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

Drew Endy endy at MIT.EDU
Thu Nov 1 17:58:14 EDT 2007 

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.
>>
>>
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