Donald Knuth announced he would make an earthshaking announcement at TUG 2010. The breaking news is the plan to release the next-generation TeX engine. Read the comments and a brief summary of the announcement in perfect Stevenote style from Slashdot.

The first public beta of Paperpile–the latest entry in the crowded arena of free reference management software–has been recently announced. As I write, a test version is available for Linux, but Mac and Windows versions should be released soon. From the screenshots gallery, it looks like Paperpile will feature a streamlined (although quite typical) 3-column interface, support for tags/labels as well as the standard Web import functionality from online bibliographic databases.

It will be interesting to see how this software compares with cross-platform biggies such as Mendeley or established tools for specific environments such as BibDesk or JabRef.

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!

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

About two years ago we talked about filehamster. It was  free, unobtrusive, and simpler than doing version control ‘by hand’ (adding numbers to filenames) or ‘by machine’ (using a proper versioning tool such as subversion or mercurial).

Well, since then filehamster has moved on to be a pain in the ass. Now the free version nags you a lot, and the paid versions are not really giving us any outstanding features. Plus as a .NET application, it eats up RAM.

Enter AutoVer. Completely freeware, no nags, and a much better interface to boot. The GUI and options make more sense too. I even use it for coding when I’m doing something small and a mercurial repo would be overkill.

Eventually, all writing applications should enable smooth versioning and real-time collaboration (Office 2010 beta does! Wave and etherpad are not alone anymore). The slider that controls versioning as in a time machine is fantastic. AutoVer would not give you that. The AutoVer model also breaks when you send the manuscript to a collaborator, and he edits it on his machine (often changing the file name). Still, it’s much better than not doing versioning at all or doing it by hand.

By the way, does anyone know an alternative that is cross-platform?

Google Scholar is probably the most useful tool on the web today for academics. However, there’s no API for it, and seems to add little to no features with time. I don’t think Google is going to give it the Axe any time soon, but … I can’t imagine ads getting clicked on scholar pages. And Google is a for-profit, so one never knows. In any case, it would not hurt to show Google that we care, and there’s one simple thing to do. If you want to support the creation of the API, you could drop by the google API forums and express your interest.

After 100,000 invites went out yesterday, the web is boiling with reviews. The best no-nonsense explanation I found is a chapter of a forthcoming O’reilly book.

If you got an account, I’ve been on the dev preview (intended for developers to build on but otherwise identical), my user is quesada@wavesandbox.com

Today I am going to share a few of the programs (on windows) that make life a little bit more easier and I can’t live without. We  might make this a series if the other ap.com bloggers want in the action.

Hotkey management and Swiss army knife – AUTOHOTKEY

I have an Autohotkey script always running, which does a bunch of different things. At the core is an autocorrect feature that corrects common spelling errors and typos taken from Wikipedia. It also will function as a text replacement utility (inserting, time, date, signatures etc…). Get it here.

Additionally, I remap some keys of the keyboard – such as Insert is now a minimise window key. 

I have some global hotkeys for launching/switching to frequently used applications (such as my favoured music player, 1plus1). They launch the app when its not loaded, switch to it when is it isn’t the active window, and minimises the app when it is the active window.

I have all my numpad button mapped (with right ctrl) to frequently used different applications.

I have a hotkey that takes the current select text and launches a google search.

I have hotkeys for controlling volume using an OSD.

Because I use a ancient buckling spring keyboard, I have my right alt button mapped to the windows key.

I also tend to create hotkeys on the fly for specific functions, essentially macros that replay certain key combinations.

Window Management – WINSPLIT REVOLUTION

A must for window management on large screens and multiple monitors. Hotkeys for moving windows and resizing round the screen in arrangements of your choosing, and I also have a hotkey for sending a window to another monitor.

Desktop management – DEXPOT

Dexpot is extremely German, and extremely good. I have four desktops, each with a different label (work, play, analysis, writing) and desktop wallpaper. I have hotkeys setup so that I can easily switch between them and send applications to each window. A minor plus is that it also adds a context menu, which allows you to set windows to be "always on top" which can be handy.

Office suite – MICROSOFT OFFICE

The only pay for software on this list. If you are on Windows and you don’t have to pay for it, then you don’t have much choice.

Text editing – Notepad2

I have this set up to replace notepad and be the default text editor. It lets you zoom in and out. Which makes me happy.

Browsing – FIREFOX

Firefox is my browser of choice because of the extensibility it offers. Most useful (non cosmetic) extensions that I use are:

Zotero – reference manager/endnote killer

Foxmarks – synchronising bookmarks across machines

Adblock – blocks flashing things

Google Gears – to get offline gmail

Application launcher – SLICKRUN

I have talked about my love of Slickrun here. I have tried other, more fully featured programs, like Ubiquity in Firefox, but the simplicity and reliability of Slickrun keeps me coming back. I put it down to reliability – when I issue a command, it works, and I don’t have to think (or look and choose between the results of a search)

Fixing windows annoyances – Autohide, CCleaner.

