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

[Bill F]

Thanks, Maureen.

I have one staring at me and I didn't realize that. Whoa. We need the
hardware section sooner than later.

B.


On Nov 1, 2007 5:48 PM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:

>  A quick comment about the barcode scanner. My mac comes with a camera
> which can act as a barcode scanner so some people may already have a scanner
> if they have a camera on their computer. I'm not sure about the software
> needed though.
> -Maureen
>
>
>
> On 11/1/07 2:35 PM, "Bill Flanagan" <wjf42 at MIT.EDU> wrote:
>
> 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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