Web 2.0 for Scientists: Where are the Applications?

The success or failure of Web 2.0 efforts for scientists depends to a large extend on the availability of cool applications that make the everyday life of a scientist easier. Many of these applications of course already exist, but I would argue that there is a lot of room for improvement. And I would also argue that in a lot of cases we just have to take the example of the Web 2.0 world and adapt it to the needs of scientists – Nature Network itself would be an example of this approach.

Meetings and Seminars
Scientific meetings and seminars are one example were we can do better. Web 2.0 is an ideal approach for this, and Upcoming is the classic application. There are of course a number of websites that list meetings and seminars for scientists, but they either focus on the big meetings or list just the seminars of a particular institution. Look at the discussion How to find a science event in Berlin in the Nature Network Berlin Forum to see what I mean.

What can we do to improve the situation?
We can wait that either one of the big players or a clever startup has a great idea. But one of the attractive features of Web 2.0 is user participation. We need more discussions between scientists and software developers on what is needed and what can be done. These discussions are of course already taking place, but science bloggers can do more to collect interesting ideas and articulate them. We want the integration of reference managers in online writing tools such as Google Docs or Buzzword, but how do we make our voice heard?

Secondly, we can write applications ourselves. The barriers of entry have become really low, and one reason are the APIs (application programming interfaces) of both science applications or conventional Web 2.0 apps:

And there were hints of a Nature Network API. With some skills in PHP, Python, Java or Ruby, anybody could create an interesting mashup with these APIs over a weekend. Maybe linking Connotea tags to YouTube videos and Flickr pictures?

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16 Responses to Web 2.0 for Scientists: Where are the Applications?

  1. Euan Adie says:

    re: the Network API – we use this internally at Nature already but it needs developer time before we can make it public to ensure that it’s compliant with privacy and data protection regs (and our T&Cs). It exposes everything on your profile page, your group memberships, your network, your activity feed and those of your friends and contacts.
    If you think that you might make use of it (or even have a good idea for a mashup that might use it) then a comment here might be a good way of voting it up the Network priorities list. ;)

  2. Martin Fenner says:

    Euan, thanks for the update. The Nature Network API could enhance NN at a few spots (e.g. better integration with Connotea, or a different representation of what is going on at NN), but nothing that is urgent for me.
    But the blog post was also about the discussion of these topics. Who decides of what gets build into a Web 2.0 software for scientists, and how can science bloggers get involved? Will software developers also attend the London Science Blogging meeting in August? Do we need a Nature Network Forum for Science 2.0 software?

  3. Neil Saunders says:

    _Secondly, we can write applications ourselves_
    Absolutely. Get writing!
    I think an API is a huge priority for NN: consider this a vote up.
    You might argue that web2.0 is a “way of doing”, rather than software _per se_. However, it’s apps that make things happen. What we need is more input from biologists. Web programmers have no end of ideas for apps, but they need to be told what’s useful and what isn’t. Alternatively, biologists need to program and as you suggest, it doesn’t take too much work to get your head around an API, read a few tutorials and give it a go yourself.
    My personal view is that we need less social, “Facebook for scientists” ideas and more apps aimed at data: aggregation, interoperability, transfer, search, online analysis.

  4. David Crotty says:

    The commenter above, Neil Saunders, has hit the nail on the head. There’s far too much effort and attention being paid to useless, time-waster sites that are just copycats of Facebook/Myspace. The really useful tools are not going to be conduits for chatting with your pals or finding collaborators online (is anyone really finding collaborators this way–aren’t you better off looking at someone’s publication record?). The real useful tools will allow new efficiencies, and will save time and effort, not demand it.
    One good example that already exists is GoPubMed, which combines PubMed searching with a folksonomy to streamline the process:
    http://www.gopubmed.org

  5. Graham Steel says:

    Spot on David !! (and of course Neil too)

  6. Maxine Clarke says:

    I hope that some of you -lot- clever programmers will be coming to Science Bloggers in August, though, as Martin suggests. Then you can tell us all about it – I’d be fascinated to learn more about this.

  7. Martin Fenner says:

    _The real useful tools will allow new efficiencies, and will save time and effort, not demand it._
    What would be on our wishlist for new Web 2.0 science applications? I had mentioned software for seminars/meetings. I would want to receive either an RSS feed or regular email updates of seminars and meetings that I have subscribed for (selectd by location and topic).

  8. Cameron Neylon says:

    _What would be on our wishlist for new Web 2.0 science applications?_
    I’ve said it elsewhere [“1″:http://blog.openwetware.org/scienceintheopen/2008/03/04/give-me-the-feed-tools-and-i-can-rule-the-world/ ,”2″:http://blog.openwetware.org/scienceintheopen/2008/03/10/a-small-feeding-frenzy/ and many of the “original ideas”:http://nsaunders.wordpress.com/2008/03/10/lifestreaming/ came “from Neil”:http://nsaunders.wordpress.com/2007/08/15/automated-bioinformatics-discovery-through-social-networking/ and “Michael Barton”:http://www.bioinformaticszen.com/2008/03/passive-research-streaming-using-twitter-flickr-and-citeulike/ but I think in many ways the technical problems of providing data feeds are largely solved. There are two outstanding problems. Getting more people to generate interesting feeds. And developing clever and easy to use tools to filter them (which might well involve building better tools that help scientists to generate them with proper tagging).
    When I can query the data web with a question like ‘what is the relationship between protein purity and crystal size’, or ‘has anyone made a novel compound that might bind to my drug target based on an in silico screen’, or “as Neil says”:http://nsaunders.wordpress.com/2007/08/15/automated-bioinformatics-discovery-through-social-networking/ ‘These people also searched for GO accession GO:0050421 (nitrite reductase (cytochrome) activity)’ then we will have the tools that make ‘Web2.0′ relevant for science.
    And as Neil says, perhaps its time to just get on and build them. Where am I going to find the time to learn to program!?!

