Citation copy-editing is one of those deceptively small burdens that have a way of taking over the working day. If left untended, the task of tidying up casually scribbled references can snowball to crisis proportions as a submission deadline approaches. Similarly, when a submission to one publisher is unsuccessful, significant effort may be required to recast its citations in the format required by another. Collaboration outside of one’s own field can bring with it an unwelcome tangle of fresh style-guide quandaries to ponder and fight through. These are things that the machines, if they want to make themselves useful, should be doing for us.

There is plenty of collective experience in this line, and as fate would have it, there are also plenty of collective solutions. In the TeX/LaTeX world, authors and their editors can today choose between BibTeX and BibLaTeX — both of them excellent utilities — with the several variants of the former supported by no fewer than four separate versions of the BibTeX program. [1] Users of WYSIWYG word processors can look to the bibliographic support built into Word or Open Office, or they can turn to an external solution such as EndNote ™, ProCite ™, Reference Manager ™, or more recently Zotero or Mendeley. Migrating data between these environments is a process fraught with uncertainty, but it is sometimes unavoidable when you need this kind of output, and it can only be produced on that kind of system …

… with so many solutions to choose from, it’s hard to go right. [2]

The citeproc-js citation processor is a Javascript implementation of the Citation Style Language (CSL), an XML schema for describing citation styles that aspires to strike this problem at its root. CSL is a general, open standard that enables fully modular control over bibliographic formatting. This means that CSL is capable of accurately describing styles used in many disciplines, from the sciences, through the humanities to law. It also means that a CSL style description can be used with any other application that understands the CSL language. And it means that the style description is separated to the extent possible from the target document; you can switch styles at any time, even after the writing process is complete. Generality, a comprehensive pooling of community resources, user-centric ease of use: all areas where, collectively, our current menagerie of productivity tools could do better.

CSL first saw wide application in the Zotero project. [3] Citeproc-js has been developed in the first instance for use in Zotero, [4] but it runs as a separate module via a (relatively) simple API, and with appropriate wrappers, it can be deployed pretty much anywhere. Potentially, any application that generates dynamic content — text processors, word processors, weblog environments, and dynamic websites — can use CSL and citeproc-js to provide publisher-correct citation and bibliography facilities without exceptional programming effort. [5]

Development of the CSL language has been spearheaded by Bruce D’Arcus. The citeproc-js processor adheres to version 1.0 of the CSL specification, [6] which has been engineered and documented during the past year primarily by Bruce and Rintze Zelle, with incidental contributions by myself and others. It will debut, together with the new processor, in Zotero 2.1, which should begin to emerge, if all goes well, during this calendar year.

Meanwhile, the processor itself is complete, documented, and more or less ready to go. [7] Here is a short run-down of some of the highlights:

Disambiguation

In author-date citation styles, works by the same author must be distinguished from one another in some way. The current Zotero processor performs name and cite disambiguation as required by the Chicago Manual of Style. There are in fact at least six other disambiguation methods in general use. CSL 1.0 and the new processor will support all of them.

Sorting

The AGU journals, in particular, impose extremely demanding sorting rules in the bibliography. [8] CSL 1.0 and the new processor support multiple sort keys with arbitrary sort order for each key. A wide variety of sorting schemes can be implemented, including the AGU sort.

Parallel citation support

Many legal styles, including the Bluebook style common in American law journals, require that law cases appearing in multiple reporters be cited to each reporter, with the case name in front, and the court and year of decision at the end. [9] The new processor supports this behavior.

On-the-fly document updates

The API of the new processor supports targeted context-sensitive updates of citations in a document that are affected by an insertion, deletion or edit, for efficient transactions with a word-processor or weblog plugin.

Localization of dates

CSL version 0.8 currently supports the use of localized terms for style-supplied labels and the like. CSL 1.0 will add sophisticated localization of dates; both the language of month names and the ordering and formatting of elements will adjust appropriately when the language of a citation style is changed.

Sophisticated names handling

A great deal of work has gone into enhancing the handling of names in CSL 1.0. European conventions on the handling of particles such as “von”, “van”, “di” and the like can be accounted for appropriately both in the sorting and in the rendering of individual names.

