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!

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.

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!

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.

Wolfram Alpha, the brainchild of Stephen Wolfram (who allegedly put its company to work on this project for several years before its official launch in May this year), has been out for a while now and is probably no more making the headlines. The long list of examples on the frontpage, organised visually or by topic, proudly shows off what Alpha is capable of. The natural language interface may still be a bit sloppy and some data may be flagrantly missing (how about a dump of the world’s scientific literature, Stephen?), but all in all it manages to live up to the promise of a universal tool to compute an impressive amount of factual knowledge. Alpha allows you, among other things, to:

• plot the sky above your head tonight at 3am
• look up your genome for occurrences of a specific sequence
• compare current unemployment rates for countries you would like to move to
• display the taxonomic tree of your favourite bug
• spell boredom in Morse
• disclose the Answer to Life, the Universe, and Everything
• you can even check your body mass! (am I really 3kg away from my ideal weight?)

Depending on your field of expertise, Alpha is likely to provide a powerful combination of computational tools and relevant data sources to calculate virtually anything you might want to know about the universe.

Apart from technical use, though, I am curious to understand whether and how people will start using Alpha as a productivity tool and integrate it in their daily workflow.

Granted, the title of this post may be overstated, as I am sure there are better ways to use Alpha to work less and live happy. Here’s my take of the 10 best productivity tips I was able to find out, please prove me wrong with better examples and I will add them to the list below.

1. Word count for humans

How often have you tried to figure out how many pages or words make 7,000 characters? Alpha can help you out, even if you speak German.

2. Convert any character

Type a character (e.g. ∞) and quickly look up its corresponding Unicode, HTML, TeX or Mathematica representation. You can obviously do a reverse lookup as well.

3. Look up URL information

You can display a nice summary of information on site ownership (from WHOIS), popularity (from Alexa) and HTML structure for any given URL.

4. Find English words matching a specific pattern

No more tip-of-the-tongue frustrations! OK, I have to think of an actual use for this one but I am sure that the poets among us will appreciate.

5. Calculate time differences

Ever wondered how much hours are left before light comes through your friend’s window in Tokyo?

6. What’s in a word

Definitions, synonyms, antonyms, word frequency, pronunciation (AmE only though…), hy–phen–a–tion patterns for any word in the English language. I even discovered that “hack” and “adulteress” are neighbours in a synonym network.

7. Where am I?

Check your current network name and IP address.

8. Tame nutritional values

If you desperately need to know how much iron is in your spinach salad or how many calories your breakfast is worth, Alpha has answers for you.

9. Convert currency

Enjoy watching how your purchasing power in Europe kept falling indefinitely over the last months, before showing some timid sign of recovery.

10. Estimate download times

Stay zen when you know that it will take slightly more than one day to download those 90GB with your 7.5Mb/s broadband connection.

Even more ideas

There are plenty of tools and Web services to do most of the above searches, but it’s nice to be able to query anything from a single search field. I obviously can’t wait for the day when the full power of Alpha will be unleashed via its API so as to be mashed with external data sources and applications, or integrated as a clever QuickSilver plugin to put the world’s knowledge at the tip of your fingers. Unfortunately it will take some time before this happens.

In the meantime, if you are looking for inspiration, you can browse the Wolfram Alpha community page: it’s a goldmine of ideas (and a good source of information on some ridiculous flaws and limitations in Alpha).

This is a killer app: Flux calculates what time of day it is and adjust your monitor accordingly. Wonderful if you stare at pdfs (lots of white!) on the screen at night. I  wonder how I lived without Flux . It also seems to help regulating sleep patterns. Recommended.

We usually try to provide at least some commentary on this site instead of just posting naked links to new and exciting things. But it’s Friday afternoon and rules are meant to have exceptions.

Some recent finds:

1. Helvetireader is a customization of Google Reader that tidies up the typography and graphic design. Perhaps a small thing but it makes reading RSS feeds much easier.
2. Readability. This rocks. Tired of trying to find the content of your favourite online newspaper amongst all the surrounding ads and other crap? Add this bookmarklet to your toolbar, browse to your favourite paper, click the button and ta da – everything disappears but the content, formatted in a nice neat column. It’s like an overzealous version of AdBlock.

Any other suggestions?

Being pathologically nitpicky about details, I tend to refactor my personal homepage very often. To do this, in the past I used to go through tedious FTP sessions or to hack my changes through the shell.

Since I started to work with wikis I realised how effective a wiki engine can be to invisibly power a website. In this post I’d like to share some tips on how I do this.

