnote (since that is what my collaborator uses), which was really annoying. This is hopefully just a minor glitch for me, but may become a problem when I am writing with collaborators who still use Endnote. I haven't had this problem in some of my own documents (updating old proposals, for example). I plan to avoid on using two reference management systems in the same document as much as possible, but be careful if you do!

Mendeley was very disappointing in one area, and that is in keeping a library synced between two computers. I used to use a laptop and a desktop, and I tried to use Mendeley to sync my library between them, but this caused me lots of grief. I had lots of duplicates in my library, and Mendeley sometimes lost track of where the pdf files were on my laptop. I have solved this problem for myself by switching to using one computer (a laptop with a dock), but this seems like a feature in Mendeley that needs a lot of work, but could be very useful.

I don't really use the online features of Mendeley much, but in theory, you can grab citations while surfing and also have access to pdfs through the Web interface. I am not sure how well this works, since I always download pdfs when I want to cite and/or read something, but this is something that might be useful to people who use Google Scholar for searching and/or don't always work on the computer where their pdf library resides.

In short, I am keeping Mendeley. That it is free is only icing on the cake!

UPDATE: Thoughts on the latest update here.