Academic Productivity

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?

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

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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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.

This is an exciting release.

In a single stroke, Zotero may have added the most important feature of online apps such as citeUlike (collaboration) and the best feature of Mendeley (metadata extraction). I have no idea how well these work, as I have just moved to zotero recently and don’t want to risk trying the beta this soon, but if they work well, this is a quantum leap.

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If you collaborate with people who use another reference management system or (to a lesser extent) word processor/typesetting program, you know that things can get messy.

I just found out Bibtex4Word, and this could be a good solution:

BibTex4Word is an add-in for Microsoft Word that allows the citation of references from a BibTex database. BibTex4Word will insert a bibliography into your document using your choice formatting style.

It is intended for three types of user:

1. LateX users who need to use Microsoft Word. BibTex4Word allows you to use your existing BibTex database and favourite bibliography style.
2. Word users who can’t afford a commercial bibliography package but need to insert citations and bibliographies into their documents. Everything you need to manage references is available free.
3. Word users who have a commercial bibliography package but who don’t like it. BibTex4Word is lightweight, transparent and doesn’t mess up your documents. It is also free.

Bibtex4Word is GPL’d. the only downside is that it depends on latex, so you might need to install MikTex (http://www.miktex.org/) and use the MikTex package manager to install any style files that you want to use.

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…)

For most academics, the standard reference management software is EndNote. It lets you keep track of all the journal articles, books, web sites, etc. that you have read and might want to cite in your papers, integrating easily with Microsoft Word to create properly formatted citations and bibliographies.

But what do you do if you use LaTeX not Word to write your papers? Traditionally BibTeX comes to rescue. It uses a formatted plain-text file to store references and with the custom-bib and natbib packages, creating citations and bibliographies is fairly painless. You can even use a graphical editor like JabRef to help manage your BibTeX database.

However there can be problems when collaborating with people who use Word. How do you share your BibTeX references with EndNote users or vice versa?

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Recently I met with someone who is the editor for one of the top journals in my field. We discussed what would increase your chances of pleasing a journal editor. He gave me three clear pointers that I thought would be interesting to the readership here. But, I also think I’m going to try a different method to get them to you: mail. There are about 2000 RSS subscribers, and only a few dozen email subscribers. I think it’s those subscribers show a lot of commit to what I have to say here and it’s about right that they get extra content. If you use RSS over email because you find it more convenient, then my apologies. You can always subscribe to get the content, then unsubscribe, although I plan to decouple the two sources and prepare extra content that goes to the mail subscribers only in the future.

As Jason calacanis and Nova Spivack put it:

Why have I been doing so much more Twining than blogging and social networking? First of all, I’m not interested in having a conversation with the entire general public, or ever being an A-List blogger, or interacting with networks of random strangers. What I want is to efficiently participate in many different specific groups and communities around particular interests and relationships I have.

I still think that ap.com could be a great community where we share really effective tips (this one email is probably one of these). Just a quick reminder that posting is open to anyone who has anything to say (posts are reviewed). There is a post describing how to make a post. And of course, the comments are open.

EDIT: Since lots of RSS subscribers felt alienated, I have added the content here. I hope you understand why I thought it might be sensible to keep it to a reduded audience. The error in my logic was that email subscribers show more commitment: in fact RSS subscribers think the technology is superior and that’s why they do not subscribe using email.

As promised in my blog post, here are three tips to increase your
chances of pleasing a journal editor (and getting your paper published).

(1) Don’t take no for an answer. This editor told me that in many cases the reviews were not completely damaging, but many authors assumed that the paper was beyond repair and never resubmitted. Sometimes, even though you didn’t get a ‘revise and resubmit’, you can write back to the editor and say that you do not agree with some of the reviewers’ points, and that you have fixed the paper. Note that you were not invited to resubmit, but you are doing it anyway. Sometimes the editor will agree with your point and keep the process going.

This little sneaky tactic can save you a lot of time waiting for another journal to start the process from scratch, not to mention psychological wear-and-tear taking rejections.

Note: my editor in question said he would be more than happy to reevaluate such cases, but he may be an exception.

(2) Write it clearly. In a world where everybody rushes papers for publication, a well-written paper feels like fresh air. How do you know your paper is well-written? Leave it alone for a week. If you come back to it and you cannot understand your own point at first read, rewrite. Use your lay-man friends, or people from a different discipline, as testers.

Another trick that I’ve seen good writers do is to use very large fonts so they concentrate on one paragraph at a time (one screen full of large fonts). They move to the next screen only when they are totally satisfied with their writing. This often involves rewriting each sentence a few times, and shortening it.

(3) Don’t resubmit in a week. It shows disrespect for the entire review process. If the reviewers and editor took a few hours of their time to make your paper better, by all means do not disregard the changes they propose. Rarely you can address all suggestions in just one week.

What happens when you take an extraordinarily large time to resubmit? I thought it’d be catastrophic, but this editor concretely thought that this is not an issue. Sometimes life gets in the way. By all means resubmit even if you think your reviews have forgotten about you. They probably have anyway even if you submit in a snap

Hope this helps!

-Jose