ONS logo

It would be nice to have a way to track all the open notebooks out there and it was suggested by Bill Hooker that those of use using open notebooks to put a logo by Jean-Claude Bradley on the webpage that the notebook is on. This is a great idea and one that posses a very interesting challenge: if ONS scientists use the logo, how do you crawl the web to find the logo so that you can curate the notebook?

At any rate, any of my notebook entries about with ONS in it will now have a logo associated with it. I’m putting “open notebook science logo” as the alternative text in hopes that maybe this can be tracked somehow.

open notebook science logo

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  1. #1 by Jean-Claude Bradley on November 27, 2011 - 7:33 pm

    Thanks for making use of the logos Andy – these were designed by Andrew Lang and Shirley Wu. Generally the way we have been using them is to select one of the 4 appropriate logos and to link the image to the ONSclaims site for descriptions of each option upon clicking on the image:
    http://onsclaims.wikispaces.com

    This way people doing Partial ONS (like only sharing Selected Content and/or with a Delay) can make that explicit. Alternatively you can specify that you share All Content Immediately with the corresponding logo – so if people check your notebook and don’t find an experiment they can safely assume that you didn’t do it yet.

    • #2 by andymaloney on November 28, 2011 - 3:17 am

      I do like the different logos and the different meanings that they encompass. I’ve changed the logo to link to the ONSclaims wiki as well and will use this style from now on.

      I especially like the generic logo as it makes sense for some to use such as myself.

  2. #3 by Carl Boettiger (@cboettig) on December 9, 2011 - 11:16 pm

    Presumably the right way to do this would be to add the appropriate meta-data to the logo the way that creative commons website does (uses the “rel” attribute as “license”) to define the relation of the badge to the thing it links to. Then you could scrape the html for licenses that point to the ons wikispaces page. Now I’d guess you could just scrape the html looking for link to the ons licenses page without that.

    A more rough-and-ready attempt is google’s search for matching images (drop image on google searchbar gives this: https://www.google.com/search?q=Open+Notebook&hl=en&client=ubuntu&hs=2Yv&channel=fs&tbs=sbi:AMhZZitZbTIBVkJkWDs3ylbH0_1QucssjUdsn9JCulNnypZcc6kxQSwUY2Ur8P06kANopPMai172k2gpAiJW2KGyUOx2ppZSiYtFOphvUTjX5pHYquKzY2XHuW65jYsCOcH-JFfimdOiQaX8PJ9h4N16ZkTK6lFcok3YRgZEPrCboMp39tUBpa7OsnBTWJKTbDg6GdV77ysXFzstRMgStn_1jXkDofOnmOgVS2hhh3NSmXe9IaUY6CCmFGH7NLgPbPPC0lhISh1q0NboiqMIT1DyQz79urRmOYYQXShXoo0_1uZIY6ToFSNpZdIyO1iH5cubJ2wIdVZpng_1HeoZcOtjfKE7_16qwAriX13pdHuug3u5BsAOPtoSbLvEG9ofSLBIpdsVqHUoZQIAy0f99dNxLJUDJCM0UeW6eadr8jHsXTXUOHM1F4rrguBWc_1Jqu-cQfGDWbHex3gbkOpIwlpMtvkSl4sMuQCXnHNhOrJZ2nAQKuVf4ZpTY5S5WFQsQLyGri1fHD4fSvCzbBTVFsNKQWenHNvcyZbQpZCS6zOy6hUn4vjD8fiSXAWgxmwSdxyPLlZM4d9CPWPGXB39FYl5MPp0Iu33cMlcCyqWdLoASfYFsr6wNCbn342Ur8zPkMiwv9IrCQQ-vs8vdE&prmd=imvns&ei=X-niTpa4FsjMiQLw-sDVBg&start=0&sa=N&biw=1280&bih=870)

    • #4 by Jean-Claude Bradley on December 10, 2011 - 10:14 am

      Carl – that is a nice way of finding all the sites using the logos. Not all researchers with Open Notebooks use them – another way of finding ONS projects is to look at those listed on Wikipedia http://en.wikipedia.org/wiki/Open_Notebook_Science

      • #5 by andymaloney on December 10, 2011 - 11:43 am

        JCB & Carl

        Wikipedia is great for showing links to some of the notebooks available however, there are still more on OpenWetWare that are not listed. Not to mention the others that pop-up from blogs or Google docs.

