From jasonk at MIT.EDU  Thu Nov  1 09:21:14 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 1 Nov 2007 09:21:14 -0400
Subject: [OWW-SC] SC Meeting next TH (11/8) at Noon
Message-ID: <7c085c480711010621i71449047l2cf043f3bd296db8@mail.gmail.com>

hey SC,

I didn't realize today was 1st TH of the month, so SC meeting will be
next TH (11/8) at Noon EST.  Sorry about that!

Chairs fill in your reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_November_2007

Please add items to the agenda:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting

Or take a look at action list from last month for left over to-do items.
http://openwetware.org/wiki/OpenWetWare:Steering_committee_actions

Number is 617-324-7520, and austin can send out details for people using sip.

Thanks!
jason


From jasonk at MIT.EDU  Thu Nov  1 09:28:22 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 1 Nov 2007 09:28:22 -0400
Subject: [OWW-SC] Nature MSB changes policy to allow derivative works
Message-ID: <7c085c480711010628v5d477f78j854bb5f08f8d18c4@mail.gmail.com>

In part due to our request to make a derivative of one of their reviews:
http://blog-msb.embo.org/blog/2007/11/open_access_derivs_or_no_deriv_2.html

hopefully other journals will follow suit!
jason


From endy at MIT.EDU  Thu Nov  1 11:12:30 2007
From: endy at MIT.EDU (Drew Endy)
Date: Thu, 1 Nov 2007 11:12:30 -0400
Subject: [OWW-SC] Nature MSB changes policy to allow derivative works
In-Reply-To: <7c085c480711010628v5d477f78j854bb5f08f8d18c4@mail.gmail.com>
References: <7c085c480711010628v5d477f78j854bb5f08f8d18c4@mail.gmail.com>
Message-ID: <14CF712E-C3B7-413F-A60F-1FECA162F1EE@mit.edu>

This should be a news items on the OWW front page.

On Nov 1, 2007, at 9:28 AM, Jason Kelly wrote:

> In part due to our request to make a derivative of one of their  
> reviews:
> http://blog-msb.embo.org/blog/2007/11/ 
> open_access_derivs_or_no_deriv_2.html
>
> hopefully other journals will follow suit!
> jason
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc



From macowell at gmail.com  Thu Nov  1 14:03:08 2007
From: macowell at gmail.com (Mackenzie Cowell)
Date: Thu, 1 Nov 2007 14:03:08 -0400
Subject: [OWW-SC] Fwd: Talk on Open Science and Scientific Publishing - MIT
	- Nov. 13
In-Reply-To: <472A12A1.3050608@creativecommons.org>
References: <472A12A1.3050608@creativecommons.org>
Message-ID: <54746a3f0711011103h15b59607j91fe6b4d3fad31f2@mail.gmail.com>

Just in case you didn't get it the first time around... see you there.

Mac

---------- Forwarded message ----------
From: Kaitlin Thaney <kaitlin at creativecommons.org>
Date: Nov 1, 2007 1:53 PM
Subject: Talk on Open Science and Scientific Publishing - MIT - Nov. 13
To: undisclosed-recipients

For those in the Boston / Cambridge area:

Join us for a discussion on Open Access and the progress of science,
co-sponsored by CSAIL, MIT Libraries and Science Commons.

WHAT: "Open Science  &  Scientific Publishing"

WHEN: Tuesday, November 13; 3:15 p.m. - 5 p.m.

WHERE: Kiva (Room 479); Stata Center at MIT; 32 Vassar Street,
Cambridge, MA.

With presentations by:

John Wilbanks (Vice President of Science Commons)
Anna Gold (Head Librarian, Engineering and Science Libraries, MIT)

Moderated by Professor Hal Abelson (Computer Science and Articifical
Intelligence Laboratory, MIT)

*This event is open to the public. Seating is first come, first serve.
Refreshments will be served.

--
................
Kaitlin Thaney
Project Manager
Science Commons
http://sciencecommons.org
kaitlin at creativecommons.org
................



-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From macowell at gmail.com  Thu Nov  1 14:38:57 2007
From: macowell at gmail.com (Mackenzie Cowell)
Date: Thu, 1 Nov 2007 14:38:57 -0400
Subject: [OWW-SC] Fwd: Fwd: Nature MSB changes policy to allow derivative
	works
In-Reply-To: <472A1817.5050102@creativecommons.org>
References: <7c085c480711010628v5d477f78j854bb5f08f8d18c4@mail.gmail.com>
	<14CF712E-C3B7-413F-A60F-1FECA162F1EE@mit.edu>
	<54746a3f0711010945k7ae24da1jc37c00c2584609bb@mail.gmail.com>
	<472A1817.5050102@creativecommons.org>
Message-ID: <54746a3f0711011138t1a7f52a0s217f236dacbbe8c9@mail.gmail.com>

Science Commons thought MCB's move toward open access was coo, but "not a
true victory for OA [open access]".

