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

[Maureen Hoatlin]

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. I¹m 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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