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

Fri Nov 2 12:19:33 EDT 2007

OK. I can give you a tag immediately to do this.

Example:

<barcode></barcode>

I'll keep it simple. Barcode will not initially give you options. It will
just create a universal unique ID for the OpenWetWare page. That way, we can
use the exact same mechanism for the labels.

Initially, you can place the tag anywhere. We can move it into the skin of
OpenWetWare and provide a 'preference page' option to enable or disable it.
That would output the tag at a known place on all pages.

Since we do have a separate CSS style sheet for printed pages, we can
restrict it to only be output via printer. Otherwise it would be invisible.

I'll put this up this afternoon.

B.

On Nov 2, 2007 8:58 AM, Tom Knight <tk at csail.mit.edu> wrote:

> So, another potentially worthwhile idea:  When you print out pages,
> provide an option to include a barcode which can be read.  Then, if you
> use a protocol that's been printed out, you can scan the barcode and
> link the correct page (including the correct version).
>
>
> On Nov 1, 2007, at 9:34 PM, Bill F wrote:
>
> > There's a $29.95 package called "evo barcode" that claims to work. I
> > downloaded and tried it with a MacBook pro camera. After whooshing
> > "A Life Decoded" in front of the scanner for 3-5 minutes, it still
> > didn't get a good scan. It may be my technique. I'll try it tomorrow
> > again. The program has a 7 or 15 day trial period. It can be scripted
> > to send the data to another app, like an input field on a web form. It
> > clearly has some possibilities.
> >
> > I also found an open source barcode reader library for the camera. But
> > the contents of the package literally is "open source" as in "source
> > code".
> >
> > This looks like a good one to track on the hardware page. Someone will
> > have a better answer than me.
> >
> > It's a great solution to the problem, however. Barry has a stand-alone
> > iSight camera that I'll try out tomorrow. Just don't tell him I'm the
> > one who stole his camera.
> >
> > Shh...
> >
> >
> >  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.
> >>>
> >>>
> >>> _______________________________________________
> >>>  OpenWetWare Steering Committee Mailing List
> >>> sc at openwetware.org
> >>> http://mailman.mit.edu/mailman/listinfo/oww-sc
> >>
> >>
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
>
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