mac

---------- Forwarded message ----------
From: Kaitlin Thaney <kaitlin at creativecommons.org>
Date: Nov 1, 2007 2:16 PM
Subject: Re: Fwd: [OWW-SC] Nature MSB changes policy to allow derivative
works
To: Mackenzie Cowell <macowell at gmail.com>

 Thanks for this. It's also been posted on Peter Suber's blog:

http://www.earlham.edu/~peters/fos/2007/11/whether-or-not-to-allow-derivative.html<http://www.earlham.edu/%7Epeters/fos/2007/11/whether-or-not-to-allow-derivative.html>

Though it's a move in the right direction to be talking about CC licenses,
it's not a true victory for OA. I say that because it is not fully in
accordance with the definition of "open access" set out in the Budapest Open
Access Declaration. The only CC license in compliance with the BOAI
definition is the Attribution license. Sharealike, non-derivatives, and
non-commercial provisions apply levels of control, not making the work
entirely OA.

OK, that's my two cents : ) But like I said, a move in the right direction!

Hope all is well,
K

................
Kaitlin Thaney
Project Manager
Science Commons
http://sciencecommons.org
kaitlin at creativecommons.org
................



Mackenzie Cowell wrote:

Off topic but exciting: did you guys here about this?  Tell your comrades!

Mac

---------- Forwarded message ----------
From: Drew Endy < endy at mit.edu>
Date: Nov 1, 2007 11:12 AM
Subject: Re: [OWW-SC] Nature MSB changes policy to allow derivative works
To: Jason Kelly <jasonk at mit.edu>
Cc: oww-sc < sc at openwetware.org>

This should be a news items on the OWW front page.

On Nov 1, 2007, at 9:28 AM, Jason Kelly wrote:

> In part due to our request to make a derivative of one of their
> reviews:
> http://blog-msb.embo.org/blog/2007/11/
> open_access_derivs_or_no_deriv_2.html
>
> hopefully other journals will follow suit!
> jason
> _______________________________________________
> 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


-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062



-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From wjf42 at MIT.EDU  Thu Nov  1 17:35:54 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Thu, 1 Nov 2007 17:35:54 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
Message-ID: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>

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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From hoatlinm at ohsu.edu  Thu Nov  1 17:48:40 2007
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Thu, 01 Nov 2007 14:48:40 -0700
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
 Working Group.
In-Reply-To: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
Message-ID: <C34F97C8.8E4B%hoatlinm@ohsu.edu>

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


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From bill.altmail at gmail.com  Thu Nov  1 17:57:16 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 1 Nov 2007 17:57:16 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <C34F97C8.8E4B%hoatlinm@ohsu.edu>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<C34F97C8.8E4B%hoatlinm@ohsu.edu>
Message-ID: <26428aaa0711011457g3a389f18j302221f7ecaf1397@mail.gmail.com>

Thanks, Maureen.

I have one staring at me and I didn't realize that. Whoa. We need the
hardware section sooner than later.

B.


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
>
>
>
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From endy at MIT.EDU  Thu Nov  1 17:58:14 2007
From: endy at MIT.EDU (Drew Endy)
Date: Thu, 1 Nov 2007 17:58:14 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <C34F97C8.8E4B%hoatlinm@ohsu.edu>
References: <C34F97C8.8E4B%hoatlinm@ohsu.edu>
Message-ID: <BF5D665B-1480-45FD-9AE7-EFF819C3DB3D@mit.edu>

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



From austin at csail.mit.edu  Thu Nov  1 18:12:50 2007
From: austin at csail.mit.edu (Austin Che)
Date: Thu, 01 Nov 2007 18:12:50 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <26428aaa0711011457g3a389f18j302221f7ecaf1397@mail.gmail.com>
	(Bill F.'s message of "Thu, 1 Nov 2007 17:57:16 -0400")
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<C34F97C8.8E4B%hoatlinm@ohsu.edu>
	<26428aaa0711011457g3a389f18j302221f7ecaf1397@mail.gmail.com>
Message-ID: <874pg5wr6l.fsf@nitsua.mit.edu>

    
    Many people probably carry around cameras and portable scanners in
    their pocket without realizing it. Making use of a cell phone
    barcode, e.g.  http://en.wikipedia.org/wiki/Semacode would be
    interesting. And your cell phone almost certainly has some form of
    data connection to the outside world. A network enabled portable
    scanner that most people already have in their pockets. What else
    do you need?

> Thanks, Maureen.
>
> I have one staring at me and I didn't realize that. Whoa. We need the
> hardware section sooner than later.
>
> B.
>
> 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

-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From tk at csail.mit.edu  Thu Nov  1 18:38:03 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Thu, 1 Nov 2007 18:38:03 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
Message-ID: <7b962bbb0198032f64cc8e0f5618530f@csail.mit.edu>

These are terrific features.  Just a note on the labels idea.  I have 
three standard labels I make.  Each has my initials and the 
(automatically created) date in the lower left and right corners and a 
spot for the main centered text.  All use the 3/4" wide tape, and are 
of these lengths:
very small, for narrow screw top bottles: 1.3"
small, for eppendorfs, cryotubes and other small containers: 1.5"
large, for everything else, mostly media bottles and flat surfaces; 
2.5"  Size on this one is not so critical.

