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A while back, I tried out Papers as a reference manager.  I liked it, but since I’m regularly using three different computers (and the license allows for two) I decided against using it and settled for BibDesk that’s also pretty good. Especially since I’m mainly using LaTeX for my writing.

Since then, though, I’ve moved to writing more and more in Word since that is what my biology colleagues are using, and there I use EndNote, but as a reference manager I don’t really like it much.  I need it for work, but for managing my references I’m just not that attracted to it.

Now I am finding myself in the situation that I need to share a reference list with some people I’m working on a review paper with.  I have no idea how to share such a list using Papers, and while it is possible with a combination of BibDesk and Dropbox, it isn’t quite as easy as I would like and I would need to to export to EndNote from time to time, so I looked around to find an alternative.

I was recommended Mendeley a while back and tried it out there, but didn’t really use it.  But I decided to try it out again, and it is growing on me.

Synchronizing the references between my computers is really easy since the reference list is on a web site, and sharing a reference list is just as easy since this is built in.

The desktop application is pretty easy to use

but I’m finding that I like the web interface more (but I would love to have auto-completion on keywords there as I have in the desktop application).

The main feature I missed when I tried out Mendeley the first time was a way to search for publications within the tool.  As far as I can see that is still missing, but if I’m using it through the web interface it isn’t such a pain.  I can search in PubMed or Google Scholar or such, Mendeley can import from search results.

I haven’t tried this yet, so I don’t know how well it works, but Mendeley can also synchronize with a BibTeX file which makes it perfect for my typical use.  It can also export to EndNote (but there’s more manual work involved here; not so much an issue for me since I don’t need this quite as often as exporting to BibTeX).  It also exports directly to Word, as far as I can see (but I haven’t tried that yet), so perhaps I can get my colleagues to use it instead of EndNote to avoid the problem completely.  We’ll see.

“Science in the open” has a very nice piece on the “author pays” publishing model.

There are several good points in the post, but in particular I want to address this one:

The more insidious claim made is that there is a link between this supposed light touch review and the author pays models; that there is pressure on those who make the publication decision to publish as much as possible. Let me put this as simply as possible. The decision whether to publish is mine as an Academic Editor and mine alone. I have never so much as discussed my decision on a paper with the professional staff at PLoS and I have never received any payment whatsoever from PLoS (with the possible exception of two lunches and one night’s accommodation for a PLoS meeting I attended – and I missed the drinks reception…). If I ever perceived pressure to accept or was offered inducements to accept papers I would resign immediately and publicly as an AE

I am an AE at PLoS ONE myself, and that is work I do for free.  Like any other editorial or reviewing job. It is part of academic life and basically just expected of scientists. I have never been paid to review or to serve as editor, so I really have no interest in making money for any publisher. The financial gain for me is exactly the same if I accept or reject a paper.  I get exactly nothing in either case.

If the author pays model was a scheme to earn money from papers that cannot be published elsewhere, it seems a bit dumb to leave the decision of whether a paper should be published with people who have nothing to gain from accepting papers over rejecting them.

As a side note, you usually have some author fees at most high tier journals as well.  They will charge you both to publish and then to read the papers.

Another point that is rarely raised is that the author pays model is much more widely used than people generally admit. Page charges and colour charges for many disciplines are of the same order as Open Access publication charges. The Journal of Biological Chemistry has been charging page rates for years while increasing publication volume. Author fees of one sort or another are very common right across the biological and medical sciences literature. And it is not new. Bill Hooker’s analysis (here and here) of these hidden charges bears reading.

I guess one of the reasons that this discussion pops up again and again is PLoS ONE’s approach to papers. That is just PLoS ONE, the other PLoS journals are a very different story, by the way.  At ONE the philosophy is to publish anything that is considered sound science. There is a lot of science that is solid enough, but where the results are not that ground breaking.  Those are hard to get published, but that doesn’t make it bad science.

A prime example is negative results. The reason we have to worry about publication bias is exactly because we are more likely to publish positive results over negative results.  We need to know about the negative results as well, but they are usually too hard to get published.

At PLoS ONE, and also BMC Research Notes where I’m also an AE, negative results are welcome.

This doesn’t mean that we will accept any paper that is submitted.  Not at all. The methods used must be of the same standard as required everywhere else. The statistics just as solid. The impact of the discoveries are just not a criteria.

If you don’t believe me, try to go to the journal and read some of the papers.  I think you will find that they are usually of the same quality as you would find elsewhere.

Is R an ‘epic fail’?

Something as popular and widespread as R can hardly be called a ‘failure’ in any meaningful sense, so of course the question is really in which aspects R is inferior to alternatives.

For most users who need a bit of data analysis, it is probably a poor first choice. R is a programming language with a lot of statistical and data visualisation support, but it is a programming language.  If you don’t want to do any programming, don’t muck about with R!  There are lots of visualisation tools and statistical tools that are much easier to use.

Of course, without a bit of programming, you are limited to what those tools can do, so if you need analysis that is not provided, you need to either find a programmer or learn how to program, and for the latter, R isn’t a bad choice.

You can get pretty far with very little effort in R, once you have learned how to program. Now learning how to program does require quite a bit of effort, but if you need to there really isn’t any way around it.  Just like there isn’t any Royal Road to mathematics (as Euclid is supposed to have said).

Sure, as a programming language R has its idiosyncrasies, but which programming languages do not?

Why use R?  Because that is what the professionals use!

The moral of the story is not that one should blindly use professionals’ tools; that can be just as bad as ignoring them. You don’t need to use Google or Facebook’s infrastructure to run your personal blog, just as developers shouldn’t employ the GPL simply because it’s the same license Linux or MySQL uses. But if you want a no-bullshit take on which technologies actually deliver, you could do a lot worse than watching what the professionals use.

I’ve never been a big fan of comments in code.  Mainly because I too often have seen comments explaining the trivial and ignoring the complex…

In most cases, clear code eliminates the need for comments, as discussed here.

I used to think commenting my code was the responsible thing to do. I used to think that I should have a comment for just about every line of code that I wrote. After my first read of Code Complete, my views changed pretty drastically.

I began to value good names over comments. As my experience has increased, I have realized more and more that comments are actually bad.

Actually, Code Complete has a more nuanced discussion on commenting code, but still…

Comments are often not needed, because they just rephrase what you can already read in the code. If at all possible, make the code easier to read rather than explain it in code.

When comments are needed, they explain design decisions that are not obvious from the code. Then there is too often the risk that the design has changed since the comment was written and that is really worse than no comment.

Still, it is when it comes to design decisions that I often miss documentation. Especially when it comes to complex class hierarchies and object interactions where there is clearly some underlying design decisions about how the objects are suppose to interact and how new classes should be added to the hierarchy to extend the code.

I rarely find that stuff documented, though.  At best I am told that for function add(a,b), “a and b are input” and “add(a,b) returns a+b” or something obvious like that…  or that the class “AbstractVisitor” is an abstract visitor class.  Duh!

I would love it if people would stop commenting the obvious but start explaining their design decisions…

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