Academic Productivity

May, 2007, we had a post on using an autocompleter to improve writing speed/save keystrokes. I recommended intellicomplete, even though it was abandonware even then.

Moving to more modern OSs (I’m running windows server 2008 64-bit), it simply didn’t work anymore. Plus it never worked well with Firefox or thunderbird. Anyway, I’ve found a much better replacement: Comfort type. It was hard to find, because reading the site, it’s not clear that it can do this kind of job. Looks like this feature is just one more for the author… which is quite impressive since it costs $20, half of what intellicomplete costed.

The main advantages over intellicomplete are:

• Multi-language support. This is killer, you can switch quickly with a shortcut, and as it learns it places words in different dictionaries
• It works on More OSs and applications.
• It also gives typewriter-like auditive feedback, which somehow makes me write more. Subconsciously, my body knows that if you don’t get the typing sound, you must be doing something passive. It’s also helpful to let people on the phone with you know when you are typing (so they don’t think an intimidating silence just started)
• It detects caret on more applications. Not very well on Tunderbird/Frefox, but better than anything else I’ve tried

The problems I can see right now are:

• It doesn’t complete with tab; only numbers, or enter. Enter can be a bit of a pain. This doesn’t bother me much because my tab finger was getting too much work anyway.
• Sometimes is not as fast as I’d like. When it completes a word, you can see it going back and retype what you wanted.
• Sometimes it hangs, but resetting it works.

What is interesting about this application is that it replaces quite a few others. For me, it replaces: Keepass (or any Password Manager) because it has encryption, and Autohotkey (for some basic templates).

Important: it doesn’t work with java applications. Could be a deal breaker. It even works when I use skype.

Frankly, there are too many reference managers today. This  is counterproductive because we all need to spend time checking the newcomers, just in case there’s a new feature that we were missing.

Most reference managers graft themselves to word or to openOffice. For example, Mendeley, and zotero both use internal reference functionality in word. In doing so, they use features that are available only on those editors. I think this is a big error for at least 3 reasons:

1. I draft my papers on a text editor or oneNote. This has a lot of advantages for me. But I would not be able to use say Mendeley or Zotero on oneNote; and I do want to keep references on my notetaking tool. Using a text editor has a lot of nice advantages over a word processor too, if you know how to use it.
2. It’s a lot faster to massage your reference the way you like it. It takes several clicks on zotero to get an Author (year, p. XX) reference. In endNote, it’d be a few keystrokes.
3. There are bottlenecks in our digital lives that are plain text. For example, emails, forum posts, and google docs are cases of writing that may need reference management but are ill-served by most current offerings. I want to copy-paste chunks of scientific writing and still carry my references; there’s life outside word processors, and quite a lot of it!

So what reference managers work ok on plain text. Well, here is the surprise: as far as I know, only bibTeX and endnote. This is surprising because they are the oldest. One would have thought that newcomers would have taken advantage of what these older tools learned.

Lurking in the Zotero forums, I saw people asking for support of this exact feature. But it seems that it’s never going to happen. It would take a lot of reengineering, and all users that are happy with the current solution (and have amassed a large body of authored docs) would complain.

so, where does this leave me? I need to either comply and write everything in word to take advantage of Mendeley and Zotero, or stick to oneNote, but use endNote references. Of course I could also do everything on a text editor and use bibTeX, but right now, it’s more trouble than it’s worth.

Does anyone know a good solution for my setting?

I want to try something a bit different in this post. Here at AP.com, we’ve talked a lot about tools, theory, trends and the general ephemera of academic productivity. But writing as academics, we should probably be trying to take this experience and build it into a cohesive model of productivity. So my goal here is to suggest a general model, one that we might use to understand what we’ve learned from previous posts and hopefully apply to our own work.

My starting point for this post was simple; I wanted to know how my productivity has changed (hopefully improved) since I first started my DPhil. From keeping a research journal, I know that some days are more productive than others and it would very helpful if I could understand when those fits and starts occur, to spot co-occuring events and thereby learn when to say “Forget work, I’m going for a run.”

In other words, I wanted to plot my productivity cycle over time. It might look something like this:

But the obvious problem with this exercise is how to measure productivity. It’s a subject that’s been tackled indirectly on this site before but going through the old posts, I haven’t yet find any attempts at a general theory – and related measures – of productivity. So drawing on the collected wisdom of previous AP.com posts, here’s a rough sketch of such a theory.
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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.

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

Exciting that an anonymous donor jumped in:

Donate to CHNM in June and your contribution will be matched twice over. Thanks to a challenge grant from the National Endowment for the Humanities, the Center for History and New Media has the rare opportunity to build a $3 million endowment to support infrastructure expenses and ongoing development across its many projects. We’re delighted to announce that now your contribution to the Center for History and New Media will be matched for a limited time. If you give within the month of June your donation will be stretched even further since an anonymous donor has agreed to double the National Endowment for the Humanities matching funds.

If you or your institution used/still pays hundred of dollars per seat on other bibliography manager, consider donations of similar size. If you can raise awareness in your institution, please do so. Zotero is a project that benefits all (Open source) and has been legally attacked (in a childish way) by Thomson before.

Zotero Blog » Blog Archive » Help Zotero by Donating to the Center For History and New Media

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

It should be no surprise that many of us love Zotero, especially since they added support for reference sharing and synchronization.

I am probably the only exception in the AP team. As a longstanding MacTeX user, I keep my references organised with BibDesk, one of the sweetest pieces of (open source) software ever written for TeX users working on Mac OS. When hunting for references, I use CiteULike as a fast and effective solution to bookmark and tag papers. My workflow usually starts with an exploratory phase based on CiteULike. As soon as I have read a paper and need to cite it, I export its reference from CiteULike into BibDesk, filing the PDFs with the help of the autofile functionality in BibDesk. So far I have been quite happy with this workflow even if it involves a little bit of fiddling to correctly import references into my local library.

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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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