During my summer blogging break, I thought I’d repost of few of my “greatest hits” from my old blog, just so you all wouldn’t miss me so much. This one is from September 3, 2008. There was some nice discussion on Friendfeed that’s worth checking out.


Some recent posts that got me thinking about various escience/science 2.0/open science issues:

First, Christina gets us rolling with some definitions:

So I’m asking and proposing that e-science is

  • grid computing – using distributed computing power to do new computational methods in other areas of science (not in CS but in Astro, in bio, etc.)
  • data curation – using computing power and information science to store, discribe, and provide access to scientific information for reuse while taking security and policy issues into account
  • supporting scientists work using social computing technologies (SCTs) to support collaboration around data and equipment (as in collaboratories) as well as collaboration to find new research partners and to discuss science
  • maybe some sort of support for benchtop computational methods or support for workflow or electronic lab notebooks?

What do you think? Is it just one of these or all or some subset?

More or less, as I said on FriendFeed, I see the terms e-science, science 2.0 and open science bandied about quite a bit these days. I tend to thing of e-science as comprising grid computing and data curation issues. Science 2.0 I think of more as social software applications in science, including lab notebooks and the like.

Open science is a newer term, I think, and a little more nebulous to me. It’s more an overarching attitude and approach rather than a set of tools. Certainly, open science includes aspects of grid computing, data curation and web 2.0 tools but all of the above don’t necessarily have to be “open.” It’s possible to curate large data sets that are private, for example, or for a wiki lab notebook to be for the lab members only; e-science and and science 2.0 don’t have to be fully open although, of course, it’s infinitely preferable that they are.

So, I’m a little uncomfortable with using open science as a catch-all term for all the four items that Christina mentions, just as I’m a little uncomfortable with e-science as the catch-all. If I had to choose, though, I’d probably go with Christina and pick e-science.

And speaking of getting more openness into science, check out this article, Era of Scientific Secrecy Near End by Robin Lloyd.

Beyond email, teleconferencing and search engines, there are many examples: blogs where scientists can correspond casually about their work long before it is published in a journal; social networks that are scientist friendly such as Laboratree and Ologeez; GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents; a site called Connotea that allows scientists to share bookmarks for research papers; sites like Arxiv, where physicists post their “pre-print” research papers before they are published in a print journal; OpenWetWare which allows scientists to post and share new innovations in lab techniques; the Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work; GenBank, an online searchable database for DNA sequences; Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles; virtual conferences; online open-access (and free) journals like Public Library of Science (PLoS); and open-source software that can often be downloaded free off Web sites.

The upshot: Science is no longer under lock and key, trickling out as it used to at the discretion of laconic professors and tense PR offices. For some scientists, secrets no longer serve them.

The article is basically about using web 2.0 tools (blogs, wikis, mashups, collaborative document creation) to create a more open scientific culture. In other words, what I’ve called science 2.0 above. It’s a very well-written article, particularly for an audience that might not be that familiar with the topic.

Of course it’s great to have all these sharing and collaborative tools available for scientists to use, but how to you actually get more than a handful of them to use them? What’s the killer app for science 2.0, in other words. Eva Amsen has some ideas!

Many, if not most, scientists are not in the habit of putting things online. The ones that are might be tempted by the concept of sharing the papers they read, letting everyone look at their lab notebook, joining a forum or writing a blog. If you’re reading this in your RSS feed or clicked through from FriendFeed , you’re probably one of those people. But think about your friends and colleagues who only turn on their computer for work and e-mail. They’re not going to tag their favourite papers or discuss the process of research with total strangers on the internet. It’s an extra thing to do that’s not already part of their lives, and no matter how appealing they might find the concept of open data or sharing information, they won’t join these sites or movements because it’s not something they are already doing.


Imagine if there was a bibliography reference manager that keeps a record of papers read, and allows users to cite papers with one click of the mouse, but does all this in a simpler way than EndNote, and perhaps has one extra feature that people really need but that EndNote doesn’t have. For example: if you’re cowriting a paper with someone else, the EndNote library needs to be on two computers. You can export it, but it’s kind of unwieldy. It would be easier to have a common shared library that both computers could use to cite in their word processing software….

Now imagine if this utopian tool they all switched to because it was so simple and fast and useful just happened to come with the default setting to share your entire collection of papers and prompted to quickly tag everything once you added it. People would leave the public setting on, and they would tag….

Please, read the whole post. It’s wonderful. Eva’s idea is that the killer app for science 2.0 is combining citation management with document preparation and making it social. A great idea, because it takes what scientists have to do already (ie. write papers) and blows it up into the miscellaneous universe.

But, are we there yet? First of all, take a look at these two conversations on FriendFeed about how to make Connotea the killer app: here and here. It’s great to know that Nature is thinking deeply about transforming what is now Connotea into something that will truly help scientists. At the same time, you have to think that the Zotero project also has great potential to be that killer app with amazing improvements in v1.5 and a social version coming up.


  1. #1 Mr. Gunn
    August 26, 2009

    I believe I or someone mentioned this on Friendfeed (and there was some discussion on twitter, as well), but Mendeley has gotten a step closer to this with the development of public collections and shared collections.

    Here’s my public collection on multiple myeloma. It’s one click to add the item to your Mendeley library, and then another click or two to add it to your Word document. If Mendeley could do the same in a Google Doc, we’d pretty much be there, right?

  2. #2 John Dupuis
    August 27, 2009

    Thanks, Mr. Gunn. I definitely agree that Mendeley is one of the select few that are working in the right direction. Zotero, of course, has a lot of similar functionality and it should be interesting to see what those two can inspire each other into accomplishing.

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