Some have said that an image is worth a thousand words, or at least a dozen or two data points. Taking measurements is a given in any lab, working in any field of science.

Therefore, we have set up an extension on OWW that allows one to easily generate some simple line, bar or pie charts by simply introducing some wiki code and comma separated values.

The charts are generated automatically via the Google Charts API and therefore any changes made to the values within the wiki code values, will generate a new chart, on-the-fly.

We have set up a page with some very simple examples on how to produce such charts. There is more info at the official extension’s page at Google Code.

If you happen to be looking for something more complex that can handle not only data points but also equations, then you are looking for another feature we also support via gnuplot. You can find more info on this feature/extension here.

There’s an interesting (but rather short) interview with Cameron Neylon and Jean-Claude Bradley on the topic of open notebooks and sharing of data on the web. Some interesting points are made by both interviewees such as Cameron’s point on the main concerns:

The main issue is the fear of rivals stealing data. The second one is: will I be able to publish? And that depends on the publisher. Most publishers regard what we do as the equivalent of presenting at a conference, or a preprint. That hasn’t been tested across a wide range of publishers, and there’s at least one — the American Chemical Society — that doesn’t allow prepublication in any form whatsoever. There’s also a legitimate concern that a lot of people will put out a lot of rubbish.

And JC Bradley’s view of an open notebook:

The basic philosophy of open-notebook science is to have no insider information. Essentially all the information that is available to the [research] group is available to the rest of the world. You have an objective, a procedure and a log section, in which you report what you actually do.

These is far more to be said about sharing data and the use of open notebooks. Both Cameron and JC Bradley have written about their experiences on their blogs. I’d recommend snooping around because there is much to read.

Alright, the title is a little of a stretch. However, the efforts of Mackenzie Cowell and Jason Bobe have demonstrated that hacking biology can and may some day become as common as hacking away on your computer (think positive!).

A recent article in the Boston Globe lists some of the issues related to doing biological work from home and how there are rules and regulations that need updating and revision.

Unlike hacking on your computer, biological work usually generates waste that may (or may not) be harmful and work is not as “straight-forward” as coding.

The movement is getting much of its steam from synthetic biology, a field of science that seeks to make working with cells and genes more like building circuits by creating standardized biological parts.

Although it’s not as simple as it’s portrayed, synthetic biology does allow for genetic transformation of bacteria and other types of cells with great ease, however it should not be something taken lightly and performed by amateurs. Or should it?

What is your opinion about DIY Bio? I’d love to hear your opinion.

wikisym2008Coming up next week is WikiSym 2008, the 4th International Symposium on Wikis, taking place in Porto, Portugal.

OpenWetWare will be presenting a poster and also a demo of how we use MediaWiki software to produce an environment that enables collaboration and sharing of scientific information among life science researchers.

So, what exactly is WikiSym?

WikiSym is the foremost conference devoted to using, developing and researching wikis. In our fourth year, only WikiSym brings together organisations that use wikis to meet face to face with leading and emerging vendors, active researchers and leading wiki consultants.

WikiSym 2008 explores and extends our thriving wiki community, building on the past 4 years to again bring together researchers, practitioners, and technical writers to gather, discuss, share best practices and develop knowledge .

For more details on the OWW poster/demo please visit “our” page on the wiksym2008 wiki.

The Boston Globe has recently published an article showcasing a few projects that belong to what they refer to as “a peaceful insurgency in science”, an open-science movement per se.

Barry Canton, Ph.D. graduate at MIT and co-founder of OpenWetWare, is portrayed as an example of this movement. By posting his work on OWW (and also to an established journal!), his work has been incorporated into 18 different projects in other labs.

Other projects mentioned are Science Commons, also based at MIT, and the Journal of Visualized Experiments (JoVE).

The Journal of Visual Experiments (JoVE), a video-publication for biological research based in Sommerville, MA has recently been accepted for indexing in the hugely accessed PubMed and MEDLINE.