I think we want some standardization of these sizes.  The small and 
very small labels can't really be larger or much smaller.  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.
I suppose a small vertical bar code would be best, or maybe one of the 
square styles.

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.  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.



On Nov 1, 2007, at 5:35 PM, Bill Flanagan 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




From bill.altmail at gmail.com  Thu Nov  1 20:45:10 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 1 Nov 2007 20:45:10 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <BF5D665B-1480-45FD-9AE7-EFF819C3DB3D@mit.edu>
References: <C34F97C8.8E4B%hoatlinm@ohsu.edu>
	<BF5D665B-1480-45FD-9AE7-EFF819C3DB3D@mit.edu>
Message-ID: <26428aaa0711011745q216183doc756d17b918306bd@mail.gmail.com>

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
>
>
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From bill.altmail at gmail.com  Thu Nov  1 21:34:28 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 1 Nov 2007 21:34:28 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <C34F97C8.8E4B%hoatlinm@ohsu.edu>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<C34F97C8.8E4B%hoatlinm@ohsu.edu>
Message-ID: <26428aaa0711011834j3fdab256j5ae6f88f22163d37@mail.gmail.com>

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
>
>
>
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From bill.altmail at gmail.com  Thu Nov  1 22:01:47 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 1 Nov 2007 22:01:47 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <7b962bbb0198032f64cc8e0f5618530f@csail.mit.edu>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<7b962bbb0198032f64cc8e0f5618530f@csail.mit.edu>
Message-ID: <26428aaa0711011901i2fe329e6w44c6fcdc65c47b2b@mail.gmail.com>

1. very small, for narrow screw top bottles: 1.3"
2. small, for eppendorfs, cryotubes and other small containers: 1.5"
3. large, for everything else, mostly media bottles and flat surfaces; 2.5"
Size on this one is not so critical.

I think we want some standardization of these sizes.
>> Excellent starting point.
>> We will have a standard set of labels each defined on an OWW page.
>> These won't be MediaWiki template pages, just print templates that can be
added by anyone.

The small and very small labels can't really be larger or much smaller.
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.
I suppose a small vertical bar code would be best, or maybe one of the
square styles.
>> I'm currently working with a standard rectangular barcode printing
library.
>> The smaller the barcode, the higher the scanner resolution required.
>> The square barcodes look interesting. Austin pointed to one system. I'm
looking into it.

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.
>> I'm still looking for info re: the Thermo system.
>> I signed up with Addgene to look at their interface.
>> Once Jason OK's me (I affiliated with Endy Lab's existing entry) I'll
have full access.

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.
>> If the Evological Mac package for using the iSight camera pans out, this
is a good place for it.
>> The evological app is fully scriptable.
>> Using a barcode reader on any computer (mac or pc) works the same way.
>> The output from either is standard keyboard codes/ ascii alphanumeric
characters.
>> We can provide a pretty simple network interface to accept the barcode
number and
>> a related set of fields from the desktop script and post it to a wiki
page.


On Nov 1, 2007 6:38 PM, Tom Knight <tk at csail.mit.edu> wrote:

> These are terrific features.  Just a note on the labels idea.  I have
> three standard labels I make.  Each has my initials and the
> (automatically created) date in the lower left and right corners and a
> spot for the main centered text.  All use the 3/4" wide tape, and are
> of these lengths:
> very small, for narrow screw top bottles: 1.3"
> small, for eppendorfs, cryotubes and other small containers: 1.5"
> large, for everything else, mostly media bottles and flat surfaces;
> 2.5"  Size on this one is not so critical.
>
> I think we want some standardization of these sizes.  The small and
> very small labels can't really be larger or much smaller.  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.
> I suppose a small vertical bar code would be best, or maybe one of the
> square styles.
>
> 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.  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.
>
>
>
> On Nov 1, 2007, at 5:35 PM, Bill Flanagan 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
>
>
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From macowell at gmail.com  Thu Nov  1 22:23:48 2007
From: macowell at gmail.com (Mackenzie Cowell)
Date: Thu, 1 Nov 2007 22:23:48 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <26428aaa0711011901i2fe329e6w44c6fcdc65c47b2b@mail.gmail.com>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<7b962bbb0198032f64cc8e0f5618530f@csail.mit.edu>
	<26428aaa0711011901i2fe329e6w44c6fcdc65c47b2b@mail.gmail.com>
Message-ID: <54746a3f0711011923j181e2427ie278e3298d4c5286@mail.gmail.com>

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: http://en.barcodepedia.com/download

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.

