[OWW-SC] November Development Update

[Bill Flanagan]

*
November Development 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.

*People*

Julius Lucks (http://openwetware.org/wiki/Julius_B._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 ( http://www.arxiv.org <http://www.arxiv.com>),  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 (http://openwetware.org/wiki/User:Skoch3) 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 (http://openwetware.org/wiki/User: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 (http://www.ecoliwiki.com), 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
(http://www.gmod.org/wiki/index.php/GBrowse<http://www.gmod.org/wiki/index.php/GBrowse>),
among many other tools. We look forward to finding ways to work with his
site.

Here at MIT, Ilya Sytchev (http://www.openwetware.org/wiki/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" (
http://www.mediawiki.org/wiki/Markup_spec/BNF/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
http://www.fckeditor.net/, 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:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007<http://openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007><http://openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007>
*
This is where you can find all of the monthly status/milestone summaries:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Milestones<http://openwetware.org/wiki/OpenWetWare:Software/Milestones>
*

*Extensions
*
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:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions<http://openwetware.org/wiki/OpenWetWare:Software/Extensions>
*
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
*

http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions/<http://openwetware.org/wiki/OpenWetWare:Software/Extensions/>
                      <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

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS/Demo<http://openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS/Demo>
*
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:

*
http://www.openwetware.org/wiki/Category:Extensions<http://openwetware.org/wiki/Category:Extensions>
*
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:

*               http://www.openwetware.org/wiki/Special:Version
<http://openwetware.org/wiki/Special:Version>

*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:*

**               http://www.semwiki.org/*
*

"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:

*              http://blog.openwetware.org/developers
*
Thanks and Happy Thanksgiving.

Bill Flanagan.
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