Nota Bene

Tools for taking notes from web pages seem to be all the rage at the moment. Here, for example, is an abstract that I lifted from the journal Bioinformatics using the Clipmarks service:

clipped from
Summary: Biskit is a modular, object-oriented python library that provides intuitive classes for many typical tasks of structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes and molecular dynamics trajectories. At the same time, Biskit offers a software platform for the rapid integration of external programs and new algorithms into complex structural bioinformatics workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, Prosa, Hmmer and Modeller; interfaces to further software can be easily added. Moreover, Biskit simplifies the parallelization of time consuming calculations via PVM (Parallel Virtual Machine).
  powered by clipmarks blog it

Are these tools useful to the bioinformatician? Let’s compare and contrast three of them: Google Notebook, Zotero and Clipmarks.

Update: Pedro adds Diigo to the list

  1. Google Notebook
    I’ve been using Google Notebook for a while now and I’m quite fond of it. By far its best feature is the browser extension, which sits unobtrusively in your status bar until required. When you come across something that you want to note, you just highlight or right-click it and up pops the mini-notebook. A link to the page is added automatically, your descriptive text is optional. You can create multiple notebooks, divide notebooks into sections and choose several sharing options: private, invited or public. Public notebooks , such as my Linux notes, appear on their own web page.

    Google Notebook is not sophisticated. It lacks tags and has a limited set of editing/formatting options. I find it most useful as I would use a real notebook – for jotting down stuff that I want to remember later, with the added advantages of hyperlinks and the sharing options.

  2. Zotero
    I’m a big fan of Zotero. Not least because I think it wipes the floor with both Connotea and CiteUlike as a reference manager – it lacks the social network features of those sites but just works so much better. However, you can also use Zotero to bookmark and make notes on websites.

    Like Google Notebook it sits in your status bar as a browser extension. This one is available only for Firefox 2 – but that’s not exactly a disadvantage. As with Google Notebook you can highlight a section of a web page to create a Zotero note. It also comes with a bunch of scrapers to extract bibliographic data from websites such as NCBI PubMed. The Zotero library is stored in an SQLite database. You can categorise your notes and references, add tags and export to multiple formats including all of the common bibliography formats.

    I find Zotero most useful when I need a “quick grab” – for instance if I’m missing a citation when writing an article. I can quickly locate it at PubMed (or HubMed), scrape the page with one click and export to e.g. BibTeX, append to my existing .bib file and cite. The only problem that I have with Zotero is that I tend to forget that it’s there, which has stopped me maximising its potential. That’s a problem with my brain, not Zotero.

  3. Clipmarks
    I was alerted to Clipmarks via Animesh’s blog – he uses it to create his posts. Clipmarks also comes as a browser extension but this one is a toolbar button – and it’s not enabled by default after installation.
    To clip a page you click the button and select what you want (up to 1000 characters). It seems that Clipmarks attempts to detect sections on a web page and the selection process is a bit wonky at first, but OK once you get used to it. You then have the option to email your clip, post it to your blog, print it or save it on a personal page at the Clipmarks website. In the latter case you can edit the clip, add tags and choose to share (or not) the clip, so creating yet another social bookmarking site.

    It’s early days for Clipmarks and me, so I’m not yet 100% convinced. The clips require rather a lot of HTML, but they look quite attractive to my eye at least. I don’t know whether a social network of clips is useful. I can imagine sharing journal abstracts, for instance, but there are other ways to do that. You could for instance subscribe to the RSS table of contents via Google Reader, star the abstracts that you like and share those feed items. Blogging a clip is a nice feature – a lazy way to generate a post if nothing else. Email – well, you could just as easily email a link with “hey look at this page”, or share your Google Notebook. Another disadvantage of course is signing up to yet another social network with yet another username and password.

    I can see potential for sharing clips with groups, such as a Google Group. In fact to go off topic for a moment, I can see a lot of potential for Google Groups if (a) group pages allowed for more than the simplest of HTML (such that you could actually create a page of e.g. clips) and (b) the groups integrated better with other services – specifically Google Calendar (again, you can’t even create a Group page with Calendar code). So I’m unsure at present if Clipmarks is useful or just a pretty gimmick.

Useful for bioinformaticians? Well, notebook services won’t help you annotate genes, predict protein folds or analyse metabolic networks. However, if you define bioinformatician as “one who deals with information management” then one or several of these services should certainly be useful to you as part of the working day.

3 thoughts on “Nota Bene

  1. Excellent post. I use both Clipmarks and Google Notebook and have only just been exposed to Zotero. After your review, a thorough run is definitely in order.

    I do like the way Clipmarks looks and works, but I always get this feeling that there are one too many clicks in the entire process.

  2. Hey Neil, excellent post man! I was thinking about writing one myself, but procrastination! Glad that you took the time out to check clipmarks… ya I know, another service, login pain etc… but once it is setup, rest is a breeze.
    Checkout the Jeteye [] too. I am really in love with this clipmark thing, a lazy way to collect and post I feel. That is why I love PERL too [shamelessly lifted off from Larry’s book].

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