Three stories about science and the web
October 19th, 2007
Collaborating on the same document
Tom, Dick, and Harry are collaborating on a paper. Tom, being the PhD student, does all the work and then writes the paper. Tom then sends a copy to Dick and Harry who edit it with their opinions. Unfortunately Dick completely removes the second paragraph of the discussion, while Harry expands it. Both then send their edited copies back to Tom.
Tom now has to email them both to discuss what to do about this paragraph. Much emailing goes backwards and forwards, and inboxes quickly get filled. Finally Dick and Harry decide to stick with the original version of the paragraph: as written by Tom. Unfortunately, in the mean time Tom’s computer has crashed and the document is lost. Tom, Dick, and Harry never work together again.
Rewind to the beginning. Instead of writing the manuscript on his computer, Tom, being quite clever, gets a Google account and writes everything in Google Docs (other options are available). Tom then sends the link to Dick and Harry. Dick and Harry sign in and start editing. Because everything is online, and in the same place, Dick and Harry are always looking at the most recent version: any changes Dick makes, Harry sees immediately. This means that Tom doesn’t have to sort out changes in two different documents. And when Tom’s computer crashes, the document is safe online, as with the different versions that are stored with it.
Harry is so pleased at how easy it was working with Tom and Dick that he invites them round for a BBQ; Tom and Harry’s sister get on famously and end up getting married, everyone lives happily ever after.
Sharing information
Dave is a PhD student, his work has been going well so far and has started writing a paper. He’s thinking about what to do after his PhD, and he’s heard that conferences are a good place to network and arrange a post-doc. Dave submits an abstract for a conference, and a month later he hears that he’s been accepted to present a poster. At the conference Dave has people come up to talk to him about his work, and gets a few contacts to talk to about a postdoc-ing. Dave is happy and looks forward to getting new job.
Meanwhile, James is a PhD whose work has been going well, and is also starting to write a paper. Like Dave, James wants to find a post-doc, so he applies and is accepted to give a poster at the same conference. However James doesn’t want to wait till then to network with other researchers; James starts a blog to discuss the finer points of the techniques that interest him, as well as the papers that he likes. Other people his area of research find his blog, read it and write a few comments.
As time goes by, James also starts to discuss certain points of his research as he writes his paper. People take an interest in a new technique that James has pioneered and ask for more information. In response James produces a video for JOVE, and writes a short description of it for OpenWetWare, both link back to James and his blog. When the conference comes round, James gets to meet a lot of people who have heard of him through is blog. One person who is particularly impressed with James is Dave’s girlfriend. James leaves with a number of offers for a post doc, a new girlfriend, and feeling very pleased with himself.
Finding scientific information
Claire is a new post doc, starting in new field in a new lab. Claire needs to get up to date on this field so she can start churning out papers.
Like most researchers Claire uses PubMed to get relevant articles and reviews. However, Claire is also clued up on how the Internet is changing the way that scientific information is disseminated, so Claire also searches for blogs in her area of research using technorati. Able to find a couple, Claire uses these to get informal opinion, that help him understand her field further. Also using Nature’s Postgenomic Claire can find blog posts that directly reference published papers. Similarly, Claire looks at Connotea where other researchers can leave comments on articles that they find of interest. Claire also read articles on OpenWetWare, watches videos on JOVE and SciVee.tv to learn about common techniques and methods in her field. Finally, Claire joins Nature Network, an online scientific community where Claire can meet and discuss her field with other researchers. Claire understands the Internet as another scientific tool, and does well in her career.
See also
Check out Mr Gunn’s related posts at Synthesis.
Creative Commons
The photo used in this post is taken from ocean.flynn on flickr and used under a creative commons licence.
October 19th, 2007 at 2:36 pm
Interesting, where are the women in this story?
October 19th, 2007 at 3:55 pm
This is an excellent point Gail. In my defense I would say that being an under-pressure third year PhD student in a bioinformatics department, I have very little time for going out and therefore contant with the opposite sex. I suspect that this is reflected in two of the stories ending with the protagonist finding a girlfriend: some one here suggested that perhaps I am projecting something of my persona into the stories.
It is a sad day when I realise I am living vicariously through fictional characters written on a bioinformatics blog.
I have updated the last story.
October 19th, 2007 at 4:06 pm
Interesting, but unfortunately it is not so simple.
Collaborating on the same document
- the interfaces of google/docs and even zoho are very uncomfortable to use. They lack various options compared to openoffice and other word processors.
For example, you can’t re-define your own styles; you can’t create automatically indexes and more other things; they are slower; and many other things.
- it is very difficult to persuade other lab members to create their own account on zoho or google/docs if they’re not ‘web 2.0 nerds’ :).
Most of the professors, are accustomed to work by printing the documents on paper and annotating it with a pen; and I believe, it is very difficult to persuade them of learning other methods.
Most of the professors use old things like word editors and sheets, but they are very experienced at using them.
However, I’ll stop moaning… because I think it is worth trying to persuade other scientists and show them these cool web 2.0 ideas. I really hope the science of the future will be like you have described in this post.
I have learned very much by using Internet and participating to forums and blogs on biology, and I think I will continue in this way.
October 19th, 2007 at 9:28 pm
It’s another reason why OpenID is so important. Even web 2.0 junkies get tired of setting up all these accounts. Support for OpenAuth will also go a long way in allowing relationships to be portable.
