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

Thu Nov 1 22:01:47 EDT 2007

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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