Mac

On 11/1/07, Bill F <bill.altmail at gmail.com> wrote:
>
> 1. very small, for narrow screw top bottles: 1.3"
> 2. small, for eppendorfs, cryotubes and other small containers: 1.5"
> 3. large, for everything else, mostly media bottles and flat surfaces; 2.5"
> Size on this one is not so critical.
>
> I think we want some standardization of these sizes.
> >> Excellent starting point.
> >> We will have a standard set of labels each defined on an OWW page.
> >> These won't be MediaWiki template pages, just print templates that can
> be added by anyone.
>
> The small and very small labels can't really be larger or much smaller.
> 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.
> I suppose a small vertical bar code would be best, or maybe one of the
> square styles.
> >> I'm currently working with a standard rectangular barcode printing
> library.
> >> The smaller the barcode, the higher the scanner resolution required.
> >> The square barcodes look interesting. Austin pointed to one system. I'm
> looking into it.
>
> 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.
> >> I'm still looking for info re: the Thermo system.
> >> I signed up with Addgene to look at their interface.
> >> Once Jason OK's me (I affiliated with Endy Lab's existing entry) I'll
> have full access.
>
> 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.
> >> If the Evological Mac package for using the iSight camera pans out,
> this is a good place for it.
> >> The evological app is fully scriptable.
> >> Using a barcode reader on any computer (mac or pc) works the same way.
> >> The output from either is standard keyboard codes/ ascii alphanumeric
> characters.
> >> We can provide a pretty simple network interface to accept the barcode
> number and
> >> a related set of fields from the desktop script and post it to a wiki
> page.
>
>
> On Nov 1, 2007 6:38 PM, Tom Knight <tk at csail.mit.edu> wrote:
>
> > These are terrific features.  Just a note on the labels idea.  I have
> > three standard labels I make.  Each has my initials and the
> > (automatically created) date in the lower left and right corners and a
> > spot for the main centered text.  All use the 3/4" wide tape, and are
> > of these lengths:
> > very small, for narrow screw top bottles: 1.3"
> > small, for eppendorfs, cryotubes and other small containers: 1.5"
> > large, for everything else, mostly media bottles and flat surfaces;
> > 2.5"  Size on this one is not so critical.
> >
> > I think we want some standardization of these sizes.  The small and
> > very small labels can't really be larger or much smaller.  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.
> > I suppose a small vertical bar code would be best, or maybe one of the
> > square styles.
> >
> > 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.  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.
> >
> >
> >
> > On Nov 1, 2007, at 5:35 PM, Bill Flanagan 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
>
>


-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From tk at csail.mit.edu  Fri Nov  2 08:58:21 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Fri, 2 Nov 2007 08:58:21 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <26428aaa0711011834j3fdab256j5ae6f88f22163d37@mail.gmail.com>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<C34F97C8.8E4B%hoatlinm@ohsu.edu>
	<26428aaa0711011834j3fdab256j5ae6f88f22163d37@mail.gmail.com>
Message-ID: <5078e517744a3c1259271b37a08f4756@csail.mit.edu>

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
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From bill.altmail at gmail.com  Fri Nov  2 12:19:33 2007
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 2 Nov 2007 12:19:33 -0400
Subject: [OWW-SC] More changes coming as part of the OWW Lab Notebook
	Working Group.
In-Reply-To: <5078e517744a3c1259271b37a08f4756@csail.mit.edu>
References: <26428aaa0711011435i436566a1wc93317291a9d1dc@mail.gmail.com>
	<C34F97C8.8E4B%hoatlinm@ohsu.edu>
	<26428aaa0711011834j3fdab256j5ae6f88f22163d37@mail.gmail.com>
	<5078e517744a3c1259271b37a08f4756@csail.mit.edu>
Message-ID: <26428aaa0711020919w25987272n2bde7f761bcfc367@mail.gmail.com>

OK. I can give you a tag immediately to do this.

Example:

<barcode></barcode>

I'll keep it simple. Barcode will not initially give you options. It will
just create a universal unique ID for the OpenWetWare page. That way, we can
use the exact same mechanism for the labels.

Initially, you can place the tag anywhere. We can move it into the skin of
OpenWetWare and provide a 'preference page' option to enable or disable it.
That would output the tag at a known place on all pages.

Since we do have a separate CSS style sheet for printed pages, we can
restrict it to only be output via printer. Otherwise it would be invisible.

I'll put this up this afternoon.

B.


On Nov 2, 2007 8:58 AM, Tom Knight <tk at csail.mit.edu> wrote:

> 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
>
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From wjf42 at MIT.EDU  Mon Nov  5 20:10:53 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Mon, 5 Nov 2007 20:10:53 -0500
Subject: [OWW-SC] OpenWetWare going down for a reboot at 11:30 PM EST this
	Friday (Nov. 9, 2007)
In-Reply-To: <26428aaa0711051708x6713b2fakdec7bea5b0383703@mail.gmail.com>
References: <26428aaa0711051706w7da19846t1cfbb74f8bd30c30@mail.gmail.com>
	<26428aaa0711051708x6713b2fakdec7bea5b0383703@mail.gmail.com>
Message-ID: <26428aaa0711051710y5ffd335x131172ad94516366@mail.gmail.com>

This is a routine upgrade of the server software. It should be no more than
5 minutes.

