Congratulations, you've reinvented Bibtex.

From the Mendeley official blog:

 

The most laborious part of any research paper for me, and probably for many of you, is making sure that the references are formatted in the proper style. Is the title supposed to be in italics? Do I need a period or a comma here? It has always seemed like exactly the kind of thing that a computer should be able to do for me, and now with Mendeley it can.

Nice to see that they're catching up with 1985 technology.  Yet mystifying why they choose to write their own rather than adopt what is already widely used.

Do you know what your colleagues are reading?

Up until Google's recent (catastrophic) changes to Reader, I used it to share and discuss interesting journal articles.  It was a near-perfect platform for this, and I'm hopeful that we'll have a replacement soon.

The great utility of it was that my colleagues are very good at discerning which articles may be of interest to others in our circle.  This is no surprise, since we have similar research interests.  The fraction of articles that are actually interesting to me, for most journal RSS feeds that I check, is 1%-5%, which means I spend a lot of time scanning article titles.  In contrast, the fraction of papers shared by my colleagues that I find interesting is probably closer to 50%!

I've found a nice way to display a public RSS feed of papers that I read*, via Mendeley (it's shown here on the right).  Now, ideally, Mendeley would allow me to publish a feed that includes all papers in my Mendeley library as I add them.  They don't, but they do something almost as good: they provide a public RSS feed showing all papers for any public Mendeley group, as they are added.  So here's what I did:

1. Create a public Mendeley group for my own library.

2. Whenever I import a new reference to Mendeley, I also add it to the group (note that you can do this via the dropdown menu in the popup that appears whenever you use the 'Import to Mendeley' bookmarklet.

3. I got the address for the feed from Mendeley (log in, click the 'Groups' tab, click 'Papers' on the left, and look for the RSS feed icon on the top right) and added a widget here on my blog, as well as on my professional webpage.

That's it.  If you want to subscribe to this RSS feed, here it is:

feed://www.mendeley.com/groups/1194891/david-ketcheson-s-library/feed/rss/

 

[*] Note that 'read' here means 'read at least the abstract.'

Managing publication lists in HTML

As an academic, it's a good idea to maintain a professional website with a list of your publications.  Ideally, this list should include links to where visitors can download the papers (PDFs) and any related code.  In my case, I also maintain a website for my research group that has another publication list. Of course, you need to maintain local reference files with the citation info for your publications (for inclusion in later publications), as well as your CV.

Maintaining all these separate lists can become very tedious, which is probably why most academics' sites are usually out-of-date.  Here's how I automate much of it:

• I use Bibtex. This allows automatic generation of bibliographies for papers and for my CV.  And it's the basis for generating HTML bibliographies, as outlined below.
• I use Mendeley. Mendeley allows me to create separate bibliographic lists (e.g., for my own publications and for those of my research group) and export them as bibtex files, using the desktop app.  It's also possible to get a bibtex file of your Mendeley publications directly on-line through BibBase.  You can even display a list of your publications on-line automatically using Mendeley, but it's not very customizable; for instance, they appear in alphabetical, rather than chronological order.
• I would use BibBase to automatically display an updated bibliography if my institutional server ran PHP or CGI scripts, but no luck there.
• My less-automatic solution is simple Python scripts that generate CSS-friendly HTML.  The scripts use the Python module bibliograph to parse bibtex entries.  I could instead use bibtex2html.  I like my solution better because the customization is all done using CSS rather than Python, so I can change the look without re-generating the HTML.  Of course, bibtex2html is a more polished and flexible tool than my 30-line script.
• Here's a CSS snippet that's used for this publication list:

#pub {padding: 5px; border-width: 2px; border-style: none; background-color: #eee4b5; font-size: 1.2em; margin-top: 20px; margin-bottom: 20px;}
#pub a{font-weight: bold; color: #09434e;}
#pub name{font-weight: bold; color: #09434e;}
#pub journal{font-style: italic;}

 

The workflow for adding a new paper to an html bibliography is:

1. Add the paper in Mendeley.
2. Export bibtex from Mendeley.
3. Run Python scripts.
4. Paste resulting HTML into the appropriate file.

Again, it would be simpler if I could use Bibbase (cutting out steps 2-4).  It's still fairly painless, and it's easy to generate new bibilographic lists or customize the look of existing ones.

