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

Thu Nov 1 22:23:48 EDT 2007

It's plausible to imagine implementing a web-based barcode scanner in flash
or java.  Someone has actually already done so here and released the source
under CCA-2.5 license: http://en.barcodepedia.com/download

I'm not sure how well it works or if it can read semacodes, but I bet we
could use it as a starting point.

Mac

On 11/1/07, Bill F <bill.altmail at gmail.com> wrote:
>
> 1. very small, for narrow screw top bottles: 1.3"
> 2. small, for eppendorfs, cryotubes and other small containers: 1.5"
> 3. large, for everything else, mostly media bottles and flat surfaces; 2.5"
> Size on this one is not so critical.
>
> I think we want some standardization of these sizes.
> >> Excellent starting point.
> >> We will have a standard set of labels each defined on an OWW page.
> >> These won't be MediaWiki template pages, just print templates that can
> be added by anyone.
>
> The small and very small labels can't really be larger or much smaller.
> You want them to fit all the way around the container so that they stick
> to themselves, but not overlap so much that the text is obscured.
> I suppose a small vertical bar code would be best, or maybe one of the
> square styles.
> >> I'm currently working with a standard rectangular barcode printing
> library.
> >> The smaller the barcode, the higher the scanner resolution required.
> >> The square barcodes look interesting. Austin pointed to one system. I'm
> looking into it.
>
> There are a lot of systems out there which use pre-coded barcodes, such as
> the Thermo system used at Addgene.  We need to support these as well.
> >> I'm still looking for info re: the Thermo system.
> >> I signed up with Addgene to look at their interface.
> >> Once Jason OK's me (I affiliated with Endy Lab's existing entry) I'll
> have full access.
>
> There should be a way of showing a bar code to the reader and having that
> barcode be remembered and associated with that lab notebook page.
> >> If the Evological Mac package for using the iSight camera pans out,
> this is a good place for it.
> >> The evological app is fully scriptable.
> >> Using a barcode reader on any computer (mac or pc) works the same way.
> >> The output from either is standard keyboard codes/ ascii alphanumeric
> characters.
> >> We can provide a pretty simple network interface to accept the barcode
> number and
> >> a related set of fields from the desktop script and post it to a wiki
> page.
>
>
> On Nov 1, 2007 6:38 PM, Tom Knight <tk at csail.mit.edu> wrote:
>
> > These are terrific features.  Just a note on the labels idea.  I have
> > three standard labels I make.  Each has my initials and the
> > (automatically created) date in the lower left and right corners and a
> > spot for the main centered text.  All use the 3/4" wide tape, and are
> > of these lengths:
> > very small, for narrow screw top bottles: 1.3"
> > small, for eppendorfs, cryotubes and other small containers: 1.5"
> > large, for everything else, mostly media bottles and flat surfaces;
> > 2.5"  Size on this one is not so critical.
> >
> > I think we want some standardization of these sizes.  The small and
> > very small labels can't really be larger or much smaller.  You want
> > them to fit all the way around the container so that they stick to
> > themselves, but not overlap so much that the text is obscured.
> > I suppose a small vertical bar code would be best, or maybe one of the
> > square styles.
> >
> > There are a lot of systems out there which use pre-coded barcodes, such
> > as the Thermo system used at Addgene.  We need to support these as
> > well.  There should be a way of showing a bar code to the reader and
> > having that barcode be remembered and associated with that lab notebook
> > page.
> >
> >
> >
> > On Nov 1, 2007, at 5:35 PM, Bill Flanagan 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
> >
> >
>
> _______________________________________________
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>
>

-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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