In-field formatting

For scientific publishing, the new processor recognizes a limited subset of HTML as markup within titles, enabling superscript, subscript, small capitals, italics, boldface. The processor also implements the flip-flopping of italic and boldface, and of quotation marks, to avoid ambiguity in rendered citations. The HTML used in markup is transformed by the processor into the selected output format (HTML, RTF, LaTeX, or whatever) during rendering.

Multi-lingual citation support

The new processor implements experimental support for multi-lingual citations, providing a flexible mechanism for the transliteration of names and titles, for the supplementary translation of titles, and for the use of alternative sort strings needed for Asian languages.

As it leaves my laptop, citeproc-js is just a bare Javascript module with some test suite wrappers to check that it actually performs as advertised. But with the widening availability and increasing efficiency of Javascript runtime tools, I do hope that it has some prospect of escaping from its cage and wreaking order on the world of bibliography management. If you’re an integrator or site administrator, the fine citeproc-js manual is your first point of reference. If you’re an end user, keep an eye out for the CSL mark, coming soon (maybe) to an application near you!

Springer announced last week the launch of LaTeXSearch.com, a free online service allowing users to search a huge database of LaTeX snippets from Springer journals and publications. This follows the launch of a similar service, a few months ago exposing Springer’s database of scientific images (which suggests a precise strategy on how to build Web services on top of content in their publication database).

LaTeXSearch does what it promises, using similarity algorithms “to normalize and compare LaTeX strings so that, if similar equations are written slightly differently, the outputs are normalized and matched, granting you the broadest possible results set”. The only glitch is that snippets are not cached but generated on the fly, with the annoying result that it can take quite some time to display the rendered version of LaTeX formulas in search results.

The last week or two has seen some serious winter weather here in the UK. Schools have been cancelled, transport delayed, idiots arrested for driving on frozen canals, and all those other things you would typically associate with places like Canada, not the balmy UK. (No, on second thought, I take back that thing about the canals. We don’t do that in Canada, unless you count this).

Anyway, the weather’s meant that a lot of us have started 2010 by working from home. Timely as always, the Guardian published a small article with some helpful tips for those new to home working. As someone who has worked from home for the past two years, I’d say the basic advice is pretty sound and worth repeating here:

1. Have a work space. Prepare a clear work space so that you can mentally, if not physically, separate home and work life. If you have a spare room to use as a home office, great; if not, clear off the kitchen table and do your best.
2. Don’t forget to take regular breaks. It can sometimes feel like you need to prove constantly that you are at your desk working, but remember: it’s very rare that an entire workday at the office would be spent staring at your computer. So listen to the radio, go for a run, do whatever you like: it’s okay to take a break now and then.
3. Be clear about what you’re working on. This is mainly a due diligence tip for those who might not normally work from home and need to demonstrate that they haven’t been wasting their time. But it’s good general advice too. Even if you are a seasoned home worker, it’s always useful to clearly set out what you hope to accomplish during a day. This is especially important for long stretches of home work when it’s all too easy to procrastinate from day to day.

One of the interviewees in the article suggests that people “stick to the work pattern they adopt at the office” and this is a good take-away message. Home work really is like working from the office, with some pros and some cons. In the past, I thought there might be more pros, like listening to music or doing a bit of laundry, but most of the time that doesn’t work. You need to have enough discipline to avoid those distractions and focus on the job at hand. This can be difficult at first but ultimately, it’s worthwhile. Once you get used to the monastic life, you may actually find that you get more done at home as there is very little outside distraction (compared with an open-plan office).

Anyone else worked from home recently? What tips do you have?

A glimpse at the hottest topics in scholarly literature according to PhdComics.