Searching the scientific literature

Many of the fundamental skills of a scientist are seldom taught. Instead, one is expected to pick them up through intuition, informal conversations, or trial-and-error. One of these essential skills is how to search the literature for journal articles related to a particular topic.

This is a challenging task with severe consequences for failure. Just ask any Ph.D. student who discovered that his thesis was focused on a problem that had already been solved. Or anybody who left grad school because of the overwhelming task of grasping and keeping up with the scientific literature related to his thesis topic.

 

Why

The purpose of a literature search is not merely to become aware of what results are already known. Rather, a good literature search provides a map of the scientific terrain, indicating the general layout of a research area:

 

• What are the main goals of research in this area?
• What kind of advances are considered significant, and why?
• What are the recognized open questions, and what impact would their answers have?
• What other research areas are most closely connected to this one?
• Are there other research areas with connections to this one that have not been recognized?
• How is this research area viewed by those who focus on related, competing topics?

How

With these goals in mind, how does one conduct an effective literature search? Here are some techniques that have served me well:

• Ask for help. You have a network of collaborators (or at least an advisor!) who each know some part of the literature much better than you. If you're starting research in a new topic where they have expertise, ask them for the most significant work on that topic. Ask their opinion of new papers that seem significant to you. Ask them for the right keywords, authors, and review articles to start with. Because they can make connections that a search engine never would, they are your most valuable resource.
• Use Google Scholar. Yes, there are countless databases and search tools out there for looking at a articles from a particular discipline or publisher. But I have yet to find one as effective as Scholar. I'm convinced that its coverage is much broader than any of the commercial academic databases available. For instance, few other databases cover the ArXiv, which is an essential source in some fields.
• Link forward through the literature. Every paper has a list of references to the works that it cites. But since you're mostly interested in learning about the state-of-the-art, it's usually more helpful to obtain a list of papers that cite the one you have. This is another major advantage of Google Scholar, which allows you to do so easily. Each search result includes a link to a list of all the articles that cite it.
• Learn how to do effective keyword searches. This skill has become incredibly valuable in the internet age, and nowhere more so than in searching for journal articles. When learning about a new topic, it can be hard to know which keywords to search for, and you should ask for help (see above). Once you know the right words, it can be very important whether search for A and B, A or B, A since year X, B authored by Y, and so forth. Learn how to refine your searches in this way.
• Learn to rapidly evaluate article titles and abstracts. You can't hope to read all the articles, or even all the abstracts published in your field. Your ability to find the most relevant ones is directly proportional to how quickly you can eliminate the irrelevant. I'm convinced that this skill can only be obtained by experience, but you can accelerate it by noticing articles that you thought would be useful but turned out not to be, as well as becoming aware of who the key authors are in an area.
• Check for articles in review journals. Most fields have some journals that publish only review articles. Such articles provide a broad overview of a topic along with a detailed bibliography; they are invaluable when starting research on a new topic. In my field, the most relevant are Acta Numerica and SIAM Review. Review articles tend to rank high in search engines because they are heavily cited, but it can be worth searching for them specifically or even browsing review journals that publish a low volume (like the two just mentioned).
• Check the websites of key authors. You can often find their preprints there long before the published article becomes available. Of course, you don't have time to do this on a large scale, so you have to be selective.

I'm planning a future post that will discuss what to do with all the relevant and significant articles you find.

What journals do you read?

As a scientist, one is defined by the kind of problems one works on, the conferences one attends, the journals one publishes in, and the journals one reads. All of these except the last are more or less publicly available information.

Only you know precisely which journals you choose to read, yet they're an essential part of your scientific identity. They determine the kind of new advances you're likely to be aware of and where your research may turn in the future.

I've made my Mendeley library public, so anyone can see in great detail not only what journals I read but which articles I read. But most of you are probably not interested in quite that level of detail, so here's a list of the journals I follow closely. I collect their RSS feeds (with Google Reader) and read at least the title of every article they publish. I've grouped them into 3 main categories, but otherwise they're in no particular order. Those listed in bold are journals where I have published; they also tend to be the journals most heavily represented in my Mendeley library.

