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The BioBricks Foundation is pleased to announce that we are now managing technical support for OpenWetWare. The BBF is a nonprofit organization that promotes biotechnology in the public interest. If you like OWW and want to support our efforts to keep it running smoothly, please consider making a tax-deductible contribution of any amount to help pay for hosting, web developer oversight, and other basic needs. You can make a contribution to OpenWetWare here.

If you have any questions or suggestions, please email us at info@biobricks.org.

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

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.

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.

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.

LaTeX logoIn the May/June issue of the Mathematics Association of America‘s news magazine MAA Focus, you’ll find an article titled “Student Collaboration using a LaTeX wiki” [pdf].

The article demonstrates the usefulness of the LaTeX extension for MediaWiki by enabling this great syntax to be used online in a collaborative environment such as a wiki.

It just happens that the LaTeX extension referenced in the article was written by Austin Che, a member of OpenWetWare’s steering committee. Which means that we’ve had a LaTeX enabled wiki for quite a while now :)

If you don’t know what LaTeX is, I’d first suggest a read at Wikipedia’s LaTeX page.

If you’ve got a grasp of what LaTeX is, I’d recommend you head over to OWW’s LaTeX page where you’ll find information on the advantages and disadvantages, software for writing LaTeX, PhD thesis LaTeX templates and more…

oww-lab-notebook-perspectiveA 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.

I’ve come across three sites that could be really valuable in imagining how to make OpenWetWare (and igem.org) better. Check them out:

UI-patterns.com is a categorized collection of 30 or so user interface design patterns (recurring solutions to solve common problems) culled from the best sites around the web. It provides generalized descriptions and links to actual instances of solutions to many common website tasks, such as tags, WYSIWYG editors, autocomplete text areas, pagination, live previews, table sorting, etc. Go have a quick look and consider if any could make OWW better.

Wikipatterns.com “is a toolbox of patterns & anti-patterns, and a guide to the stages of wiki adoption.” They categorize and describe ~100 common methods of optimizing how wikis work and are used, similar to ui-patterns.com. Here are some interesting entries: Set Window of Discussion, IdentityMatters, Built-in obsolescence, BarnRaising.

Aboutus.org has nothing directly to do with running a wiki. I’m including it because it is a stunning example of how mediawiki can be re-themed to look absolutely great and how the structure of mediawiki URLs can be simple and logical; for instance, the aboutus.org entry on openwetware is simply aboutus.org/openwetware.org.

I think these sites are great resources for helping us improve OWW and I hope you get a chance to check them out.