Log into <a href="http://beta.openwetware.org">beta.openwetware.org</a> and try it out.<br><br>The page you sent me is too magic: the product page mapping to the BamHI ID needs a lookup to get there.<br><br>But.... <br><br>
Their rebase page has all the info on it. The link works to that database.<br><br>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. <br><br>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.
<br><br>Let me know where you want it to go. <br><br>B.<br><br><br><div class="gmail_quote">On Nov 1, 2007 5:58 PM, Drew Endy <<a href="mailto:endy@mit.edu">endy@mit.edu</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Bill,<br><br>Your email and work are terrific, at many levels.<br><br>It is fun to imagine having a magic link for restriction enzymes<br>(also at many levels).<br><br>Perhaps, just to demo something we could try something for New
<br>England Biolabs. "NEB BamHI" would link to: <a href="http://www.neb.com/" target="_blank">http://www.neb.com/</a><br>nebecomm/products/productR0136.asp<br><br>I think that this would be a pretty interesting experiment for us.
<br>First, the NEB website has the best information on their restriction<br>enzymes (they are a special company). Second, on longer time<br>scales, maybe NEB would start to appreciate OWW for directing traffic<br>in their general direction. This last statement implies a lot, and I
<br>don't mean to skip over any conversations about how OWW works and<br>what our values are, but I still think that this idea is sufficiently<br>interesting and important that we should try a pilot experiment, if<br>
we can afford it.<br><br>All best,<br><font color="#888888">Drew<br></font><div><div></div><div class="Wj3C7c"><br><br><br> On 11/1/07 2:35 PM, "Bill Flanagan" <<a href="mailto:wjf42@MIT.EDU">wjf42@MIT.EDU</a>
> wrote:<br>><br>>> I'd like to thank Steve Koch for both the way he helped pull<br>>> together last month's Lab Workbook Brainstorming Session and his<br>>> continued assistance in working all of you to come up with what's
<br>>> turning into an exciting project.<br>>><br>>> We're now starting to implement features coming out of the Working<br>>> Group. We hope to have a follow-up session after we finish with<br>
>> next weeks OWW Board and Steering Committee meetings. Steve has<br>>> already indicated that he'll be moderating the next session as well.<br>>><br>>> Two particular features are starting to move forward that I want
<br>>> to briefly mention. I welcome your comments on them as well. One<br>>> is going to be introduced into OpenWetWare over the next few days.<br>>> The feature is an extension of a feature in MediaWiki called
<br>>> "Magic Links". Any time you type the term 'PMID' and put a number<br>>> next to it, MediaWiki creates a usable link to PubMed when you<br>>> save the document. With no special linking characters, these
<br>>> references allow a reader of the page to go to PubMed via NCBI and<br>>> view the associated document. This also works with Internet RFC<br>>> document and, to a lesser degree, with ISBN book numbers.
<br>>> Thompson and Francois St. Pierre, PhD candidates in the lab my<br>>> wife now calls my home, told me about this feature. I had been<br>>> working on MediaWiki for quite a while and never ran across it
<br>>> before.<br>>><br>>> We've now extended the original magic link concept to include<br>>> GenBank accession numbers, BioBrick parts, and references to<br>>> Cornell's ArXiv (Archive X). Julius Luck's Atom-based network
<br>>> interface to that system is how we implemented it.<br>>><br>>> In the case of GenBank accession numbers, we came up with an<br>>> interesting way to allow the data to be viewed. We're generalizing
<br>>> it to the other network document repositories as time permits.<br>>> I'll keep you all up to date as we move forward.<br>>><br>>> When you hover your mouse over an accession number that has been
<br>>> linked, a small dialog box pops up. It initially will contain the<br>>> title of the GenBank record for the part. These links will only be<br>>> present if a valid part number is entered. In the dialog box, a
<br>>> download tag is present. If you click it, OpenWetWare will<br>>> download the sequence from NCBI and stream it down to your<br>>> desktop. If you have an application that knows about the '.gb'
<br>>> tag, the sequence and associated header information will be<br>>> directly loaded into your application. Vector NTI and CLC Free<br>>> Workbench 4 are a few apps we've tested with. Once the sequence is
<br>>> downloaded the first time, it stays in our OWW cache and will zoom<br>>> down to you or anyone else requesting it for anytime forward. Tom<br>>> Knight asked for an extension to this that I'm just finishing up.
<br>>> If you enter a term such as, "GENBAN U49845:12-1024", only base<br>>> pairs 12-1024 will be downloaded.<br>>><br>>> The other feature, originally suggested by Tm Knight, was a way to
<br>>> print labels from OWW. This has turned into a very fun feature.<br>>> I've created a new tag, "<label>". The Label tag will permit you<br>>> to enter a label into your lab notebook (or any OWW document).
<br>>> When you save the page, an image of the label will be visible. If<br>>> you click on the associated 'print' icon, the label will pop up<br>>> in a separate window along with a print dialog box. If you have a
<br>>> label printer available to you, you can print the label to it. I'm<br>>> creating a new section called "OpenHardWare" to allow people to<br>>> share their experiences about which printers work best. I'm
<br>>> putting my money ($29.95! on ebay!) on a Brother USB label printer<br>>> as our test platform.<br>>><br>>> The label will feature a barcode. Steve made a great suggestion to<br>>> tie the use of the labels back to OpenWetWare. The barcode will be
<br>>> a unique pointer, across all of OpenWetWare, that will associate<br>>> the label with the page it is printed from. We want to create<br>>> templates for a few different kinds of labels used in the lab. We
<br>>> will have a way for anyone to create and contribute templates for<br>>> specific sizes and layouts. Any petri dish in a lab using<br>>> OpenWetWare for creating these labels will find, if available, the
<br>>> exact context of where the page originally came from. Those stacks<br>>> of plates you just found in the corner? Scan first, blame for<br>>> taking up too much bench space later.<br>>><br>>> I'm experimenting with a $10 barcode scanner, the CueCat, as a
<br>>> "necessary and sufficient" scanner for this activity. We also have<br>>> access to more sensitive and expensive bar code readers but out<br>>> goal is to work with the absolutely most affordable barcode
<br>>> scanner we can find.<br>>><br>>> If anyone has suggestions as to what else we can do with this<br>>> information, let me know. We'll be rolling out a very "beta"<br>>> version over the next few weeks. More features will follow as soon
<br>>> as we make them work.<br>>><br>>> We have several more tricks up our sleeves that I'm flushing out.<br>>> More will follow.<br>>><br>>> When MediaWiki ceases to be useful for doing what we need to do,
<br>>> we are extending it. The built-in archiving is a feature we<br>>> desperately want to keep in the middle of everything we do. But<br>>> how we create the documents and what happens when we read them may
<br>>> vary from the standard product. Lab scientists have different<br>>> requirements that Wikipedia readers. We want to make sure those<br>>> needs are accommodated without breaking OWW's essential 'Wikiness'.
<br>>><br>>> As I said, please let me know what you all think.<br>>><br>>><br>>> _______________________________________________<br>>> OpenWetWare Steering Committee Mailing List<br>>>
<a href="mailto:sc@openwetware.org">sc@openwetware.org</a><br>>> <a href="http://mailman.mit.edu/mailman/listinfo/oww-sc" target="_blank">http://mailman.mit.edu/mailman/listinfo/oww-sc</a><br>><br>> _______________________________________________
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</a><br><br></div></div></blockquote></div><br>