        Use of the logo is a great idea but, it is far from standard as the Google search shows. It would appear that there is a need for a standard curation of open notebooks as the movement is gaining momentum.

      • #6 by Jean-Claude Bradley on December 10, 2011 - 12:18 pm

        Andy – the last time I checked OWW I tried to identify all of the users who use the system to maintain Open Notebooks where all their experiments (and all associated raw data) are recorded in near real-time. Are you aware of any new ones that meet those criteria?

  3. #7 by Jean-Claude Bradley on December 10, 2011 - 12:32 pm

    Andy,
    Regarding “curation” of Open Notebooks, I’m not sure if I understand exactly what you mean. If experiments are recorded as they are done, it isn’t possible to have “experts” constantly monitor edits. For the students that I mentor I do try to give feedback reasonably quickly but not instantaneously. And even there I do not comment on every conceivable way of interpreting the experimental details. One of the fundamental points of ONS is that it is not “validated” by some arbitrary people. Instead, feedback will come if and when someone actually needs to use the experimental details (or interpretations). ONS ensures that all the raw data will be available for others to perform any desired analysis.
    Where there is some more systematic curation is in the abstraction of selective data for incorporation in specific databases (in our case solubility, melting points and reactions). But this is not technically part of the notebook, it is part of derivative processes after the experiments are recorded.

    • #8 by andymaloney on December 10, 2011 - 2:27 pm

      JCB: What I meant by curation was having a place where all ONS posts could be hosted or, a place that automatically linked to ONS pages as they were created. I’m thinking more along the lines of a website that is completely designed for ONS. Something similar to OWW but, as simple to use and as expandable as WordPress. Places like Linkedin or the book where you plaster your face on exist because there is a community backing it. While open scientists do have a community, we don’t have an agreed upon spot to put our notebooks. I’m curious if something like this existed, would we use it? Could it be sustainable? Or, is it just a silly idea?

      • #9 by Anthony Salvagno on December 12, 2011 - 12:23 am

        It’s not silly, could be sustainable through NSF, and it would be usable, but it would have to be really expansive and very easy to use. Most scientists won’t do it unless there is next to no learning curve and it is very easy to go from bench to notebook.

        I don’t think now is that time though. I mean open scientists can’t even decide where to share information: friendfeed, twitter, google plus (it’s hard to follow everyone posting different things in all these places and still get research done!). And if such a place existed we would need to be all in despite how unusable it would be in the beginning (and more than likely it will be pretty unusable).

  4. #10 by Carl Boettiger (@cboettig) on December 11, 2011 - 5:04 pm

    An alternative to the google image search is a google search for pages linking back to the onsclaims page (google: link:http://onsclaims.wikispaces.com/, my search results may be different), though it doesn’t get every page that has the link.

    I think offering a way for researchers to declare their work as Open Notebook Science in a machine readable way would be very interesting and very valuable. The manual curation on wikipedia is clearly out-performing my machine-search methods, but it doesn’t really scale, and doesn’t offer the potential benefit of “branding” that the icon does. For instance, here are two notebooks I only know because they are in my field, that use the icons, link back to the onsclaims page, but don’t make the wikipedia list:

    http://genefish.wikispaces.com/
    http://leeworden.net/lw/notebook
    http://www.math.ualberta.ca/~mpineda/evolution-in-fluctuating-environments/docs/notebook/

    I’m sure adoption of the icon is much wider, it’s just hard to find. ResearchBlogging.org has authors embed a piece of code along with their icon, which feeds their content to it’s database, so users have a one-stop-shop to search for all blogs on the published literature that use their icon. Obviously that’s a (small) subset of the total number blogging on science literature, but it’s still a very extensive, searchable database. Perhaps we need something like this to go along with the icon?

  5. #11 by Jean-Claude Bradley on December 12, 2011 - 8:57 am

    Andy,
    Since an Open Notebook is just a mechanism to record and share experiments in any field it has to be very flexible. I still believe that a general purpose free hosted wiki is an ideal platform – especially when linking to Google Spreadsheets to store data. Researchers could also use OWW. But I think it is healthy for researchers to experiment with different platforms to see what works best for them.

  1. Some Notes on Open Notebooks, Open peer review practices. – Carl Boettiger

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