As I contribute to the development of the open source wiki engine I refer to in the following examples, this is obviously my software of choice (hint). There is however a range of excellent free software you can use to this aim (provided they have good ACL support and allow you to easily modify the look and feel of the output via CSS, as I’ll show later).

Let me first clear one major confusion about what wiki software is for. One common misunderstanding about wiki engines is that they can only be used to run actual wikis (or web-based collaborative projects such as the Wikipedia). Wiki engines are, on the contrary, simple and flexible tools for maintaining and managing different kinds of non-wiki websites, without bothering with FTP sessions.

The following are common sources of misunderstanding about wikis that typically blur the distinction between a wiki as software and the function of a wiki:

1. anyone can edit the content of a wiki;
2. wikis look wikish;

Both arguments are false. The truth is that editing privileges in most wiki engines (with some flagrant exception!) can be set on a per-page basis through Access Control Lists. You can then easily restrict read-, comment- or write-ACL for a specific page so that no user other than you, a specific user or more users can access the page.

As to (2), wiki-related features typically include: recent changes links, login links, last edit information, last author information, history/revision links and comments. A simple touch of CSS is sufficient to hide all this information from graphical browsers (not from crawlers and text browsers though, if you want to do this you will have to actually modify the page template!).

For the actual details on how to configure your wiki to enable ACL and hide unnecessary elements from graphical browsers you can read this tutorial.

Here I would just like to suggest three aspects that make wikis a fantastic solution for fast and hassle-free content management:

• they allow you to edit and modify content at the speed of light;
• they allow you to easily embed all sort of contents in a page;
• they allow you to set granular access privileges for specific pages, which is a very powerful solution for collaborative work with colleagues and coauthors;

The screencast below should give you an idea of how easy these three tasks can be made using a wiki.

I hope this is a convincing argument to show the power of an invisible wiki and I look forward to your comments and feedback.

Powerpoint is ubiquitous in academic presentations, yet it is often roundly criticised. One of the major problems with powerpoint is that it focuses on form over content. Powerpoint is a what-you-see-is-what-you-get editor. This makes it easy to spend more time on the form than content, as if you start writing a presentation in powerpoint from scratch, the bells and whistles can easily be distracting, and rather than writing your presentation you can end up spending hours tweaking fonts. Powerpoint can help, however, in structuring a talk. Much of this structuring ability comes from the use of powerpoint essentially as an outlining tool. Indeed, powerpoint has an outline tool built in. However, what I recommend is not to use the inbuilt outlining tool, because it is very hard to resist playing round with the formatting. You need to separate form from content completely.

Instead, use a different tool for outlining. Chances are, if you use powerpoint, you also use word, which has a reasonable outlining feature. Go into outline view on word, switch off “show text formatting”, and write your outline using level headings. I use the ctrl-alt-1/2/3/4 keyboard shortcuts to create headings and indents.

When done, save as a normal word file, and open in powerpoint. Powerpoint will make every first level heading the title of a slide, and lower level headings will be converted to bullet points within slides.  You will need to add graphics at this stage, as importing pictures from word to powerpoint doesn’t work. I use figure names in the outline to remind me what figures I need to insert. Your pictures should come last, as like formatting, it is easy to waste time looking for clipart when you should be focusing on your content.

So once you have your content sorted, now it is time to worry about its presentation. You can then apply one of the inbuilt templates. Alternatively, for greater control and your own unique style, go to the view menu and choose Slide Master. Change the formatting of the top level slide master (choose your colour scheme, fonts, background etc…) and then all your slides will be automatically updated. You can also edit of the existing layouts or add your own. For example, I sometimes use slides with just a single line of text in the middle, so I create a new master for title page for this and name it “single title”. Then, I go back to the slide view and change the layout for particular slides to new slide master layouts I have created.

Using slide masters is key to control over visual presentation in powerpoint and becoming a power user. Rather than going through slides and making individual changes, you can make global changes that affect all slides. And if you create a slide master you like, it is worth saving them as a powerpoint template to the form the basis of future presentations.

For some inspiration and 10 top tips on good powerpoint design, see Garr Reynolds.

One thing to note is that with what some consider really good powerpoint design, the pictures can be more important than the text, and therefore you might want to build your powerpoint around visual points instead of a text outline. But I don’t think that type of style of presentation works for so well for the technical and specialist talks that academics typically give. Maybe you can pull it off. As always, you have to consider your content, your audience, and the message you want to communicate.

I better stop posting now and finish outlining the presentation I was working on before writing this post…

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