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

Fri Nov 2 08:58:21 EDT 2007

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
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 8220 bytes
Desc: not available
Url : http://mailman.mit.edu/pipermail/oww-sc/attachments/20071102/db22a3bc/attachment.bin