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It’s been a while since my last update. But lest anyone have any doubts about the ongoing direction of OpenWetWare, rest assured, things are moving forward.

Not dead yet….

Server Move Details

This week (June 1 – June 5), OpenWetWare.org will be moving from our current server at Rackspace to a new Rackspace Cloud Server. The server will be around the same class of machine and will be running on Ubuntu Linux rather than the existing RedHat Enterprise Linux release. All backups will be done to Rackspace Cloud Files. All MySQL database backups , and image files will be stored external to the server via Cloud Files. For those of you who are wondering why OWW will be using Ubuntu rather than Red Hat, it’s because Wikimedia uses Ubuntu for all of their MediaWiki servers; using it will keep OWW close to the infrastructure that MediaWiki is tested and developed¬† on.

The move will be done Tuesday night around 11:00 PM EST. We don’t anticipate problems but the server will briefly go down as the IP address is changed. The new server has been configured and, just after changing the IP address, the most recent snapshot of the MySQL databases from the current server will be loaded to the new one and a final file sync will be executed.

There should be no changes in the way MediaWiki and any extensions are handled. LaTex has been installed on the new server.  All extensions are working or are being tweaked before the move.

There will be no upgrade of OWW’s MediaWiki software release until the move is complete. Hard-won experience dictates that reducing variables is the right way to maximize the probability of a successful major server task.

Since OWW uses many virtual hosts, all of these will be tested briefly to make sure they are all accessible. This can’t be tested completely until the change. No problems are anticipated but if there are problems, this is the most likely place it will be.

Please submit any comments or questions to me. Either reply here or use this link and follow the contact instructions in the OpenWetWare wiki.

Thanks again.

Bill Flanagan

OpenWetWare.org

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 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.

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 del.icio.us. 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!

OWW Lab NotebookTomorrow, July 10th at noon EDT, we’ll be having another one of our open town hall meetings at OWW. Anyone is invited to take part in the meeting, either via conference call or online chat. Details to get connected can be found here.

This month’s meeting will be focused around Lab Notebooks. We’ll be discussing what has already been done at OpenWetWare and what features should be added (or removed!), among other things…

If you happen to be interested in this topic, feel free to join in on the conversation and share your thoughts. If you can’t make it to the meeting, you can either leave your comments on this blog post or on the wiki, here.

Jonathan over at Working the bench has just recently posted about how impressed he is by OpenWetWare and the available protocols:

It takes a little digging, but the website is really sweet simply because it gives you the feel that, for any given protocol, you are looking at something that works. It’s been tested, validated, and in many cases even commented on and modified by any number of additional people.

Jonathan makes a good point here where he mentions that you are looking at something that has been tested, validated and in many times worked on collaboratively by a group of OWW members.

What Jonathan doesn’t mention is that although OWW is a great resource for protocols, there are other great features like the materials section, indexed reference sources and above all, a large community of researchers from all over the world.

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.