Software

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.

In 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…

A 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.