Friday, October 28, 2011

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Maintaining all these separate lists can become very tedious, which is probably why most academics' sites are usually out-of-date.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:

#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.

Thursday, October 27, 2011

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.



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?


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.

Friday, October 21, 2011

Springer denies scientist access to her own research

The modern scientific method goes something like this:
  1. Obtain grants to fund your research.
  2. Conduct research.
  3. Write up results of your research.
  4. Submit your written work to a scientific journal.
  5. Sign a copyright transfer giving up all rights to your work.
The last step may sound crazy if you're not an academic, but we usually don't think twice about it. After all, the publisher you're giving the rights to would always give you access to your own work if you needed it.

The following letter from Dianne O'leary, Professor of Computer Science at the University of Maryland, is reproduced here with permission.

From: Dianne O'Leary
Date: Tue, 11 Oct 2011 13:42:18 -0400
Subject: Rejected Springer reprint request

On September 9, I wrote to Springer asking for a pdf file of one of my
Wang and O'Leary, Adaptive use of iterative methods in
predictor-corrector interior point methods for linear programming
Numerical Algorithms, 25 (2000) 387-406.

It took until October 8 for them to answer my request, and they
decided that I was not entitled to the pdf file of my own paper.

This doesn't seem to be the way to maintain the good will of the
community. They might have the legal right to make this decision, but
it seems to me that it is bad logic and bad business, since they rely
on us to provide, without financial compensation, the content for
their journals and the refereeing of other manuscripts.

My university does not subscribe to this journal -- too expensive --
so I was wondering if anyone had an idea of how I can obtain this pdf

Thanks much.

Dianne O'Leary

One more reason to be careful about the journals you submit to.  SIAM, for instance, allows the author not only unlimited use for personal purposes, but also to post the final version of the article on his/her institutional webpage.
By the way, Prof. O'Leary now has over 200 copies of her article -- so there's no need to indundate her inbox with more.  And apparently someone from Springer has now (on Oct. 19) given in and provided her official access to her article.

Update from Prof. O'leary on Nov. 1:

In response to my posting of trouble getting a pdf file of one of my
Springer-published papers, I received over 200 messages of support and
advice.  It is a great community!

M.J.D. (Mike) Powell was inspired to contact Springer, and in
response, I very promptly received the pdf file (which I have learned
that Springer is willing to supply to every author) and legal
permission to post it on my website (which Springer does not
ordinarily give).  This gives me exactly what I wanted, and I am

I had sent my original request to Springer from the website of the
article, clicking the "permissions and reprints" button at  Apparently,
this gives the wrong outcome if you are the author.  The people who
processed my request did not forward it to the appropriate person, the
editor, found using the "contact" button on the journal's homepage.

A week after my posting, Claude Brezinski, editor-in-chief of
Numerical Algorithms, wrote me saying that my message might be
interpreted as criticism of him and the editorial board of the
journal.  I meant no such criticism.

Elizabeth Loew of Springer has been very helpful in trying to solve
the problems and clarify the issues.  It is in the current Springer
copyright agreement that authors cannot post the journal pdf files to
their own websites.  Authors are allowed to email the pdf to

As Steve Vavasis noted last week, authors who care about making their
articles more available need to look into mechanisms such as the SPARC
copyright addendum:

See also the SHERPA/RoMEO site that provides the copyright policy for
many journals:

Friday, October 14, 2011

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?