  9. David Crotty says:

    _What would be on our wishlist for new Web 2.0 science applications?_
    I’ve talked about what I see as some of the more promising directions “here”:http://www.cshblogs.org/cshprotocols/2008/04/03/web-20-for-biologists-are-any-of-the-current-tools-worth-using/, way down towards the end.
    I think there’s great promise in the mashup approach, where data from a variety of sources is combined into a new, more meaningful interface. The example I used was “Epispider”:http://www.epispider.org/
    I like the idea of sites that 1) aggregate data from a variety of places, saving you time as you now don’t have to go to multiple sites, and that 2) combine that data to glean new insights into the data. Which is all pretty vague but at least it’s a direction that shows promise.

  10. Martin Fenner says:

    Interesting that most of the suggestions are about data aggregation. And David’s detailed blog post has some promising examples. My own thinking was rather along the lines of facilitating the daily tasks of a scientist: doing experiments, searching the literature, writing papers, going to seminars, etc.

  11. David Crotty says:

    Well, “GoPubMed”:http://www.gopubmed.org certainly addresses literature searches. There have been a few recent announcements about “semantic search sites”:http://www.powerset.com/ lately, but but they don’t yet seem to work all that well (“here”:http://therehearsalstudio.blogspot.com/2008/05/playing-with-powerset.html and “here”:http://therehearsalstudio.blogspot.com/2008/05/what-askwiki-told-me.html). I expect as this technology improves we’ll see more and more useful tools on that end.
    I also tend to think that more mainstream calendar and organizational sites might suffice for some of the everyday stuff as well. Again, it would be more efficient for me to have one place to check all my meetings/seminars as well as my obligations outside of work (carpool, etc.).

  12. Martin Fenner says:

    I’m sure that many of the popular general Web 2.0 tools are useful for scientists as well. But writing about using “Basecamp”:http://www.basecamphq.com, “last.fm”:http://www.lastfm.com, “Google Calendar”:http://calendar.google.com, “Remember the Milk”:http://www.rememberthemilk.com/, “Dopplr”:http://www.dopplr.com, etc. (to name just a few that I use) is probably enough material for a separate blog post.

  13. Cameron Neylon says:

    I think many of the generic tools are pretty good, but have limitations (referencing tools in GoogleDocs anyone?).
    We use blogs to record experiments but that is at a very crude level at the moment really but you can see where it is going. The key to me as David says is bring it all together and processing it where and how you like. That’s why I focus on aggregation (of anything, whats going on, who’s said what, where I’m supposed to be [oops, in the lab :) ], and what people are writing and thinking). These kind of work, but the filtering bit is where the real work needs to be done in my view.
    There’s another interesting discussion (prompted by David’s mention of carpools) of whether this promotes a blurring of the work/life line. You can’t afford to separate carpool issues from where you are supposed to be and when, but is it healthy for us? Or, where personal data might be involved, even safe?

  14. Neil Saunders says:

    Thinking a little more about this: perhaps the web at large defines “social” differently to scientists. Most social web2.0 apps mean “keeping in touch with your friends”. Perhaps web2.0 for scientists apps means “keeping in touch with data”.
    @Martin indeed, many of the popular tools are very useful for science and perhaps one goal is to use those APIs to bring them together. You can imagine an electronic lab notebook cobbled together from an online wiki, editor, calendar and source code repository, for example.
    I’m hoping to see some great science apps out of Google App Engine any day now…

  15. Martin Fenner says:

    I looked again at some of the popular Web 2.0 tools. A common observation seems to be that they serve only 90% of the needs of a scientist:
    * “Google Docs”:http://docs.google.com. No integration of references.
    * “Backpack”:http://www.backpackit.com. Nice tool to organize your ideas, could work as electronic lab notebook. But no integration of research papers.
    * “Upcoming”:http://upcoming.yahoo.com. Great tool for events. But no special category for science.
    How do we fill the gap of the remaining 10%? By creating a science version – with 90% duplicated functionality? The better approach would be the use of an API or other extension that adds the missing 10%.
    “Google App Engine”:http://code.google.com/appengine/ looks promising. But it still involves a lot of programming (in Python). “Yahoo Pipes”:http://pipes.yahoo.com/pipes/ and “Microsoft Popfly”:http://www.popfly.com/are alternative that involves far less programming skills. Both the Pipes and Popfly website have a few science-related examples.
    “My Space DataAvailability”:http://dataportability.tumblr.com/post/34138755, “Facebook Connect”:http://developers.facebook.com/news.php?blog=1&story=108 and “Google Friend Connect”:http://www.google.com/friendconnect/ were announced just the last few days and also promise better data integration.
    My suggestion: we hold a Yahoo Pipes contest for the most interesting science mashup.

  16. Martin Fenner says:

    Good timing. Yahoo today “announced”:http://www.ysearchblog.com/archives/000583.html SearchMonkey, their new open developer platform. To get SearchMonkey started, they have a developer challenge with a chance to win up to $10.000.