Autohide mostly fixes problems with windows auto-hide taskbar settings, and CCleaner does cleans your computer every now and again.

Backup and sync – MS MESH

Microsoft Mesh is one of the tools that has transformed by computing experience. Back in the day I used to take my laptop to work everyday. No more. Mesh syncs selected folders to the “cloud” (the next big thing in computing, apparently) and allows for 5GB of data for free, which is enough for my needs. It syncs all files in any folders you specify across machines and also on Microsoft servers for backup.

It means I can work on a document on my laptop at home, and without being having to do anything I can turn up at my office and continue working on the same document where I left off. No more emailing myself documents, or storing to a flash disk. And it means in theory I should never ever loose data, as anything important is being continually backed with multiple redundancy.

I have a single folder on my local drive which I keep everything I could want to sync, and create ad hoc syncs for particular purposes.

Microsoft was also kind enough to throw in a very handful remote desktop tool for all your computers connected to the MESH, which saves having additional software for this purpose. It also allows for sharing, if you like sharing.

The summer conference season is slowly drawing to a close and we can all put our feet up, right? After all, the papers are done and presented and it’s a least a couple of months before organizers want your abstracts for next year. But before you kick back and relax, it’s worth pausing for a second to reflect on how things have gone and what you might want to do differently next year.

I gave a couple of talks this summer and while they went well, I wasn’t happy with the behind-the-scenes workflow. Some problems:

• Creating figures in one piece of software, exporting to the right image format, inserting them into PowerPoint, discovering that you made a mistake, re-doing the figures…
• Trying to shoe-horn a nice story about the results into 10 tight slides
• PowerPoint, PowerPoint, PowerPoint – having to use someone else’s PowerPoint template, ugly text and math, big files, etc.

A lot of these issues can be fixed using tips here on the site. Outlining your talks for example helps get away from the staccato style of PowerPoint and as commenters have pointed out here, there are lots of ways to mix slides and narrative in one source file. But I want to go step further and show how you can combine narrative, slides and content (i.e. figure creation) in one file.

To achieve this goal, we need use the concept of literate programming, yet another one of Donald Knuth’s contributions to the world. LP “represents a move away from writing programs in the manner and order imposed by the computer, and instead enables programmers to develop programs in the order demanded by the logic and flow of their thoughts”.

So in the case of a technical presentation, the idea is that we:

• write our talk in a loose conversational style, just as we hope to deliver it
• whenever we think we need to illustrate a point, we create the necessary slide
• wherever we need a figure for the slide, we insert code to perform the analysis and create the figure

Sounds like voodoo? Nope it’s straight-forward thanks to LaTeX, beamer and R/Sweave. Here’s the basic workflow (after you’ve installed all the software).

1. Create a source file with a .Rnw extension. This should contain only the preamble and body of a LaTeX document. Here’s a minimal working example to download: myfile.Rnw.
2. Write your talk in the body of your Rnw file. Wherever you want to insert a slide, use the \begin{frame}{Title}{Sub title} \end{frame} environment as described by the beamer documentation.
3. Wherever you want to perform some R analysis, add an R code block. While Sweave lets you format these blocks in multiple ways, here are two useful templates.

   A basic code block to perform calculations. The code will not show up in the final document.
   
<<echo=FALSE>>=
x <- 1:100
y <- x + rnorm(100,0,1)
@


   A basic code block to show a plot, again without displaying the underlying code.
   
<<echo=FALSE,fig=TRUE>>=
plot(x,y)
@


4. Compile your Rnw file using R. Assuming you’ve started R from the same directory as your Rnw file, the syntax is:
   
Sweave("myfile.Rnw")

   You can change the working directory with setwd("path").

   This will create all the necessary figures and generate a tex file called myfile.tex.

5. Process one of the two following examples with LaTeX to generate either your slides or the lecture notes (e.g. pdflatex slides).

   Slides (slides.tex)
   
\documentclass[ignorenonframetext]{beamer}
\input{myfile}


   Notes (article.tex)
   
\documentclass{article}
\usepackage{beamerarticle}
\input{myfile}


That’s it. I’ve used this process to prepare my presentation for an upcoming event and it’s much easier than the old PowerPoint/R shuffle. The resulting PDF is fully portable as all you need is a reader of some sort. Load it up, press CTRL+L to get full screen mode and away you go!

Edit:
As a private emailer pointed out, there are a few other beamer tricks that might be worth mentioning:

• With a bit of practice, you can style slides however you want. But there are also some presets: e.g. in the slides.tex file above, insert the package declaration \usepackage{beamerthemesplit} to get a blue format with a title of contents/breadcrumb trail.
• The fragile option and \footnotesize commands can be useful for formatting verbatim text output. For example:
  
\begin{frame}[fragile]{Results of linear regression}
\footnotesize
<>=
summary(lm)
@
\end{frame}


Thanks to Patrick from Berlin for those tips.