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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

Hello!  Is this thing on?  The last 12 months have seen significant life changes (seemingly successful) for many of the people within and around the OWW community.  Because OWW is a community (of researchers) we are past due for an update on how we are doing and open discussions of where we might want to be heading.

First, a few of the changes:

  • All of the founding researchers who created and obtained funding in support of OWW managed to  earn their PhDs from MIT.  Many of these folks have successfully launched a new company, Ginkgo BioWorks, in order to help make biology easy to engineer.  Indeed!
  • Lorrie LeJeune, who was our Managing Director was lured away to become a Senior Editor at Nature Education, which is an incredible opportunity for her to impact the lives of many learners.  Good luck Lorrie!
  • The Endy Lab wound down at MIT and has been reborn at Stanford.  Personally, I’ve moved twice, sold one condo, bought one house, helped to design and manage the construction of a new laboratory, and have been assembling a new research team.  Phew.

Second, what’s not changed:

  • Bill Flanagan remains gainfully employed at MIT, working to make OWW better and helping to put out the fires that flare up.  Simply put, Bill is an incredible resource for OWW and we are ridiculously lucky to have somebody at his skill level and with his strategic perspective at the heart of OWW.
  • We currently maintain funding from the US National Science Foundation in support of OWW.  To clarify one point in the recent and fantastic article by Jakob Sukale, the NSF grant expires 30 April 2010.  This grant currently pays for Bill’s salary and our server costs.  We are currently underspending on this grant and I will likely ask for a no-cost extension which, if granted, could extend our existing funding runway to April 2011.

Third, who is OWW?

  • I’ve found it very useful to understand who is actually using OWW.  I’d suspected that some people tend to talk about OWW and openness in research but that fewer folks are actually living the dream, so to speak.  Well, turns out that thanks to Bill, OWW maintains a statistics page here.  There are ~6000 registered OWW users (roughly doubling over the past year).  About 50 different users make edits to OWW pages on any given day.  About 500 unique users make edits each month.  Over 100,000 unique visitors browse OWW each month. This is incredible!
  • From a different perspective, OWW is incredibly small.  We also represent a broader experiment in changing the process of research that is very much in a fragile intermediate stage of its development.  Michael Nielsen did a good job of capturing some of the issues in his recent article, “Doing Science in the Open.”  Stated differently and from a personal perspective, I would currently be hard pressed to make a successful argument that supporting and using OWW has made the research in my own laboratory significantly better, as judged by our traditionally published results.  On the one hand, we had a great experience using OWW as a platform for developing a shared reference standard for measuring promoter activity in vivo. On the other hand, using OWW as it exists today has led to increased frustration with the slow inanities to be found within the conventional research publication process, while simultaneously and naively reducing the pressure to publish more formally and enabling others outside the (v. small) OWW community to “borrow” results without giving credit.  Perhaps this shouldn’t be surprising. All said, I’m more invested in OWW than ever before, and am convinced that we are figuring out a new way to do research.  We just have a lot of work to do in order to make the transition complete.

So fourth, what’s happening in terms of thinking about where we might go?

  • Lorrie LeJeune and Jason Kelly did a tremendous job exploring the entire process of research, from brainstorming ideas to promulgating results.  Some of these ideas are summarized here.  Many interesting questions and debates arise from considering this framing.  For example, is OWW about the information and knowledge maintained on our servers, or is it about the community of researchers that produces this content?  (personally, I think that the answer is both).  Stated  differently, should OWW support the process of research or should we focus on the capture and promulgation of research results?  (again, I’d vote both).  As a different example, does OWW exist primarily in order to stand as a shining beacon of openness in research, or are we simply trying to make the research process better which, given today’s information and communication technology platforms, tends to select for doing many more things in the open? (more on this third example below).
  • Bill Flanagan and I have been churning through the exciting opportunities that seem to continuously emerge given ongoing advances in information and communication technologies.  Some people refer to OWW as a wiki.  This makes me cringe.  Wikis are great but we likely need to transcend this framing in order to best realize solutions that could be developed in service of our community and our work.  You can find many early examples of this, such as Bill’s pilot efforts to integrate OWW with online document systems (e.g., Google Docs).

So, where should we go?  My own sense is that we should go meta and support the integration of many web-based tools and communities in support of making the research process better.  We will end up doing many more things in the open as a result.  We also need to partner more effectively with existing modes and channels of peer review and recognition.  But this is just my sense, so please chime in with your two cents, either via our Google discussion group, in the comments below, or by editing the appropriate OWW page.  We need to hear from the people who are depending on OWW, or who would use OWW if <blank> happened.  Also, for those of us for whom OWW is an essential part of our research existence, please participate in discussions about how to best guarantee the future funding of our operation.  We have time to work through different models, but need to start doing so now. Our Discussion list is
just a click away
.

Cheers, Drew

My life at OWW has been an endless stream of messages articulating Austin’s far-too-old feature and technology suggestions that I slowly get around to adding. The “flash” (of insight) to “bang” (of getting the idea online) is not great; I would hope the time will diminish eventually. But for now, this is what it is!

The latest is a big one. That would make it a “big bang”. So maybe a better way of saying it would be a “marginal thud” to a “moderate drop”. I’ve started the process of adding support to OWW for Javascript Gadgets. This is a centrally managed method of deploying ‘sanctioned’ Javascript that then can be enabled or disabled by every user. This extension is already in use on various WikiMedia servers; we are long overdue.

What it means is that there are scores of ways people more javascript-savvy than me have created small extensions to MediaWiki that do all sorts of useful things. The ‘quick-nav’ item on the sidebar, written by Austin, as an example, could be included in this general category. I created an extension to enable it for everyone since it is so useful to anyone who has ever forgotten the last 15 pages he/she visited.

I’ll provide a full list of these extensions when I’ve completed the import of them.

Once we have access to all of them, I would imagine that a set of much more research- and life science-specific entries would be useful. Since the Venn diagram representing “biologists”, “OWW users and viewers”, and “Javascript hackers” may be initially limited to Austin, it may be a while before we have many OWW-specific extensions available.

Personally, I think we should all do our best to start keeping him company.

If there’s something you have to do over- and over- again in OWW to do your work, consider using the discussion area I’ll add in order to get the ideas flowing.

Expect the first set of Gadgets, with instructions, to be available this week.

If anyone wants to volunteer to help out with testing Gadgets prior to our including them in the central library, please let me know. We’re not limiting inclusion of Gadgets because we want to suppress open science, by the way. It’s just that in programming, anything that can fail, will. I just don’t want an infinite number of new lab notebook pages to be created just because someone wanted to automate his or her own task and didn’t test!

Here’s a link for more information on MediaWiki Gadgets:

wikimedia.org: Gadgets

By the way. Don’t confuse Gadgets with Widgets. We may add Widgets as well. Unlike Gadgets, once enabled, Widgets can be added by anyone to any of their pages. Where Gadgets are more related to creating content and using OWW, Widgets will be useful for extending OWW to interact with external data.

Thanks.
Bill

PS: Thanks again, AC.

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.

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.