It's plausible to imagine implementing a web-based barcode scanner in
flash or java. Someone has actually already done so here and released
the source under CCA-2.5 license: <a href="http://en.barcodepedia.com/download" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://en.barcodepedia.com/download</a><br><br>I'm not sure how well it works or if it can read semacodes, but I bet we could use it as a starting point.<br><br>Mac<br><br><div><span class="gmail_quote">On 11/1/07, <b class="gmail_sendername">
Bill F</b> <<a href="mailto:bill.altmail@gmail.com">bill.altmail@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
1. very small, for narrow screw top bottles: 1.3"<br>2. small, for eppendorfs, cryotubes and other small containers: 1.5"<br>3. large, for everything else, mostly media bottles and flat surfaces; 2.5" Size on this one is not so critical.
<span class="q"><br><br>I think we want some standardization of these sizes. <br></span>>> Excellent starting point.<br>>> We will have a standard set of labels each defined on an OWW page. <br>>> These won't be MediaWiki template pages, just print templates that can be added by anyone.
<span class="q"><br><br>The small and very small labels can't really be larger or much smaller. <br>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.
<br>I suppose a small vertical bar code would be best, or maybe one of the square styles.<br></span>>> I'm currently working with a standard rectangular barcode printing library. <br>>> The smaller the barcode, the higher the scanner resolution required.
<br>>> The square barcodes look interesting. Austin pointed to one system. I'm looking into it. <span class="q"><br><br>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.
<br></span>>> I'm still looking for info re: the Thermo system. <br>>> I signed up with Addgene to look at their interface. <br>>> Once Jason OK's me (I affiliated with Endy Lab's existing entry) I'll have full access.
<span class="q"><br><br>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.<br></span>>> If the Evological Mac package for using the iSight camera pans out, this is a good place for it.
<br>>> The evological app is fully scriptable. <br>>> Using a barcode reader on any computer (mac or pc) works the same way.<br>>> The output from either is standard keyboard codes/ ascii alphanumeric characters.
<br>>> We can provide a pretty simple network interface to accept the barcode number and <br>>> a related set of fields from the desktop script and post it to a wiki page.<div><span class="e" id="q_115fe1805b3d2ad5_9">
<br> <br><br><div class="gmail_quote">
On Nov 1, 2007 6:38 PM, Tom Knight <<a href="mailto:tk@csail.mit.edu" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">tk@csail.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;">
These are terrific features. Just a note on the labels idea. I have<br>three standard labels I make. Each has my initials and the<br>(automatically created) date in the lower left and right corners and a<br>spot for the main centered text. All use the 3/4" wide tape, and are
<br>of these lengths:<br>very small, for narrow screw top bottles: 1.3"<br>small, for eppendorfs, cryotubes and other small containers: 1.5"<br>large, for everything else, mostly media bottles and flat surfaces;
<br>2.5" Size on this one is not so critical.<br><br>I think we want some standardization of these sizes. The small and<br>very small labels can't really be larger or much smaller. You want<br>them to fit all the way around the container so that they stick to
<br>themselves, but not overlap so much that the text is obscured.<br>I suppose a small vertical bar code would be best, or maybe one of the<br>square styles.<br><br>There are a lot of systems out there which use pre-coded barcodes, such
<br>as the Thermo system used at Addgene. We need to support these as<br>well. There should be a way of showing a bar code to the reader and<br>having that barcode be remembered and associated with that lab notebook<br>
page.<br><div><div></div><div><br><br><br>On Nov 1, 2007, at 5:35 PM, Bill Flanagan wrote:<br><br>> I'd like to thank Steve Koch for both the way he helped pull together<br>> last month's Lab Workbook Brainstorming Session and his continued
<br>> assistance in working all of you to come up with what's turning into<br>> 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 next
<br>> weeks OWW Board and Steering Committee meetings. Steve has already<br>> indicated that he'll be moderating the next session as well.<br>><br>> Two particular features are starting to move forward that I want to
<br>> briefly mention. I welcome your comments on them as well. One is<br>> going to be introduced into OpenWetWare over the next few days. The<br>> feature is an extension of a feature in MediaWiki called "Magic
<br>> Links". Any time you type the term 'PMID' and put a number next to it,<br>> MediaWiki creates a usable link to PubMed when you save the document.<br>> With no special linking characters, these references allow a reader of
<br>> the page to go to PubMed via NCBI and view the associated document.<br>> This also works with Internet RFC document and, to a lesser degree,<br>> with ISBN book numbers. Thompson and Francois St. Pierre, PhD
<br>> candidates in the lab my wife now calls my home, told me about this<br>> feature. I had been working on MediaWiki for quite a while and never<br>> ran across it before.<br>><br>> We've now extended the original magic link concept to include GenBank
<br>> accession numbers, BioBrick parts, and references to Cornell's ArXiv<br>> (Archive X). Julius Luck's Atom-based network interface to that system<br>> 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 it<br>> to the other network document repositories as time permits. I'll keep<br>> 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 download<br>> the sequence from NCBI and stream it down to your desktop. If you have
<br>> an application that knows about the '.gb' tag, the sequence and<br>> associated header information will be directly loaded into your<br>> application. Vector NTI and CLC Free Workbench 4 are a few apps we've
<br>> tested with. Once the sequence is downloaded the first time, it stays<br>> in our OWW cache and will zoom down to you or anyone else requesting<br>> it for anytime forward. Tom Knight asked for an extension to this that
<br>> I'm just finishing up. If you enter a term such as, "GENBAN<br>> U49845:12-1024", only base 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. I've<br>> created a new tag, "<label>". The Label tag will permit you to enter a<br>> label into your lab notebook (or any OWW document). When you save the
<br>> page, an image of the label will be visible. If you click on the<br>> associated 'print' icon, the label will pop up in a separate window<br>> along with a print dialog box. If you have a label printer available
<br>> to you, you can print the label to it. I'm creating a new section<br>> called "OpenHardWare" to allow people to share their experiences about<br>> which printers work best. I'm putting my money ($29.95! on ebay!) on a
<br>> Brother USB label printer as our test platform.<br>><br>> The label will feature a barcode. Steve made a great suggestion to tie<br>> the use of the labels back to OpenWetWare. The barcode will be a<br>
> unique pointer, across all of OpenWetWare, that will associate the
<br>> label with the page it is printed from. We want to create templates<br>> for a few different kinds of labels used in the lab. We will have a<br>> way for anyone to create and contribute templates for specific sizes
<br>> and layouts. Any petri dish in a lab using OpenWetWare for creating<br>> these labels will find, if available, the exact context of where the<br>> page originally came from. Those stacks of plates you just found in
<br>> the corner? Scan first, blame for taking up too much bench space<br>> 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 goal<br>> is to work with the absolutely most affordable barcode scanner we can<br>> 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" version<br>> over the next few weeks. More features will follow as soon as we make<br>> them work.<br>><br>> We have several more tricks up our sleeves that I'm flushing out. More
<br>> will follow.<br>><br>> When MediaWiki ceases to be useful for doing what we need to do, we<br>> are extending it. The built-in archiving is a feature we desperately<br>> want to keep in the middle of everything we do. But how we create the
<br>> documents and what happens when we read them may vary from the<br>> standard product. Lab scientists have different requirements that<br>> Wikipedia readers. We want to make sure those needs are accommodated
<br>> without breaking OWW's essential 'Wikiness'.<br>><br>> As I said, please let me know what you all think.<br>><br></div></div><div><div></div><div>> _______________________________________________
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