Monday, January 26, 2009

Update on Our New Open Science Activities

I think it's been about a month since I started these blogs and joined friendfeed. It's been a whirlwind, really. I've e-met dozens of scientists around the globe in that short time, most of them much farther along than I and my lab are in terms of open science. The community of scientists out "here" is incredibly welcoming and helpful, and I want to send a thank you out to whomever of you read this post.

It's also been a time of huge change in terms of our lab's open science activities. We have started a lot of new open activities, and I thought I would make a list of them here. I'll only list those things that are new since mid-December, and I think it's quite a lot.


Of course, I started blogging. We also started a blog that I and our lab members to contribute to. So far, only Anthony and I have contributed to it, but that will evolve over the year, I think. So far for me, blogging is a treat and I've been able to rationalize doing it based on potential synergies with the activities I'm supposed to be doing :)

Posting grants in public

We started posting our grants on Scribd. I chose this site from advice from Jean-Claude Bradley and Cameron Neylon. So far, I've liked the site as a place for sharing grants and other documents and it seems to work well. As an example, here is the grant we submitted last week. Posting grants has been really helpful so far and I expect it to continue to be helpful. We've received helpful comments from a couple people, and also made some science connections because of it. For example, Cameron and I realized we have a lot of science interests in common!

Paper preprint

A big step we took is we drafted our first paper out of our lab and we posted it on Nature Precedings. Larry Herskowitz is the lead author on this paper. We posted it a week ago, and we immediately received very helpful comments, questions, and suggestions from Richard Yeh. We're using OpenWetWare to talk about the paper with Richard and any others who want to join. My opinion right now is that OpenWetWare is a better place for these kinds of detailed lists of questions and suggestions, because we'll easily be able to break it into different topics, create sub-pages, and post supporting data, figures, etc. (In contrast, we found that trying to write the paper on a wiki just did not work for us at all.)

Open research projects

We have also taken some big steps towards "open notebook science" in the past month. We've been using a private wiki for about two years now, hosted by OpenWetWare. As I understand it, providing us with a private wiki was part of an experiment to see if it could draw in more users and lead them towards open science. You can't scientifically extrapolate from our experience, but then again, you don't have to approach it, my opinion is that providing the private wiki worked out beautifully for OWW's mission. I think they should continue to provide private wikis, including for select new users on a trial basis. It's quite possible (impossible to prove, though) that none of the open science activities I'm describing in this post would have been started had not Jason Kelly offered me the private wiki two years ago. Thank you Jason & all the OWW founders! I'd also like to thank Bill Flanagan who has helped me tremendously in many areas of the public and private wikis.

Having prepared via our "warmup time" with the private wiki, many of the students in my lab have begun to take open notebook steps in the past few weeks. You can find links to these on our open-research projects section. Anthony Salvagno has started doing real open-notebook science, keeping his daily notes on OWW, using the Lab Notebook system that Ricardo and others developed. Anthony is about to start learning molecular biology in our collaborator's lab, with guidance from Kelly Trujillo. The lab is not accustomed to e-notebooks, so it's going to be really tough for Anthony to not be driven to use a paper notebook. We'll see how it goes, I'm hoping he can show them the way!

Caleb Morse is embarking on some MediaWiki projects and we're trying to do our communication via OWW. There are many interesting things he might pursue this semester, many of them improvements to OWW and / or MediaWiki that can make the conduction of open research much easier. For example, he's currently working on modifying an extension to MW that uses cookies to prevent data loss when the browser crashes or closes while editing a page. This would be a huge plus for OWW.

Finally, Andy Maloney joined our lab in October and has learned to use the wiki very quickly. He recently took his first leap into the public wiki by posting his incredible instructions on how to build a laser diode control system from OEM parts. I'm also pushing him to post some of his earlier research accomplishments on OWW, including a custom microscope he built for imaging ultrasonic fields via the sonoluminescence. His Google SketchUp drawings and fly-by animations of the thing are amazing and I want you all to see them!

Open teaching

I've also started posting teaching material on Scribd. I'm trying to be careful about copyrighted material, so I'm not sure whether I can keep that up. One of the things I try to do after lecturing is to "debrief" to help with next year's lecture. So, combining blogging with Scribd is a good way to do that.

Back Pat

Looking back over that list of new things we started doing only recently has made me feel great about our lab. Obviously that rate of science "opening" can't continue. But I really do think we'll be able to keep up most of the things we've started, and I'm excited about that. On our private wiki, use a template that Anthony wrote for giving yourself a pat on the back. You just add {{BP}} to a page to use the template, and then you get an electronic pat on the back and feel good about yourself. Or at least some of use do. So, I'm going to put {{BP}} on this article and it's for me and all the students in our lab for these accomplishments. It's also a {{BP}} for all of the scientists I've been talking to recently and who have helped us take all these steps. They've provided very valuable advice and examples about how to do it, as well as encouragement and feedback for the steps we've taken. Thank you!


  1. This is all extremely encouraging! Please keep us posted when Anthony posts a wet lab experiment on the Open Notebook. I would be happy to look at the interpretation of the data and give feedback.

  2. Hi Steve,

    A friend and I (both physics undergraduates) are currently building a website called CoLab to help scientists perform online collaborative projects. We're centering the site around 'Issues' for which scientists can create 'Discussions' (threaded comments) and wikis (conclusions drawn from the discussions for instance).

    What features do you find yourself wishing for that are not available with current tools? Are there features that are currently available but you wish were all available in one place?

  3. Hi DJ, I currently use OpenWetWare which is a MediaWiki-based tool that provides a lot of what we need. But there is no perfect solution out there to solve our general need of just making it very easy to electronically capture what goes on in the lab. There's a lot of discussion of these issues on FriendFeed by a lot of people more knowledgeable than me. I'd suggest you take a look there. The "Science 2.0" room would be a good start ... and posts from members of that room (Jean-Claude Bradley, Cameron Neylon, and many others)

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