JoVE was founded in late 2006 as the first video-publication for biological research. With an editorial board including 20 scientists from leading academic institutions such as Harvard and Princeton. The online journal has grown to include over 200 video-protocols in fields such as immunology, neuroscience, microbiology and many others.

The National Library of Medicine (NLM) advisory board decided to include what is now the first and only video-publication in their large publication database and by doing so demonstrates openness to new and innovative ways of sharing science.

Moshe Pritsker, Ph.D., co-founder of JoVE in an email sent to us states:

“Inclusion in PubMed/MEDLINE is a big milestone for JoVE, and for the scientific publishing in general. It demonstrates the official acceptance of new approaches to science communication, such as video online, by the scientific community. Overall, it will increase the interest of the scientists to communicate their findings in video, making biological sciences more transparent and efficient.”

The Do-It-Yourself (DIY) movement has been growing quite significantly recently. I should say regrowing, given the fact that I recall reading Popular Mechanics do-it-yourself encyclopedias at least 15 years ago!

Anyhow, enter the Forbes DIY e-gang. Forbes has put together a short list of prominent names in the newly revived DIY movement like Dale Dougherty & Tim O’Reilly (Make Magazine), Neil Gershenfeld (Fab Labs), Jim Newton (TechShop), just to name a few.

Ginkgo BioWorks Transformation GuideAmong the group spotlighted in Forbes is Reshma Shetty (Ginkgo BioWorks), a PhD graduate from MIT and also co-founder of OpenWetWare.

Shetty and colleagues (also MIT PhD graduates and co-founders of OpenWetWare) recently demonstrated how microorganisms can be manipulated quite easily to produce interesting results. In this case, they genetically transformed bacteria (E. coli) to produce a red glow. All this was done in a few simple steps as illustrated.

On a side note, I found it interesting that there was no mention of DIYbio, a group recently founded by Mackenzie Cowell and Jason Bobe in Cambridge, MA. Although not yet quite as grand as the DIYers mentioned in Forbes, but still noteworthy.

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.

Earlier today fellow OWW blogger Cameron Neylon gave a talk at the Institutional Web Managers Workshop in Aberdeen and did so, not only for those present at the venue, but also to anyone with internet access.

Cameron set out to stream the talk via webcast, have updates via FriendFeed and also microblogging via Twitter.

The presentation was viewed by quite a few folks and many participated on FriendFeed. Cameron even stated that he noticed 20 new followers on his twitter account!

Giving talks can be stressful as is, so this requires some congratulating for the effort. Great work Cameron!

As many of you may have noticed, we’ve been adding a few new features to OWW’s side bar over the last few days. Among them you’ll find the quick nav, the feedback box and invite box.

Let me go over some of these new features so that you can take full advantage of them. Keep in mind that some of these features are only available for OWW community members. If you are not yet an OWW member, feel free to join us.

Quick NavThe Quick Nav
The quick nav is a cool dropdown select menu that displays your last 15 or so moves around OWW. This comes in handy when you are bouncing between pages. Just click and you’re there.

Bookmarking linksBookmarking tools
We’ve added a few little icons that link to bookmarking tools like Connotea, CiteULike and This will allow you to quickly save the revision of the page you’re currently looking at with all the relevant content required by these bookmarking services.

Feedback is goodThe Feedback box
As a way to further interact with our visitors and community, we’ve set up a quick feedback box that allows anyone to let us know their opinion regarding a specific question we happen to display within that box. It’s just a matter of typing in your short comment and click! It’s that simple.


Invite a researcherInvite a friend
We are always interested in having new and interesting people join OpenWetWare. Therefore, we’ve set up a quick invite box that allows current OWW community members to invite their friends/colleagues to join.

We are cooking up the next batch of cool features… Do you have any ideas or suggestions for features you’d like to see developed/implemented on OWW? Let us know!

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