[via FlowingData]

Peter Sefton wrote a series of posts on wave. He has published on Scholarly HTML so I read attentively what he has to say. What follows is some highlights of his posts, and my thinking about where things are going. There are at least four things that bother me about wave –as it is today:

1- It’s not really HTML

I thought that waves being XML documents would be a good thing because it’d separate content and formatting. But it seems that they made some strange decisions about how to represent formatting with “very tenuous relationship to HTML”. For example

While there is talk of ‘XML documents’ in the whitepapers etc, a wave document in the current implementation is apparently a series of lines of text. All formatting and what you might think of as structure, such as whether something is a heading or not, is considered an annotation.

This is important right now because the only way to get the resulting doc is to dump the html to a file, or ‘copy-paste’. So, in a way, losing formatting like this would completely incapacitate wave for serious paper writing. I have had some success just copy-pasting and keeping most formatting, but I cannot risk to write a long paper and lose all formatting. Which won’t happen, because…

2- It doesn’t work too well for long, structured documents

Having a large blip for the entire paper with many people editing it seems to perform poorly. And having each person write their own blip-per-paragraph is not very pretty. It’s in fact distracting. I don’t discard wave’s usability to go through the roof once people start making things with it (robots). But it all depends on how well the API is designed. For example, following the mailing list, it seems that there’s no easy way to reorder blips programatically. This sounds like bad design to me.

3- It doesn’t integrate well with citation tools

It may be a matter of time before all the bibliographic tools we like get integrated. For example, Igor does offer some basic integration but this is far from satisfactory.

4-Formatting is simplistic

Wave has no table support. Figures are also not what you would expect, even for a notetaker. Captions are not implemented, nor footnotes. finally, LaTeXy is not the most convenient way to get equations done, I’m afraid, and it doesn’t go both ways.

Clearly, the content/form separation in wave is not designed for academic collaboration, and it shows. The questions is whether we can make this happen by writing robots[1]. Whether wave is the open platform that would make academic writing 2.0 happen.

Wave is just a tool. Why does this matter so much?

You may think that thinking too much about tools is counterproductive. But the way things are, it looks like tools are more and more important. Right now, we are stuck with the paper metaphor. Authors can produce pdfs, and publishers too. A publisher may make a prettier one, but that adds little value. We are equaled in terms of tools. However, publishers such as Elsevier want to get away from the paper metaphor (which is a good thing). As a consequence, authors will not be able to produce HTML as rich as the publisher’s. Here, the difference in tools matter.

In this case, Wave does look like an easy way to craft an interactive experience with little effort. So, even if you discard wave’s usefulness as a collaboration tool, it has quite a lot of value.

But it could very well be that wave doesn’t fulfill its promise. Microsoft Office 2010 offers similar functionality (close to real time edits). And of course, word has unparalleled features such as track changes, integration with endNote, etc. It could be that people adopt this new way of collaborative writing in real time without using wave. What worries me is that openOffice looks seriously left behind now. If it looks like a half-assed implementation of word 2003 features now, imagine when real-time hits mainstream. You need a serious server infrastructure to support that, which is possible for Google or MS, but not for a –smallish- open source foundation. I hope they find a way to jump in the train before it’s too late. Wave has a lot potential, because it is open. If openOffice could support that wave protocol, it could be a big achievement for open source.

If you have had any experience drafting a long doc in wave, please post it in the comments.

[1] For more on this, see my Wave intro for RuPy 2009.

Call for participation for a workshop at CSCW 2010
[submission deadline: November 20, 2009]

The confluence of two major trends in scientific research is leading to an upheaval in standard scientific practice and collaborative technologies. A new generation of scientists, working in large-scale collaborations, is repurposing social software for use in collaborative science. Existing social tools such as chat, IM, and FriendFind are being adopted and modified for use as group problem-solving facilities. At the same time, exponentially greater and more complex datasets are being generated at a rate that is challenging the limits of current hardware, software, and human cognitive capability. A concerted effort to create software that will support new scientific practices and handle this data tsunami is redefining the collaboratory and represents a new frontier for computer supported cooperative work.

This follow-on event to a similarly themed workshop at CHI 2009 is intended to foster community among researchers and practitioners from multiple disciplines interested in the changing dynamics of scientific collaborations.

