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.

One of the themes we’ve been discussing here is the idea that prestige and attention are the main currencies of academia. So it only makes sense that you want your online presence to be an accessible and positive reflection of your work and, at the very least, you want to be distinguishable from all of the other John Smiths in the world.

MIT has recently put together a tool called Personas which attempts to figure out this question of online identity. I say attempts because to be honest, it’s a bit hit and miss. The design looks pretty good but the results seem to change each time you run it, you can’t review the underlying data and it doesn’t even have a roll-over to quantify each chunk of your profile (e.g. percent of total, source documents etc).

[click for bigger]

It’s a noble effort though and it got me thinking that there are two sides to the question of online identity.

• User perspective: It’s a pain having a different user name and password for every website so initiatives like OpenID and Shibboleth should make things easier by providing common log-on standards. Similarly APML (Attention Profile Markup Language) is an emerging technology for customizing content based on your interests and habits. Both technologies are valuable for improving your online experience.
• Search perspective: The second issue is being able to search for someone and know that the results pertain to a specific person. The user perspective technologies discussed above can help in this regard, as they establish a common link between all of your online activities. And although I’ve misplaced the link somewhere, I’ve heard of some researchers using generic online data to reverse-engineer a unique identify (e.g. a Joe from California on Facebook here, a Joe who works at UCLA in biology there, etc.).

Clearly there are a lot of privacy issues involved as marketers (and governments) would love to have this sort of detailed record of who went where doing what. But let’s come back to the question of academic online identity. For a user perspective, I think we’re getting there. I can’t speak for everyone obviously but at Imperial, my single sign-on gives access to my publications database, the online journals, administrative data and many other facilities both on the local network and the wider web.

From a search perspective, there’s a way to go before we can amalgamate our various online activities into a consistent verifiable public identity. Yet the academic environment is the perfect place to start building and testing these identity systems. There’s a wealth of metadata available in journals (citations, institutions etc) and one could establish fairly well-defined problem boundaries for example by using the .edu, .ac.uk or journal publisher domains. Google Scholar probably already does this to some extent but when searching for an author, it doesn’t suggest different unique authors. Instead I would love to have one portal, accessed by a single identity which is verified by some official higher education authority, that could crawl the web and aggregate publications, blogs, newspaper articles, conference appearances, etc and combine this with social meta-data from citations or other sources (e.g. LinkedIn). Users could create public profiles and the private data could be useful for determining discipline rankings and influence (e.g. the IDEAS ranking of economists) and so on.

There’s a lot going on in this area and I’ve probably only skimmed the surface. But I wanted to raise the issue and see if anyone had any thoughts about how online identity issues for academics could be handled. At the very least, have a play with the Personas thingy and see if you, like me, are 5% illegal.

Springer launched yesterday a new service allowing users to search, browse, annotate and reuse scientific images from their huge database of publications.

SpringerImages is a growing collection of scientific images that spans the scientific, technical and medical fields, including high-quality clinical images from images.MD. The continually updated collection – currently over 1.5 million images – gathers photos, graphs, histograms, figures, and tables, and is available to libraries and their patrons via a searchable online database. The SpringerImages interface enables users to search faster, more broadly and more accurately, through captions, keywords, context and more, even jumping from the image to the source article. Users can create personalized image “sets,” and can easily export images for use in their own presentations or lectures.

The service offers a range of potentially innovative features.

Being able to search, organise and download high quality images as PDF from a large corpus of books and journals might represent a breakthrough in the dissemination and reuse of non-textual content from the scientific literature. Usage factors related to images may provide additional metrics of scientific impact for authors and journal editors. From the end user’s point of view, the collaborative annotation functionality is an interesting addition, although it may not be obvious to convince users to massively start tagging and annotating images. Last but not least, a prominent button allows users to bookmark images via CiteULike (a Springer partner) in the same way as references (images available from SpringerImages will be the displayed as thumbnails from the correspondent article page). It is worth reporting details on the access conditions, as the full availability of the service (in particular access to full-resolution images) is tied to Springer’s institutional subscriptions. The set of freely accessible images is–helas–a tiny portion of the complete database.