Please let me know if this conflicts with anything you folks may be aware
of.

Thanks.

Bill Flanagan
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From jasonk at MIT.EDU  Wed Nov  7 15:05:24 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Wed, 7 Nov 2007 15:05:24 -0500
Subject: [OWW-SC] Reminder: SC meeting tomorrow (TH) at Noon EST.
Message-ID: <7c085c480711071205k6194cbf7rae1b618bfb1f48c8@mail.gmail.com>

Please post discussion topics here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting

And update chair reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_November_2007

The number is 617-324-7520 and also join the chat (just in the lounge).

thanks!
jason


From julius at younglucks.com  Thu Nov  8 13:20:29 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Thu, 8 Nov 2007 13:20:29 -0500
Subject: [OWW-SC] Change to Welcome Email Content
Message-ID: <774F37FC-A303-4141-B187-DED30D343795@younglucks.com>

Hi SC,

As discussed at the meeting today, I am proposing to change the  
content of the welcome email to new users to be simpler, and to draw  
them to their automatically created User page, which now has  
introductory material as part of its text.  Please have a look at the  
content below (or at this link http://openwetware.org/wiki/ 
OpenWetWare_talk:Welcome_email), and edit as you see fit.  Once we  
have finalized the content, we will go ahead and implement the changes.

EMAIL CONTENT _START_

Welcome to OpenWetWare!

Your new account has been created with username UMS_NAME. To get you  
started, we have created a User page for you at

http://openwetware.org/wiki/User:UMS_NAME

Your User page contains some basic information about you that you  
gave us in your account application, as well as a mini-tutorial on  
how to use the wiki with links to more detailed information.  We  
encourage you to edit your User page to familiarize yourself with the  
wiki, and to introduce yourself to the OWW community.

If you are interested in finding out more about OpenWetWare itself or  
would like to help out, consider signing up for the discuss AT  
openwetware DOT org mailing list here:
http://mailman.mit.edu/mailman/listinfo/oww-discuss

Thanks again, and we look forward to seeing your edits!

OpenWetWare Admin Team

admin AT openwetware DOT org


_END_

Cheers,

Julius

------------------------------------------------------------------------ 
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------ 
----------------



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From bill.altmail at gmail.com  Thu Nov  8 18:58:33 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 8 Nov 2007 18:58:33 -0500
Subject: [OWW-SC] Change to Welcome Email Content
In-Reply-To: <774F37FC-A303-4141-B187-DED30D343795@younglucks.com>
References: <774F37FC-A303-4141-B187-DED30D343795@younglucks.com>
Message-ID: <26428aaa0711081558v238af3c3v166be9c1101a807b@mail.gmail.com>

I have updated the page as you specified. The changes are effective
immediately.

B.


On Nov 8, 2007 1:20 PM, Julius B. Lucks <julius at younglucks.com> wrote:

> Hi SC,
> As discussed at the meeting today, I am proposing to change the content of
> the welcome email to new users to be simpler, and to draw them to their
> automatically created User page, which now has introductory material as part
> of its text.  Please have a look at the content below (or at this link
> http://openwetware.org/wiki/OpenWetWare_talk:Welcome_email), and edit as
> you see fit.  Once we have finalized the content, we will go ahead and
> implement the changes.
>
> EMAIL CONTENT _START_
>
> Welcome to OpenWetWare!
>
> Your new account has been created with username UMS_NAME. To get you
> started, we have created a User page for you at
>
> http://openwetware.org/wiki/User:UMS_NAME
>
> Your User page contains some basic information about you that you gave us
> in your account application, as well as a mini-tutorial on how to use the
> wiki with links to more detailed information.  We encourage you to edit your
> User page to familiarize yourself with the wiki, and to introduce yourself
> to the OWW community.
>
> If you are interested in finding out more about OpenWetWare itself or
> would like to help out, consider signing up for the discuss AT openwetware
> DOT org mailing list here:
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
> Thanks again, and we look forward to seeing your edits!
>
> OpenWetWare Admin Team
>
> admin AT openwetware DOT org
>
>
> _END_
>
> Cheers,
>
> Julius
>
>
> ---------------------------------------------------------------------------------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>
> ----------------------------------------------------------------------------------------
>
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
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From wjf42 at MIT.EDU  Sat Nov 10 16:23:12 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Sat, 10 Nov 2007 16:23:12 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
Message-ID: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>

We've added a feature to help displaying special characters and character
string to OpenWetWare documents. If you've used this feature in Wikipedia,
it now works exactly the same in OpenWetWare.

