One recent SciFoo related post that caught my eye was Mario Pineda-Krch’s thoughts on the idea of distributed open notebook science. Yes, distributed.

As Mario mentions, by using a client based wiki setup like Tiddlywiki, the user has more flexibility by not having to rely on network access. Furthermore, a version control system like Git brings redundancy allowing anyone to download the latest version of the notebook. The wiki + the data with full control.

The idea of open notebook science is not necessarily a new one. The term was coined by JC Bradley roughly two years ago. However, it’s been tough to go mainstream due to the fact that notebooks are usually foreseen to be private, thus failing in the “open” department. However, this hasn’t stopped many from setting up lab notebooks online like Jean-Claude Bradley, Garrett Lisi or any of the dozens of OpenWetWare lab notebook users.

It’s almost officially Summer here in the northern hemisphere but there is still time to do some spring cleaning.

As you can see, we’ve changed the name of our main blog from Steering Committee to Community, to reflect what we thing it should be about - Not only the steering committee’s views and operations but what the OWW community at a whole has to show the world.

The name change is just the first step among many new features we’ll be bringing to the OWW Community blog over the next weeks. To keep up-to-date, we suggest that you visit us regularly or subscribe to our feed.

Note: Although we’ve changed the title and subsequently the blog’s address, our RSS subscribers should not see much of a glitch. If you do happen to find anything broken, please let us know.

With the ability to get information anywhere in the world in seconds, and the virtually immediate obsolescence of any printed work, why are journals such an important part of academic research?

This question, under the heading “Are Academic Journals Obsolete?” was posted yesterday on Ask Slashdot. As you might expect, the comments are wide ranging and interesting.

When page layout software was first introduced and do-it-yourself desktop publishing became popular, many people wondered if publishers would become obsolete. Now, twenty years later, we have blogs, newsfeeds, and even better DIY publishing tools like blurb.com. Anyone can publish anything and reach a wider audience than ever before. And publishers still exist.

The arguments about whether academic journals are obsolete is a long and complex one, and you’ll see a wide range of opinions on this and other questions like it. Perhaps the print journal is a vanishing breed, for many of the reasons stated in the Slashdot posting. But much of the value, such as peer review, that academic publishers bring to their work is still very valid. Either way, until the systems for academic tenure and funding change, the academic journal in print or web-based form is unlikely to vanish.

Having a presence on OWW can help a lab gain exposure in some unexpected ways. Last week the French, Keymer, and McKinney labs, all of whom maintain wikis on OWW, were mentioned in Virtual networking for microbiologists, a Nature review about Web 2.0 applications and science. Check out the full review at http://www.nature.com/nrmicro/journal/v6/n6/full/nrmicro1922.html.

OpenWetWare is a strong supporter of iGEM (iGem.org) the International Genetically Engineered Machine Competition, which is now shifting into high gear for 2008. iGEM and OpenWetWare share some important core values including openness, community, and sharing of information. Check out the 2008 iGEM team wikis on OWW and on the iGEM site. If you’re on an iGEM team that hasn’t yet started a team notebook, check out OWW’s new One-Click Lab Notebook. It has lots of great new features.

Registration for iGEM 2008 closes on Friday, May 9, at 6pm U.S. EDT, so if you haven’t already done so, be sure to complete your registration in time!

A part of our mission at OpenWetWare is to lower the technical barriers to sharing and dissemination of knowledge in biological research. In carrying out this mission we implement new tools and technologies that make it easier to introduce, organize and present biological research data. One such tool is the new OWW open lab notebook.

By harnessing the powerful features that mediawiki provides and creating some custom features, we’ve made it possible to setup an electronic lab notebook on OpenWetWare with little more than a few keystrokes and a click of the mouse!

The new OWW lab notebook was built with three key groups in mind: individual users, iGEM teams and labs.

The lab notebook now includes these new features:

• A dynamic calendar that allows you to create or view project entry dates with a simple click.
• Local search that allows you to easily find content located only within your project.
• Improved navigation that allows you easily jump back and forth between entries.
• Customizable template pages specifically for your project. These pages automatically pull in any logo, project title or graphics every time you make a new entry)

These are just a few of the new features we’re working on. There will be more in the coming months.

If you are an OWW member, what are you waiting for? Go to our new one-click setup tool to create your personal lab notebook. If you are not an OWW member, request an account today and let us know what you think!

To keep up with the latest lab notebook developments, visit our OWW Lab notebook page.

Today, April 17, from 12noon to 1pm, the OWW steering committee will be online at http://openwetware.org/chat/ to chat with the community about the latest goings on at OWW. Anyone is welcome, so please join us.

To join, click the above link and log in using your OWW user name and password. When the chat window opens, click on “conferences” at the bottom of the page. At the next window, double-click on “Lounge” to enter the chat session.

OWW is pleased to announce a new addition to our system: ROD:Research on Demand. ROD enables the creation of research results that meet the demands of your publication and graduation schedules. By design, ROD is never 100% correct, and includes errors as subtle or as blatant as you would find in actual research results. With ROD you get the time, AND the reasons, to complete your work.