Mike … fabulous post. Technologies like Google Docs are still very young, but are already getting very advanced. In a year or two, I can’t think of too many reasons not to collaborate over the web.
You are already seeing efforts that integrate services. It is also another reason why open APIs are required allowing people to mash up services.
October 20th, 2007 at 1:15 am
There are other ways to collaborate writing documents then sharing with google etc. Just like your source code, your documents should be under revision control. We’ve been using mercurial for ours and its proven very effective. I’ll admit that since we’ve been writing in LaTeX, our documents do very very well in revision control but it do able in other word processors as well. This also solves problems of who can do what with your data (today google is trying to do no evil, but what happens when they refocus their business and decide google doc’s aren’t worth it). So why force everyone to use a new tool, when existing ones they’re probably already using work?
October 20th, 2007 at 1:47 am
As of right now ThinkFree.com beats Google Docs, from my experience –especially if you’re used to MS Office. Google is likely to catch up eventually, but they’re not there yet
October 21st, 2007 at 12:46 pm
Most of what you propose can and does work. The technology will keep changing and people will tend use what is easy and free.
The point of publishing is to communicate research and network. In addition to journal articles we now have Web2.0 tools that will give those who choose to use them a competitive advantage.
October 21st, 2007 at 1:20 pm
@Giovanni
Yes I agree that online word processors do lack a lot of the functionality compared with those that can be installed on your computer, however they do have the advantage of being always the latest version, and you don’t have to worry about maintaining them either. The fact that they’re always there when you have an internet connection is useful too.
I also agree that using online tools is not for everyone either, but like so many things I have found in science so far, you have to muddle along making compromises as you go.
@Deepak
That is a great point, so many “walled gardens” are a hindrance especially when switching to a new and better tool, and you have to create a username and id. However, I’d say that OpenID is still somewhat esoteric to use, but once it becomes easier, I think I will be using it more.
@Jacob
What I have always wanted to see is some kind of svn-google docs-wiki standard interface, so people can use which ever type they prefer, but all the changes are sent to the same document repository.
For example I use Google Docs to edit the document, but you prefer LaTeX and svn, so when you update the repository my Google Docs changes are translated into the LaTeX in the svn repository you are using, and vice versa.
@Jake
I’ve never heard of that, but it looks good. Thank you pointing it out.
@Jean-Claude
Easy and free are definitely important considerations. Both equally important, but ease of use it what is going to attract the non computer based biologists to using these technologies.
October 21st, 2007 at 8:00 pm
Great post Mike. One small thing - there’s still Alex in the last story :).
One of the concerns I heard about using Google Docs for collaboration on the scientific paper was privacy issue. Google’s privacy agreement is not the best available and my colleagues were worried about showing their work to Google (and risk a leak to the public via search engine). While I don’t see a possible data leak as an issue (we are about the open science, aren’t we?), other people still do. This is somehow complementary to the issues Jacob raised - it’s all about trust in externally/privately hosted services (yes, in this light, Facebook is also not-good).
October 22nd, 2007 at 10:14 am
hi, Why your RSS is not available? I wanta subscribe your blog.
Thanks!
October 24th, 2007 at 10:58 pm
I was just coming up with some “use cases” for an intro to scientific blogging article I was writing. I like yours better.
October 24th, 2007 at 11:00 pm
[…] out the three stories about scientists using the web at Bioinformatics […]
October 30th, 2007 at 3:33 pm
Thought this might be of interest in terms of how useful Google Docs is for collaborating on documents (short answer–the key word is “beta”):
http://www.neilgaiman.com/journal/2007/10/simplicity-of-black.html
“I’ve been using Google Documents to share ODD AND THE FROST GIANTS with people who needed to see it… and just realised that none of the little corrections and fixes I’ve been entering — and dutifully saving — have been saved. Instead it seems to have taken a version of the document open in Google Documents on another computer somewhere in the house as its master text, which means the saves I’ve done on the downstairs computer I’m on have apparently not taken. (I’ve sat there going through all the old saved versions it’s kept — 121 of them and they only seem to go back and forwards between a couple of versions in which a But changes to a Still, because at a guess it’s open in two different tabs somewhere on whichever computer it’s on that Google is paying attention to…) Between the people who can’t get in to see it and write me grumbly emails, and the way Google Documents sometimes fails to send the letters inviting people to look at it (but still lists them as now having access to the document), I think I should have paid a bit more attention to the word BETA underneath the words Google and Documents.”
November 1st, 2007 at 12:30 am
[…] Barton from Bioinformatics Zen posted three stories explaining how web technologies may improve scientific communication, plus he shared his thoughts […]
November 1st, 2007 at 7:15 pm
@Pawel
Thanks, I fixed that mistake. As for Google docs, I think you can choose to keep your document hidden. I think they would get into trouble if the document showed up on the net without your consent.
@zhang
Could you tell me what problem you’re having. I haven’t had any RSS problems recently, though in past there were problems with FeedBurner.
@Mr. Gunn
I enjoyed reading your article, I look forward to the next entries.
I added a link to the original article.
@Dave Crotty
Thanks for that link Dave.
The only I think I can say is check out Zoho, or as Jake suggested ThinkFree.com.
Competition is always good.
January 21st, 2008 at 2:04 pm
[…] a previous post I wrote about how great new web tools are making it easier for scientists too collaborate, find information, and share information. The […]