Articles by Ricardo Vidal

Ricardo Vidal is a graduate student in Biological Engineering at University of Algarve (Portugal) and is also currently the Community Developer at OpenWetWare.
He also maintains a personal blog called My Biotech Life.

The nice folks at MediaLab-Prado in Madrid, Spain brought to our attention the Garage Science Workshop-Seminar that will be taking place between January 28th and February 14th 2009.

What is a Garage Science Workshop-Seminar, you ask? MediaLab-Prado explains:

The socialization of technology and the accessibility of information available on the Web make it increasingly easy for anyone to have the possibility of building a home laboratory. Garage science is nothing new but home laboratories are connected now more than ever before. There are home laboratories of all kinds: technology factories, chemistry or biology labs, artists’ studios, places to rehearse, etc.

These home laboratories have a worldwide scope via the Web, which serves as a space for the dissemination of projects and the exchange of knowledge and techniques. These online communities are accompanied by a proliferation of onsite events, such as dorkbots, barcamps and hackmeetings, where people who only knew each other via the Web can meet face to face and share their achievements and experiences.

The communities formed this way provide citizens with the capacity to develop scientific-technical knowledge comparable to what is produced in the major laboratories. “Citizen science” can serve to explore questions such as: How are the foods we eat made? What possibilities exist in biogenetic research? What is the code that makes the machines we use work? How are those machines manufactured? Based on this knowledge, experimental and critical formulations and objects can be produced proposing new paths and goals in these fields.

Interactivos?’09 aims to explore these practices, where art, science and technology meet. We invite the participants to turn medialab into a garage laboratory where low-cost, accessible materials are used to develop objects and installations that combine software, hardware and biology. There’s license to fail!

As you can see, this event looks to be quite interesting and should be quite inviting for the DIYBio folks and their projects.

Keep in mind that final call for projects and papers is December 14th 2008.

According to Scientific American, the not-so-open-access publisher Springer has just acquired the very open access pioneer site BioMed Central.

Regarding if BioMed Central will continue to be open access:

Those in the open access movement had watched BioMed Central with keen interest. Founded in 2000, it was the first for-profit open access publisher and advocates feared that when the company was sold, its approach might change. But Cockerill assured editors that a BMC board of trustees “will continue to safeguard BioMed Central’s open access policy in the future.” Springer “has been notable…for its willingness to experiment with open access publishing,” Cockerill said in a release circulated with the email to editors.

No information yet as to how much this acquisition cost.

What do you think about this? Will Springer just “experiment” with open access publishing for a while and then close the gates? Or is this a genuine attempt to join the OA movement?

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.

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