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

Thu Nov 1 20:45:10 EDT 2007

Log into beta.openwetware.org and try it out.

The page you sent me is too magic: the product page mapping to the BamHI ID
needs a lookup to get there.

But....

Their rebase page has all the info on it. The link works to that database.

What I will do later is to make up a sort of index card version of the page
that can be displayed via a popup box.

But you folks tell me. Do you want the product page? I can probably get
their catalog adn load it into our database so we go straight to the product
order page.

Let me know where you want it to go.

B.

On Nov 1, 2007 5:58 PM, Drew Endy <endy at mit.edu> wrote:

> Bill,
>
> Your email and work are terrific, at many levels.
>
> It is fun to imagine having a magic link for restriction enzymes
> (also at many levels).
>
> Perhaps, just to demo something we could try something for New
> England Biolabs.  "NEB BamHI" would link to: http://www.neb.com/
> nebecomm/products/productR0136.asp
>
> I think that this would be a pretty interesting experiment for us.
> First, the NEB website has the best information on their restriction
> enzymes (they are a special company).    Second, on longer time
> scales, maybe NEB would start to appreciate OWW for directing traffic
> in their general direction.  This last statement implies a lot, and I
> don't mean to skip over any conversations about how OWW works and
> what our values are, but I still think that this idea is sufficiently
> interesting and important that we should try a pilot experiment, if
> we can afford it.
>
> All best,
> Drew
>
>
>
>  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
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20071101/4c73b33c/attachment.htm