When you edit any page or choose to download a new file, OpenWetWare will
now display a list of characters and tags at the base of the page. By
clicking on any of these characters or tags, the ascii code will be inserted
into the page being edited at the current cursor location.

The range of special sequences includes the following:

MediaWiki Markup
Greek
Cyrillic
Other special characters.

All of the current special tags supported by OpenWetWare will be included in
the list.

If there are special vocabularies or character sets anyone wants add to this
list, please consult with me. We can add them quickly.

Thanks.

Bill Flanagan
OpenWetWare.org
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From tk at csail.mit.edu  Sat Nov 10 17:01:59 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Sat, 10 Nov 2007 17:01:59 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
Message-ID: <D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>

On our pages, the micro (mu) and degree sign are so common that I  
think they deserve special attention.  I don't have a clear idea of  
what to do, but this feature (for me) does not help. It's easier to  
type &mu; and &deg;


On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:

> We've added a feature to help displaying special characters and  
> character string to OpenWetWare documents. If you've used this  
> feature in Wikipedia, it now works exactly the same in OpenWetWare.
>
> When you edit any page or choose to download a new file,  
> OpenWetWare will now display a list of characters and tags at the  
> base of the page. By clicking on any of these characters or tags,  
> the ascii code will be inserted into the page being edited at the  
> current cursor location.
>
> The range of special sequences includes the following:
>
> MediaWiki Markup
> Greek
> Cyrillic
> Other special characters.
>
> All of the current special tags supported by OpenWetWare will be  
> included in the list.
>
> If there are special vocabularies or character sets anyone wants  
> add to this list, please consult with me. We can add them quickly.
>
> Thanks.
>
> Bill Flanagan
> OpenWetWare.org
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc



From bill.altmail at gmail.com  Sat Nov 10 19:59:44 2007
From: bill.altmail at gmail.com (Bill F)
Date: Sat, 10 Nov 2007 19:59:44 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
Message-ID: <26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>

Entering the HTML tag for those characters works. The character tags for
them are as follows:
*
    Mu: &micro;
    Degree: &deg;*

This is a little better than the use of the table at the bottom of the form.


An alternative that isn't any shorter than the above expression would be by
using an extension I modified:

    *{{deg:}} or {{mu:}}
*
I've enabled this via an extension in beta. It's pretty clumsy. Using this
method, we can add any tags of interest. But it's pretty ugly.

The curly braces tell the parser this is a parser extension, while the ":"
is present to allow arguments to be appended.

It's possible to make this more compact if needed, but this is what's
immediately possible,

We can directly augment the parser if needed if you need a more compact way
to label either of them.

If anyone else has suggestions, let me know.


On Nov 10, 2007 5:01 PM, Tom Knight <tk at csail.mit.edu> wrote:

> On our pages, the micro (mu) and degree sign are so common that I
> think they deserve special attention.  I don't have a clear idea of
> what to do, but this feature (for me) does not help. It's easier to
> type &mu; and &deg;
>
>
> On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
>
> > We've added a feature to help displaying special characters and
> > character string to OpenWetWare documents. If you've used this
> > feature in Wikipedia, it now works exactly the same in OpenWetWare.
> >
> > When you edit any page or choose to download a new file,
> > OpenWetWare will now display a list of characters and tags at the
> > base of the page. By clicking on any of these characters or tags,
> > the ascii code will be inserted into the page being edited at the
> > current cursor location.
> >
> > The range of special sequences includes the following:
> >
> > MediaWiki Markup
> > Greek
> > Cyrillic
> > Other special characters.
> >
> > All of the current special tags supported by OpenWetWare will be
> > included in the list.
> >
> > If there are special vocabularies or character sets anyone wants
> > add to this list, please consult with me. We can add them quickly.
> >
> > Thanks.
> >
> > Bill Flanagan
> > OpenWetWare.org
> >
> >
> >
> > _______________________________________________
> > 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
>
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From bill.altmail at gmail.com  Mon Nov 12 15:01:03 2007
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 12 Nov 2007 15:01:03 -0500
Subject: [OWW-SC] New interwiki links (ecoliwiki and mediawiki)
Message-ID: <26428aaa0711121201w234cd656ycb34a2923aa7cda6@mail.gmail.com>

I've added both ecoliwiki and mediawiki to the list of interwiki links we
have in our database.

For those not familiar with interwiki links, these are tags that can be used
in regular OWW links to allow sharing of content in external wikis.


For instance, using a link without a wiki-style link to the ecoliwiki
website, the following would be the format to link to their 'lacZ' page:

       [http://ecoliwiki.net/colipedia/index.php/lacZ]

Using an interwiki link, the link would look like this:

       [[ecoliwiki:lacZ]]

If you have other wikis you would like to have included in the table, please
let me know.

Thanks.