Anyone can create an account and search the free and Open Access images indexed by SpringerImages. Access to the complete collection is available via subscription to libraries, research institutions and individuals. Images obtained from SpringerImages can be used for almost all noncommercial purposes, including integration into presentations and PDF documents.

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 post describes a very efficient way to digitize large amounts of books. Why is this important? If you are an academic you (1) have amassed a large collection of books and (2) are bounded to relocate more than a few times i n your life. Moving books is no fun. Plus being able to grep through your books, and read them even if you are away from home (conference, coffee shop, retreat) is really priceless.

The general agreement is that mail is broken. We all use it but kind of hate it too. Well, it seems that Google came up with a very good alternative (ambitious, and technically impressive): Google Wave.

A long video of Wave’s capabilities here.

It’s very long at 1:20hrs, but worth it. It’s peppered with random bouts of applause, something I’ve never seen in a scientific/technical presentation before. About minute 1:04, Lars Rasmussen presents real-time translation and he gets about a minute of standing ovation.

Why is this important for academics? Looks like sending a word document back and forth with version numbers in the file name is no fun. And setting a VCS with a bunch of .tex files plus figures is not much better (mainly because doing diffs on LaTeX files is pretty horrible). One could always convince a collaborator to use Google Docs, but then you have no way to use a proper reference manager, figures are a mess, etc. In short, scientific paper collaboration is not really pleasant right now.

In fact, it might be more appealing than desktop equivalents (say MS word) to write papers with collaborators, and better than a long thread of mails to simply organize a dinner out. So I won’t be surprised if many people jump on this as soon as it’s out. Wave is solving so many problems so well that it’ll be a rotund success. Here’s the interface:

The basically new thing is that you can see your collaborator typing away in real time, maybe in different parts of your manuscript. Although similar things have been around for a while (see for example etherpad), the way Wave integrates with other google offerings such as chat/email –may well be enough to gain adoption.

Wave supports images, and more editing features in general than etherpad.

One thing we get for free is version control: you can even move a slider to see how changes happened in your document. It’s pretty spectacular.

While Wave won’t be out for a while, there are developer accounts where one can sign up and get a preview.

Surprising: It’s open source, both client and server (!). I have no idea how they plan to disentangle the server side from the rest of Google’s infrastructure… Unless they ask you to reproduce all of part of it on your server – which is unlikely- I’m not sure how you could get this thing running.

Sciplore has produced an interesting hybrid between a mind mapping and reference management tool. Freemind Scholar adds two basic features over the excellent Freemind: you can have references (at this time, only bibTeX) inserted, and you can drag and drop hig hlights on pdfs (the pdf is linked).

This looks like the perfect IDE for sketching notes while reading papers. I use oneNote for this, but I’ve tried mind maps before and could easily revert to it.

As soon as they implement zotero/endnote references, I can imagine many people finding this tool very useful.

Freemind Scholar is in alpha right now. Feel free to try it out and send them your comments, chances are they will implement your feature requests since they are just starting.

According to Wikipedia, “the semantic web is expected to revolutionize scientific publishing, such as real-time publishing and sharing of experimental data on the Internet.” The W3C HCLS group’s Scientific Publishing Task Force is going to explore how this could happen.

Currently, one describes experiments in a more or less ad-hoc way. The mapping between experiments, papers, and titles is… well, not the most consistent ever.

Do you want to know if the experiment you have in mind is done already? Good luck mining the literature. Although mostly everyone is well-versed on building queries in scientific search engines, the task is far from accurate.

Maybe the problem is in the way we write the literature. If we could write a description of every experiment in some kind of agreed format that both humans and machines understand, searches would be trivial.

An alternative would be to use an ontology to describe experiments. The ontology should not be too complicated to use. If a user feels overwhelmed by the large number of parameters required to describe an experiment, this user may hesitate to do it. Of course, every field would need to built its own ontology. The effort to integrate ontologies across fields may be titanic.

There is some progress in the direction of using named entity extraction as metadata already. For example, the pubmed interface gopubmed is above and beyond anything I have seen. It uses facets (left sidebar) to show metadata. I do not know the details on how it works, but going back to say Web of Science after gopubmed feels like going 5 years back in time. Is there any hope to have a similar interface for all scientific databases? I sure hope so.