We encourage papers on the following topics, especially those with a focus on changing practices in these areas:

• Collaborative scientific applications concerning data gathering,
  analysis, sharing, and visualization
• Case studies concerning data gathering, analysis, sharing and visualization
• Socio-technical research on scientific collaborations
• Social networks of scientists
• Repurposing social software for science
• Participatory design and/or rapid prototyping for scientific software
• Distributed data gathering and analysis
• Time-critical scientific applications
• Studies of generational differences in how science is done
• Cross-functional applications and comparisons of a scientific to
  a non-scientific field

For more information, please see the workshop web site:
http://www.sci.utah.edu/cscw2010/

Organizers:

• Cecilia Aragon, Lawrence Berkeley National Lab, CRAragon@lbl.gov
• Jeffrey Heer, Stanford University, jheer@cs.stanford.edu
• Charlotte Lee, University of Washington, cplee@u.washington.edu
• Claudio Silva, University of Utah, csilva@sci.utah.edu

When I started my DPhil, I set myself assignments in order to cover the lit review in easy bite-sized chunks. This worked pretty well but the collated material was scattered across different Word documents, which meant that I couldn’t look at everything at one glance or search the content.

However at about the same time, I also started free-writing to generate ideas. If you’re not familiar with the technique, it’s simply writing for a fixed amount of time without stopping. You don’t delete anything on the fly and just go, writing down anything that comes to mind until the timer sounds or your wrists cramp up, whichever comes first.

Instead of putting this writing into Word documents though, I decided to set up a local installation of the blogging engine Movable Type. In retrospect, I think this was probably just an excuse to play with blogging software but it turned out to be a good decision. I could add content from any computer with access to the server, the basic input form meant that I focused on content not style, and of course, I had all the blogging bells-and-whistles attached. Comments could be added at a later date, the information sorted and searched, shared with my supervisor and so on.

I’m not sure why I didn’t think of it at the time but I would now recommend combining the two ideas: use a blog to write your lit review. (I say “write”, but I really mean “draft”. The structure of blog writing is quite different from academic writing and besides, you’ll want to tidy up references, tables, etc. for the final version. But a blog post is still big enough to cover the bulk of the material and help you organize your thoughts.)

The final stumbling block of course is how to get the content out of the blogging engine and into a presentable format. Fortunately, there’s a script called WPTEX that will convert your Wordpress blog into a LaTeX document. I found this software about six months ago and it does what it says on the tin: give it some basic details and it will parse all of your posts, tidying up the code and creating LaTeX source files which you can then compile as a standalone PDF book or for inclusion as part of your thesis.

The script’s not perfect and I can think of several improvements, particularly in the way that it converts URLs for paper presentation. But if you’re starting a PhD, I’d recommend giving it a go. A blog-sized lit review is a great way to manage this difficult task and of course, if you make the blog public, you can engage with the wider community in your field, getting feedback and maybe even making a bit of a name for yourself. Happy blogging!

My colleague Alastair is conducting a survey about online academic collaboration, use of tools and attitudes to technology in the Academia as part of the Qlectives project. All participants who supply an email address (and complete the questionnaire by the 14 November) will be entered into a prize draw.

The Qlectives project based at the University of Surrey is conducting a survey to investigate how scientists collaborate and use technology. The questionnaire should take around 20 minutes to complete and is being conducted anonymously and confidentially.

As a way of saying thank you to those who take part, we will hold a prize draw for 5 x £20 Amazon vouchers when we have finished
collecting data (we anticipate that this will be around the 14 November 2009). To be considered in the prize draw, simply leave your
email address on the final page of the questionnaire, and we will contact the lucky winners.

A more detailed description of the Qlectives project and this study can be found on the first page of the questionnaire. Please also feel
free to share the study with other colleagues who you think would be interested in taking part.

CC-licensed image courtesy of Enrique Burgos Garcia

It was a matter of time before someone wrote a robot that grabbed latex  and returned an image after latex processing. LaTeXy does exactly that and has just increased tenfold the usefulness of wave for academics.

Peter Drucker: "There is nothing so useless as doing efficiently that which should not be done at all."