The variability of results from scientific experiments has traditionally been a major inhibitor of research progress and matriculation. Complex protocols, expensive materials, exotic equipment, trained staff, and meticulous attention to detail are typically needed to obtain quality results required for publications, clients, and various intellectual property (IP) protection agencies. Having access to all of these components at the right time and, getting desired outcomes, can be challenging at the best of times. When deadlines loom, getting consistent results may be impossible.

With OWW’s ROD, “good enough to stay in the game” results needed to address complex external dependencies are algorithmically constructed for you. In fact, ROD delivers flawed data so well, in some cases, you may never even need to finish your experiment. Should you choose to, ROD gives you extra leeway to create delays that even your toughest PI’s will agree to. Think of ROD as the “dog ate my homework” for scientists.

How Does ROD Work?

OWW’s ROD system seamlessly merges the vast array of publicly-available published information with software technology from some of the world’s most prestigious labs to produce a realistic, but subtly flawed, mash-up of any data set you need.

Example Techniques Supported

Here is a partial list of the techniques that can be included in your ROD results:X-Ray Crystallography: Resolution just low enough to produce inconclusive but “interesting” results 100% of the time.

PCR: Samples that appear to show the specific sequences required but are artfully flawed with substrates that, upon secondary analysis, will always come up negative.

Microscopy: High quality JPEG images that, on a second viewing, revert to the family travel photos you submit to us. Pet photos or opening frames from YouTube videos may also be substituted.

Using ROD, OWW guarantees you will have negative results for any findings you submit. We give you publication-quality assets that are be remarkably realistic but, under further scrutiny, will never pass peer review. However, the time you gain by using ROD assets will give you that decisive edge in pulling together the actual data.

What Users Are Saying About ROD

Here’s testimony from some of our beta testers:“If my thesis committee didn’t get off my case, I never would have finished my degree. ROD gave me the time to do it right. OK. Maybe not ‘right’, but at least, ‘better’. My committee was convinced what I had submitted was worth reviewing. When they saw the negative results but understood the plausible reason for it failing, my senior advisor actually took me out to dinner. Thanks OWW!”

“ROD got me my first-choice post-doc. The data set I submitted looked great. I got lucky; the data was never reviewed but if it were, they would have noted that the reason it was wrong was not my hypothesis but that it was the data for another experiment cited in one of my papers. The “honest mistake” angle made me feel confident that if anyone digs into my past, it can’t be used against me. This is great. I love Open Science!”

“The FDA bought every line of the report ROD submitted for me. Our review was so well accepted that the entire lab is using it for all of our new clinical trial applications.”

“I never thought I’d get out of my lab position. Thanks to ROD, I’m now managing a major facility. I don’t even need to redo my experiments. The quality of ROD info is THAT high. My start-up page is OpeWetWare now! Thanks, ROD!”

Availability

The system is still beta. ROD will be available for general use at some point in the near future….

Lorrie LeJeune writes: All of us who work online or with computers live in fear of The Big Crash. Sure, we make backup plans, and sometime the backups themselves, but we still wonder what will happen when the system goes down. Ironically, experiencing a major failure is often the event that drives us to build a stronger, more failsafe system. This is the case at OpenWetWare.

Two weeks ago OpenWetWare experienced a database crash. Yes, we did have backups, but in rebuilding the system we realized that these backups weren’t as robust as we wanted them to be. Over the last two weeks we’ve designed a new, multi-tiered backup procedure. In addition to our standard nightly backups, all data and images are now incrementally captured every five minutes and stored in several locations. These new processes will allow us to very quickly recover from even the most serious system crash, and will make OpenWetWare more durable than it’s ever been before.

Hello everyone. I’m Lorrie LeJeune, and two weeks ago I came on board as managing director of OpenWetWare. I’ve spent most of that time learning about its history, culture, and goals, and I think we’re moving in some exciting directions. Over the next few months we’ll be working to more fully realize OWW’s three-part mission of lowering technical barriers to information sharing in the sciences,  building a community of researchers who value open information sharing, and integrating OWW into the existing publishing and rewards model for science.

One example of how we’re working to lower the technical barriers is our new wiki-based lab notebook tool. The OWW Lab Notebook has all the functionality of a paper notebook and more. In particular, your OWW lab notebook is searchable and can display your work both by entry date or by project. We’re still shaking out the bugs, but Lab Notebook is currently available to all users. Look for the link in at the top right corner of your window after you log into your OWW account.

We’re also exploring both online and real-world ways of building the OWW community. This includes organizing a series of real-world meet-up sessions, and materials to help communicate the values of open science. If you’re interested in attending or hosting a local open science meet-up session, or talking about OWW at a conference, drop a note to me at lorrie@openwetware.org.

Finally, we’re looking at ways of integrating OpenWetWare into the existing publishing models for science. We want to be able to cite work that’s posted on OWW, and eventually we want to explore models for publishing original content. We’re also looking at how to post content like  protocols and supplementary materials that often falls between the cracks of traditional academic publishing.

If you have any ideas to help us carry out our mission more effectively, please follow the feedback link in the navigation bar on the OWW main page, or contact me directly at lorrie@openwetware.org. Information sharing in the sciences has come a long way since I worked at the bench and I’m looking forward seeing where the OpenWetWare community can take it.