Open science discussion

Question: does the open research world need a single access point?

You do open research. You write about it in your blog. Feedback comes in the form of blog comments. Great, but undoubtedly others can learn from the discussion – if they can find it. Do people find it?

If a blogger has research questions and you have the answers, consider creating an article on the Nodalpoint open research discussion wiki page. I’m not suggesting that this become the place to go for answers (although that would be nice), but it’s a place.

11 thoughts on “Open science discussion

  1. Question: does the open research world need a single access point?

    I don’t think so. Too many eggs in one basket; better to maintain cordial relations with a few search portals (PubMed, Google, Google Scholar, OAIster) and make sure they know about your offerings. Then people will find you when they need you.

    This is not to say that the wiki page in question is a bad idea — far from it. I’m glad to see Rosie Redfield’s sequence comparison problem is getting the “enough eyeballs” treatment.

  2. I agree. So long as we have the tools to aggregate information from diverse sources, let’s have diverse sources rather than competition to be the “best”.

  3. I think the key criterion is that the open research is indexed on Google. That way people (or machines) who are looking for the information that you have will find it even if they don’t know about it initially. Based on our SiteMeter referrals, that seems to be the main way info is found on UsefulChem.

  4. I also think that the key is searchability rather than centrality. One problem I can think of with respect to google and other search engines is that I’ve heard they only index the first part of large pdf files. I just posted my lab notebook on the web as a giant pdf. But if google doesn’t index it, I might as well print it out and leave it on park benches in Cambridge – more people would find it that way.

  5. Jeremiah,
    Yes if you want people to find your research you’ll have to break down that huge file at least into smaller pdf’s. You might post them on Nature Precedings so people can comment on each piece maybe. Another problem with pdf’s is the lack of version tracking, that you get automatically with a wiki. But since you already have the document you might as well try to use it with minimum hassle.

  6. Does anyone know of any good examples where a wiki is used (and well organized) for an electronic notebook?

  7. Does anyone know of any good examples
    About the only example that I’m aware of is Jean-Claude’s UsefulChem project.

    I think that a wiki makes an excellent ELN. I see 3 problems in getting more people to use this solution. (1) Your lab needs a sysadmin to set up the wiki, unless you use an online service. (2) The users have to learn wiki syntax – and some of them just won’t. (3) Wikis are freeform – how you organise pages is up to you. Some (many?) users prefer a more structured web page where they enter data – so again, a sysadmin has to write forms for them.

    Most biologists just assume that somewhere out there on the web is the perfect, downloadable ELN package. The idea that you can build a solution yourself from components is really hard for them to grasp, for some reason.

  8. Neil brings up some good possible objections.

    1) People may think they need a sysadmin but I think that is not necessary, and even undesirable for most scientists. Your group should focus on science, not on maintaining a server. There are currently some awesome free hosted services out there – we use Wikispaces. Use of a hosted service also gives you that valuable third party time stamp to prove when information was posted.

    2) Learning wiki syntax: here is another reason why we use Wikispaces – it has a visual editor and a simplified syntax for text editing compared with MediaWiki. Most students can learn to do simple editing extremely easily.

    3) Freeform editing – well this is exactly why freeform physical editors (blank laboratory notebooks) are still used in labs – it is hard to predict everything you will need to describe when doing real research. True, forms would make it easier to convert experiments to semantically rich documents but if those forms don’t work to capture everything then people won’t use them. My view is to make sure that the science gets captured first then we can experiment with converting the freeform record into something more amenable to automation (i.e. use of InChI’s, CML, etc.).

    My impression from the interactions I have had with several people is that wikis are being used as laboratory notebooks more and more but that it is hard to quantify because they are not public.

  9. Your group should focus on science, not on maintaining a server
    That’s why groups employ bioinformaticians, in my experience :) Beware, young scientists, of falling into an unofficial IT support role.

    I use our lab wiki (private) every day as a notebook, but I’m the only member of the group who does. Admittedly I’m the lab geek, but I wonder what holds other users back, if anything.

  10. Hi Neil,

    Sorry for the slow response to this. I think this is a great idea. The thing about open science, that I see, is that it’s undefined. No one really knows what it means. The best thing to test it is to try things out and see what sticks. We’ll work things out as we go along. The only thing that does seem certain is that closed science will eventually be eclipsed by the open approach. The discussion page already seems popular on the nodalpoint wiki. Rosie Redfield and Jean-Claude Bradley also seem to be enjoying a disproportionate amount of success as well.

    As an aside, I’ve started up my own open science blog at I’m not trumpeting it about though, people in my department are still a bit wary about me being scooped. I don’t think baby steps will hurt. Maybe we could have a bioblogs issue in the future where we can encourage 100 adventurous people to start an open science blog, then list them in this issue.

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