[OWW-SC] More changes coming as part of the OWW Lab Notebook Working Group.

[Bill Flanagan]

I'd like to thank Steve Koch for both the way he helped pull together last
month's Lab Workbook Brainstorming Session and his continued assistance in
working all of you to come up with what's turning into an exciting project.

We're now starting to implement features coming out of the Working Group. We
hope to have a follow-up session after we finish with next weeks OWW Board
and Steering Committee meetings. Steve has already indicated that he'll be
moderating the next session as well.

Two particular features are starting to move forward that I want to briefly
mention. I welcome your comments on them as well.  One is going to be
introduced into OpenWetWare over the next few days. The feature is an
extension of a feature in MediaWiki called "Magic Links". Any time you type
the term 'PMID' and put a number next to it, MediaWiki creates a usable link
to PubMed when you save the document. With no special linking characters,
these references allow a reader of the page to go to PubMed via NCBI and
view the associated document. This also works with Internet RFC document
and, to a lesser degree, with ISBN book numbers.  Thompson and Francois St.
Pierre, PhD candidates in the lab my wife now calls my home, told me about
this feature. I had been working on MediaWiki for quite a while and never
ran across it before.

We've now extended the original magic link concept to include GenBank
accession numbers, BioBrick parts, and references to Cornell's ArXiv
(Archive X). Julius Luck's Atom-based network interface to that system is
how we implemented it.

In the case of GenBank accession numbers, we came up with an interesting way
to allow the data to be viewed. We're generalizing it to the other network
document repositories as time permits. I'll keep you all up to date as we
move forward.

When you hover your mouse over an accession number that has been linked, a
small dialog box pops up. It initially will contain the title of the GenBank
record for the part. These links will only be present if a valid part number
is entered. In the dialog box, a download tag is present. If you click it,
OpenWetWare will download the sequence from NCBI and stream it down to your
desktop. If you have an application that knows about the '.gb' tag, the
sequence and associated header information will be directly loaded into your
application. Vector NTI and CLC Free Workbench 4 are a few apps we've tested
with. Once the sequence is downloaded the first time, it stays in our OWW
cache and will zoom down to you or anyone else requesting it for anytime
forward. Tom Knight asked for an extension to this that I'm just finishing
up. If you enter a term such as, "GENBAN U49845:12-1024", only base pairs
12-1024 will be downloaded.

The other feature, originally suggested by Tm Knight, was a way to print
labels from OWW. This has turned into a very fun feature. I've created a new
tag, "<label>". The Label tag will permit you to enter a label into your lab
notebook (or any OWW document). When you save the page, an image of the
label will be visible. If you click on the associated  'print'  icon,  the
label will pop up in a separate window along with a print dialog box. If you
have a label printer available to you, you can print the label to it. I'm
creating a new section called "OpenHardWare" to allow people to share their
experiences about which printers work best. I'm putting my money ($29.95! on
ebay!) on a Brother USB label printer as our test platform.

The label will feature a barcode. Steve made a great suggestion to tie the
use of the labels back to OpenWetWare. The barcode will be a unique pointer,
across all of OpenWetWare, that will associate the label with the page it is
printed from. We want to create templates for a few different kinds of
labels used in the lab. We will have a way for anyone to create and
contribute templates for specific sizes and layouts. Any petri dish in a lab
using OpenWetWare for creating these labels will find, if available, the
exact context of where the page originally came from. Those stacks of plates
you just found in the corner? Scan first, blame for taking up too much bench
space later.

I'm experimenting with a $10 barcode scanner, the CueCat, as a "necessary
and sufficient" scanner for this activity. We also have access to more
sensitive and expensive bar code readers but out goal is to work with the
absolutely most affordable barcode scanner we can find.

If anyone has suggestions as to what else we can do with this information,
let me know. We'll be rolling out a very "beta" version over the next few
weeks. More features will follow as soon as we make them work.

We have several more tricks up our sleeves that I'm flushing out. More will
follow.

When MediaWiki ceases to be useful for doing what we need to do, we are
extending it. The built-in archiving is a feature we desperately want to
keep in the middle of everything we do. But how we create the documents and
what happens when we read them may vary from the standard product. Lab
scientists have different requirements that  Wikipedia readers.  We want to
make sure those needs are accommodated without breaking OWW's essential
'Wikiness'.

As I said, please let me know what you all think.
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