OpenWetWare:Software/Milestones/November 2007/Update

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November 2007 Update

There’s only so much time in a month, especially when there are 2-3 holidays in it. I’ll do my best to keep updating the individual projects on a regular basis. If you have specific features that you’re looking for that aren’t being worked upon, let me or anyone on the OWW Board of Directors know about it and we’ll do our best to accommodate your request. It may not be immediate but I assure you that we’ll do our best to stay on top of all of them.


Julius Lucks generously donated his time this month to work with us on a number of development tasks. We’ve implemented a way for his project, a new Atom-based API for Cornell’s arXiv archive (, to be displayable within OpenWetWare. We’ll move it to the main server soon. Julius has also been very helpful in outlining ways in which we can start implementing ways to start creating more formal ways in which individuals and their labs can be connected together.

Steve Koch ( continues to help us develop Lab Notebooks. We are in the middle of implementing prototypes for various features for the notebooks. He’s sent us a number of requests for email-enabling wikis that would help both the notebooks and a multitude of other aspects of OpenWetWare. We’ll do our best to get inbound email up and running. We’re constrained by the need to finish off other parts of the system before moving on to this one. I haven’t forgotten it, however!

Cameron Neylon ( visited with us a few weeks ago. He demonstrated some of the work he’s been doing on lab notebooks. His work is extremely interesting. He’s spent a long time working through the line between structured and unstructured applications for supporting lab science. We look forward to continuing to collaborate with him as we move forward.

We also met with Jim Hu from Texas A&M. For those not familiar with his project, e-Coli Wiki (, check out his site. We have a lot to learn from him in the way he has built up his site. He’s also walking the line between a classical “formal” application for curating genomic information related to e-coli and providing a more fr–form wiki-based system for allowing others to co-curate. His site features a very nice integration with gbrowser (, among many other tools. We look forward to finding ways to work with his site.

Here at MIT, Ilya Sytchev ( continues to amaze me with his ability to predict the future. He told me to wait at least a few months before upgrading to Leopard on my Mac. It’s not a bad upgrade. The problem is the amount of time one needs to spend fixing problems when so few others have had to contend with them already. Installing developer tools on Friday really can make the rest of the weekend disappear. The moral is never to lse your ‘tar’ executable. And never doubt Ilya! Ilya’s keen eye can find a problem in OWW from 300 yards. My continued thanks to him for his vigilance.


Magic Links and Printable Labels

I’m still in the process of moving the “magic links” to the main server as well as providing label printing support. I’ll keep you posted on both of these topics. The mention of using a bar-code scanner generated a good deal of email traffic. I’m still working on the implementation of the label printing. I created a new extension to handle the extended “Magic Links” ( We chose to wait until we move to the next release of MediaWiki to roll it out on the main OpenWetWare server. The original version was implemented directly in the OWW MediaWiki core and was intended for test. Expect to see it on the main system soon.

GUI Editor

A GUI editor, based on the Javascript-based FCKEditor HTML editor, was experimented with this month. There are a LOT of details still to be handled before this meets the needs of everyone. In the short term, I have it deployed on an OWW copy. Our initial enthusiasm for it was quelled by some of the more daunting usability and stability problems present with it. But we’re still working with the FCKEditor team to see how much it will take to get to the point where it’s no longer “not quite ready for prime time”. It’s a great project.

November Milestones

Although we’re still centered upon improving lab notebooks, there are several other items we’re working on. I was tardy on posting the November update but it can be found here:

This is where you can find all of the monthly status/milestone summaries: [1]]



I’ve also cleaned up documentation on extensions. All of the extensions are now linked into the main Extensions page which can be found here:


For each extension, there’s currently a main page. My goal is to write and document lab-centric examples for each extension. Anyone who wants to add these should feel free to do so. Currently, extension pages are named as follows <Extension name or Type>

Demos for each extension will also be present. They will be located directly below the name/type in a document, Demo. As an example, the full path of the RSS extension (XFeeds) demo document is

If you don’t see a demo for an extension and would like to add to the docs or create a document for it, please feel free to do so.

All active extension pages are now connected together as a single category. The category page is located here:

I’ll eventually add additional categories to improve discovery. I’ve imported the original doc pages for some of the non-OWW-developed extensions so people can find them. It may be more appropriate to link to some of these pages in general, but I wanted to allow the text to be searchable from within OpenWetWare.

One other note. You can also find out about all of the current OWW extensions by checking the Special:Version page here:

This is the “official” source of what is and is not running on the server. This is a list of all currently active extensions published by the MediaWiki server. if it’s not there, it ain’t runnin!

Semantic Wiki

We’re just starting to work with Semantic Wiki. This isn’t just an extension but a way of ordering all of the information contained within OWW. The jury is still out as to how we’ll use it. I’ll keep all of you posted as we figure out exactly where it fits in. For more information, check out the following: “OpenWetWare Developers” blog

This and other OpenWetWare development messages will be posted inside OpenWetWare as well as on the new “OpenWetWare Developers” blog. I intend to publish there on a regular basis. it can be found here:

Thanks and Happy Thanksgiving.

Bill Flanagan