Academic Productivity

This could be a blessing. There are occasions where you (or your organization) have a lot of content in word files that would be better off in some form of collaborative/searchable repository. Wikis are very handy in these cases. However, it takes quite a lot of footwork to reformat all tables, headings etc to wiki parlance. This plugin for openOffice takes care of it.

Some people have chosen a wiki for their scientific homepage (Dario posted a tutorial in How to run an invisible wiki). I have considered it myself, although I’m more inclined to use a wordpress blog (post on how to set it up to maximize google scholar’s chance of getting your pubs coming soon!). One of the advantages of a blog over a wiki is that one can use a very good WYSIWYYG tool, windows live writer. Unfortunately only for windows. Now, this advantage is gone: one could reasonably set up and update without having to ftp files around or use crappy editors that come built-in with most wikis.

Good news for FOSS and the entire industry, really. Thomson Reuters claim didn’t hold on court. In an ecosystem where all competitors are launching new creative features every day (Mendeley, Zotero, citeSmart, jabRef, etc), development of endNote seems glacial.

EndNote maker’s lawsuit over open-source Zotero dismissed – Ars Technica

If you are interested in scientific blogging and collaborative tools for research and happen to be in the UK this summer, here’s an event not to be missed:

Science Online London 2009 will explore the latest trends in science online. How is the Web affecting the work of researchers, science communicators, journalists, librarians, educators, students? What can you do to make the best use of the growing number of online tools?

The event is cohosted by Mendeley and Nature Network. More information available here:

• www.scienceonlinelondon.org
• twitter.com/soloconf

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.

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Would you like to highlight parts of webpages? I do that all the time with pdfs, so I miss this functionality when I’m online. Sometimes I bookmarked a site, but when returning to it I don’t see the part that interested me. This problem has been solved by diigo.

As you may have observed, here at ap we are fans of social bookmarking and collaboration (we have the delicious bar under each post). Showing what people have bookmarked gives us feedback, and it is Up to now the leading contender in this space was delicious. But after finding Diigo, I cannot understand how delicious lost their competitive advantage so fast. Diigo is a killer app, and it works in many browsers.

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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).
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A reader writes:

“Dear Academic Productivity,

After having finished a phd project, I am starting a new research project together with a colleague. As a collaborative project requires, well, collaboration and coordination, I wonder if you or perhaps your readers happen to have any good advice, both on best practices and concrete suggestions for web-based collaboration tools. (more…)

Michael Nielsen has a great post on why open science is failing to take off. His main point is that science was never that open to start with, but thanks to the communication needs of the time and the technology available people developed the peer review system. A system that is now hauting us, while top scientists disregard current technology (mostly web-based) that makes the current system look silly.

By the way, Nielsen knows what he is talking about; he wrote the standard text on quantum computation the most highly cited physics publication of the last 25 years according to Google Scholar.

The first example he uses is Nature’s open peer review system:

Inspired by the success of amazon.com and similar sites, several organizations have created comment sites where scientists can share their opinions of scientific papers. Perhaps the best-known was Nature’s 2006 trial of open commentary on papers undergoing peer review at Nature. The trial was not a success. Nature’s final report terminating the trial explained: There was a significant level of expressed interest in open peer review… A small majority of those authors who did participate received comments, but typically very few, despite significant web traffic. Most comments were not technically substantive. Feedback suggests that there is a marked reluctance among researchers to offer open comments.

His second example is the usual suspect: wikipedia.

Seigenthaler has described Wikipedia as "a flawed and irresponsible research tool".

Nielsen marvels as scientists missing the point of wikipedia:

[...] You’ve bought into the current game, and take it for granted that science is only about publishing in specialized scientific journals. But if you take a broader view, you believe science is about discovering how the world works, and sharing that understanding with the rest of humanity.

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I found a (badly scanned) paper on how to concentrate. It’s a so-so article, but there is at least one gem in it:

remember that solitude has always been, in all the history of mental achievement, a requisite for great work. (…) The great poems written in lonely garrets—the masterpiece paintings conceived by the artist amid the fields—the divine harmonies first heard by the musician communing with the stars—the sublime oration which first stirred the soul of the orator as he tramped in the forest—all attest that the best comes to man when he is alone.

This is interesting. I always found that some people complained I spent too much time in front of the computer… maybe that is what it means to be lonely. The funny thing is that nowadays it is a lot harder to be alone. Maybe alone is just a romantic surrogate for ‘uninterrupted’ I don’t think the mood implications of lonely help in any way, unless you are producing poetry, music or plastic arts… but certainly not papers.

So, do you feel lonely? Do you seek time apart from ‘the world’? It’s true that most academics’ social lives suck (not mine ). But what is the right causal path here? Do we kill our social lives so we can get ‘in the state’ more often and be productive? Or is it the other way around: we are ‘in the state’ so often that social relationships just die off?

One thing is true: having an internet connection provides constant, second-class (in the sense that it’s not as rich as real-life interaction) social stimulation; being in front of the computer is not a certain way to achieve ‘the state’ (lonely or not). But maybe a good solution is to concentrate a lot (no surrogate activities, like me writing this blog post while I should finishing up my paper), and then get a lot of first-class, ‘live person’ social action.

(Conference announcement via Gerry McKiernan)

Science in the 21st Century: Science, Society, and Information Technology

Waterloo, Ontario, Sep 8-12, 2008.

Times are changing. In the earlier days, we used to go to the library, today we search and archive our papers online. We have collaborations per email, hold telephone seminars, organize virtual networks, write blogs, and make our seminars available on the internet. Without any doubt, these technological developments influence the way science is done, and they also redefine our relation to the society we live in. Information exchange and management, the scientific community, and the society as a whole can be thought of as a triangle of relationships, the mutual interactions in which are becoming increasingly important.

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