Numerical Analysis and scientific computing:

• BIT Numerical Mathematics
• Journal of Scientific Computing
• SIAM Journal on Scientific Computing (SISC)
• SIAM Journal on Numerical Analysis (SINUM)
• Mathematics of Computation
• Numerische Mathematik
• Applied Numerical Mathematics (APNUM)
• Computational Science and Discovery
• Journal of Computational and Applied Mathematics
• Journal of Computational Physics (JCP)
• Computing in Science and Engineering (CiSE)
• International Journal of Numerical Methods in Fluids (IJNMF)
• IMA Journal of Numerical Analysis
• ACM Transactions on Mathematical Software (TOMS)
• Computer Physics Communications
• Acta Numerica
• math.NA on ArXiv

 

I would add Communications in Computational Physics and Computational Methods in Applied Mathematics, but as far as I know they have no RSS feed.

Nonlinear waves:

• Physica D: Nonlinear Phenomena
• Nonlinearity

 

Here I would add Communications in the Mathematical Sciences, which also has no RSS feed.

General applied math:

• SIAM Review
• SIAM Journal on Applied Math
• IMA Journal of Applied Mathematics

 

Although ArXiv isn't a journal, I've included it here. Indeed, I find useful articles in that feed much more often than for most of the listed journals.

What does your list look like?

Mendeley's PDF import has improved dramatically

Looks like the folks at Mendeley have been quietly making some big improvements.

When I first started using Mendeley, I decided to drag a folder of one hundred or so PDFs into it, since it could extract the bibliographic metadata from PDFs. The consequences were disastrous, with a dozen documents named "Society" and all published in "Science". Overall, less than half were correctly imported, and many entries were unrecognizable.

Since then, I don't drag PDFs into Mendeley. This means that bringing in a new document requires a few steps: get the metadata from a journal webpage (automatically using a bookmarklet), download the PDF, and finally associate the PDF to the document.

Today, by accident, I happened to drag a PDF into Mendeley. To my surprise, it was imported perfectly, with all bibliographic data correct. I decided to try another. And a few more. All came in perfectly. I also found that dragging a PDF of a paper already in my library DID NOT create a duplicate.

Thanks, Mendeley developers. Please keep it up.

Why I won't be a Mendeley university advisor (for now)

Mendeley, my tool of choice for bibliographic reference management and sharing, just announced their "University Advisor" program. Basically, they're asking academics to advocate for them on campus in exchange for free premium accounts.

I already advocate for Mendeley unofficially, because I think it is useful and its usefulness will grow in proportion to the number of people who adopt it. But I'd rather not be officially associated with Mendeley, mostly because it's not yet a sufficiently polished product.

Mendeley is a useful product with a lot of potential, but it still has a lot of serious problems. Some of these seem like telltale signs that the basic software and data infrastructure on which Mendeley is built has fundamental and dangerous flaws.

For instance, my Mendeley collection has 516 documents according to both the Desktop app and the web app. But the "my library stats" page says I have only 328 articles. This doesn't cause any real problems, but the idea that somehow a count of these items is being maintained in a way that it can get permanently out of sync is disturbing. Furthermore, I had an e-mail exchange with Mendeley support about this a couple of months ago, and they admitted it was a problem but they've been unable to solve it.

Duplicates. This is a huge problem with Mendeley. If I import a document twice, even from the same source, I get duplicates. If I drag a document from my library to a "group" twice, I get duplicates. The latter behavior is really inexcusable, since this operation occurs entirely within Mendeley. It also makes it very painful to use groups (so painful that I've stopped using them). I have a group called "Runge-Kutta stability regions", and I'd like to keep all papers in my library with the tag of the same name in that group. This would be easy if I could just periodically select the tag and drag all papers to the group, but that's a recipe for disaster since I'll end up with duplicates. CiteULike sync is also a disaster, as it generates many duplicates.

Bibtex. Mendeley just doesn't seem to pay enough attention to bibtex-centric user needs. In the desktop app, citation keys are not shown by default. When one right-clicks on a document and selects "copy citation" (with citation style set to bibtex), the citation generated is different than what one gets from "export citation" (the cite keys don't agree). Mendeley mangles bibtex fields on import. When articles are removed from Mendeley, they may persist in the auto-synced bibtex file. Combined with the duplicates problem, this can be a nightmare.

Sharing. Mendeley is supposed to facilitate sharing, but unfortunately it also restricts sharing in one very important way: my library is not publicly accessible, and I cannot make it so. Why not? Do people have something to hide in their library of scholarly references?

I could go on, but you get the idea. Mendeley has a lot of things going for it, not the least of which is a very active development team, and I hope it succeeds in achieving what its developers intend. It's my tool of choice, but as its name indicates, it's still beta.