Bill Flanagan
-------------- next part --------------
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From wjf42 at MIT.EDU  Mon Nov 12 15:44:37 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Mon, 12 Nov 2007 15:44:37 -0500
Subject: [OWW-SC] New OWW interwiki link list page/extension added
Message-ID: <26428aaa0711121244m4fb23d6ahf8e96a6f81b7245e@mail.gmail.com>

There's a list of all of the Interwiki links provided via an extension
I just added to OpenWetWare.

Check the following page for a complete list of all of the Interwiki
links currently supported via OpenWetWare:

                  http://openwetware.org/wiki/Special:Interwiki

This page can be edited by anyone with Sysadmin or above access. The
page allows for creation and deletion of Interwiki links in addition
to viewing the list of all available links.


From rshetty at MIT.EDU  Mon Nov 12 20:10:02 2007
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Mon, 12 Nov 2007 20:10:02 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
Message-ID: <6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>

Bill and I've modified the set of characters available at the bottom further.

We've stripped out many of the symbols and have added some that are
particularly relevant to biological research like those for
concentration, volume and temperature.  (This is in keeping with what
Tom was suggesting.)

Check out any edit page or modify the list at
http://openwetware.org/wiki/MediaWiki:Edittools
(Thanks Bill!)

Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools

-Reshma

On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
> Entering the HTML tag for those characters works. The character tags for
> them are as follows:
>
>     Mu: &micro;
>     Degree: &deg;
>
> This is a little better than the use of the table at the bottom of the form.
>
> An alternative that isn't any shorter than the above expression would be by
> using an extension I modified:
>
>     {{deg:}} or {{mu:}}
>
> I've enabled this via an extension in beta. It's pretty clumsy. Using this
> method, we can add any tags of interest. But it's pretty ugly.
>
> The curly braces tell the parser this is a parser extension, while the ":"
> is present to allow arguments to be appended.
>
> It's possible to make this more compact if needed, but this is what's
> immediately possible,
>
> We can directly augment the parser if needed if you need a more compact way
> to label either of them.
>
> If anyone else has suggestions, let me know.
>
>
>
>
> On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
> > On our pages, the micro (mu) and degree sign are so common that I
> > think they deserve special attention.  I don't have a clear idea of
> > what to do, but this feature (for me) does not help. It's easier to
> > type &mu; and &deg;
> >
> >
> >
> >
> >
> > On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
> >
> > > We've added a feature to help displaying special characters and
> > > character string to OpenWetWare documents. If you've used this
> > > feature in Wikipedia, it now works exactly the same in OpenWetWare.
> > >
> > > When you edit any page or choose to download a new file,
> > > OpenWetWare will now display a list of characters and tags at the
> > > base of the page. By clicking on any of these characters or tags,
> > > the ascii code will be inserted into the page being edited at the
> > > current cursor location.
> > >
> > > The range of special sequences includes the following:
> > >
> > > MediaWiki Markup
> > > Greek
> > > Cyrillic
> > > Other special characters.
> > >
> > > All of the current special tags supported by OpenWetWare will be
> > > included in the list.
> > >
> > > If there are special vocabularies or character sets anyone wants
> > > add to this list, please consult with me. We can add them quickly.
> > >
> > > Thanks.
> > >
> > > Bill Flanagan
> > > OpenWetWare.org
> > >
> > >
> > >
> > > _______________________________________________
> > > 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
> >
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>


From tk at csail.mit.edu  Tue Nov 13 00:01:47 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Tue, 13 Nov 2007 00:01:47 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
Message-ID: <90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>

I added some comments.  Has anyone else noticed that the way to get  
to a talk page is to click on the "discussion" link at the top of the  
page?  I find this rather unnecessarily confusing.  The name of one  
or the other should be changed.


On Nov 12, 2007, at 8:10 PM, Reshma Shetty wrote:

> Bill and I've modified the set of characters available at the  
> bottom further.
>
> We've stripped out many of the symbols and have added some that are
> particularly relevant to biological research like those for
> concentration, volume and temperature.  (This is in keeping with what
> Tom was suggesting.)
>
> Check out any edit page or modify the list at
> http://openwetware.org/wiki/MediaWiki:Edittools
> (Thanks Bill!)
>
> Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools
>
> -Reshma
>
> On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
>> Entering the HTML tag for those characters works. The character  
>> tags for
>> them are as follows:
>>
>>     Mu: &micro;
>>     Degree: &deg;
>>
>> This is a little better than the use of the table at the bottom of  
>> the form.
>>
>> An alternative that isn't any shorter than the above expression  
>> would be by
>> using an extension I modified:
>>
>>     {{deg:}} or {{mu:}}
>>
>> I've enabled this via an extension in beta. It's pretty clumsy.  
>> Using this
>> method, we can add any tags of interest. But it's pretty ugly.
>>
>> The curly braces tell the parser this is a parser extension, while  
>> the ":"
>> is present to allow arguments to be appended.
>>
>> It's possible to make this more compact if needed, but this is what's
>> immediately possible,
>>
>> We can directly augment the parser if needed if you need a more  
>> compact way
>> to label either of them.
>>
>> If anyone else has suggestions, let me know.
>>
>>
>>
>>
>> On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
>>> On our pages, the micro (mu) and degree sign are so common that I
>>> think they deserve special attention.  I don't have a clear idea of
>>> what to do, but this feature (for me) does not help. It's easier to
>>> type &mu; and &deg;
>>>
>>>
>>>
>>>
>>>
>>> On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
>>>
>>>> We've added a feature to help displaying special characters and
>>>> character string to OpenWetWare documents. If you've used this
>>>> feature in Wikipedia, it now works exactly the same in OpenWetWare.
>>>>
>>>> When you edit any page or choose to download a new file,
>>>> OpenWetWare will now display a list of characters and tags at the
>>>> base of the page. By clicking on any of these characters or tags,
>>>> the ascii code will be inserted into the page being edited at the
>>>> current cursor location.
>>>>
>>>> The range of special sequences includes the following:
>>>>
>>>> MediaWiki Markup
>>>> Greek
>>>> Cyrillic
>>>> Other special characters.
>>>>
>>>> All of the current special tags supported by OpenWetWare will be
>>>> included in the list.
>>>>
>>>> If there are special vocabularies or character sets anyone wants
>>>> add to this list, please consult with me. We can add them quickly.
>>>>
>>>> Thanks.
>>>>
>>>> Bill Flanagan
>>>> OpenWetWare.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>>



From sjkoch at unm.edu  Tue Nov 13 00:19:53 2007
From: sjkoch at unm.edu (Steven J. Koch)
Date: Mon, 12 Nov 2007 22:19:53 -0700
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com><D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu><26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com><6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>
Message-ID: <001801c825b4$d2c5ab90$785102b0$@edu>

I remember that being confusing to me when I signed up on OWW earlier this
year.  I was a newbie to wikis at the time, but I think OWW will be dealing
with newbies for a long time, so it is important to consider.  A downside of
changing the name is that newbies may have edited Wikipedia first (which I
think also has the confusing talk/discussion naming).  The fact that OWW was
"the same" as Wikipedia was a big plus at the beginning (and also now).

A related confusion is that on OWW it's often not clear whether to put edits
on the talk or the main article page.  In Wikipedia, it's usually more clear
given that most of the pages are encyclopedia articles.  Whereas on OWW it
seems like the main point of an article is often a discussion in the first
place (such as brainstorming ideas).  Or, in the case of grading, I don't
like to use the Talk: page, because I have a bunch of little comments, so I
use a little hack template that's like adding comment bubbles in a PDF or
Word.  (See this for an example:
http://openwetware.org/wiki/Physics307L:People/Knockel/formal).  I think in
my entire Physics307L class, we haven't used the Talk: page ever.

OK, not sure if I have a productive suggestion buried in those comments, but
I do agree with TK's post and think it may be a real barrier to edits for
new people.

--S

-----Original Message-----
From: oww-sc-bounces at mit.edu [mailto:oww-sc-bounces at mit.edu] On Behalf Of
Tom Knight
Sent: Monday, November 12, 2007 10:02 PM
To: Reshma Shetty
Cc: Steering Committee
Subject: Re: [OWW-SC] EditTools helper enabled (Greek characters, etc).

I added some comments.  Has anyone else noticed that the way to get  
to a talk page is to click on the "discussion" link at the top of the  
page?  I find this rather unnecessarily confusing.  The name of one  
or the other should be changed.


On Nov 12, 2007, at 8:10 PM, Reshma Shetty wrote:

> Bill and I've modified the set of characters available at the  
> bottom further.
>
> We've stripped out many of the symbols and have added some that are
> particularly relevant to biological research like those for
> concentration, volume and temperature.  (This is in keeping with what
> Tom was suggesting.)
>
> Check out any edit page or modify the list at
> http://openwetware.org/wiki/MediaWiki:Edittools
> (Thanks Bill!)
>
> Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools
>
> -Reshma
>
> On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
>> Entering the HTML tag for those characters works. The character  
>> tags for
>> them are as follows:
>>
>>     Mu: &micro;
>>     Degree: &deg;
>>
>> This is a little better than the use of the table at the bottom of  
>> the form.
>>
>> An alternative that isn't any shorter than the above expression  
>> would be by
>> using an extension I modified:
>>
>>     {{deg:}} or {{mu:}}
>>
>> I've enabled this via an extension in beta. It's pretty clumsy.  
>> Using this
>> method, we can add any tags of interest. But it's pretty ugly.
>>
>> The curly braces tell the parser this is a parser extension, while  
>> the ":"
>> is present to allow arguments to be appended.
>>
>> It's possible to make this more compact if needed, but this is what's
>> immediately possible,
>>
>> We can directly augment the parser if needed if you need a more  
>> compact way
>> to label either of them.
>>
>> If anyone else has suggestions, let me know.
>>
>>
>>
>>
>> On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
>>> On our pages, the micro (mu) and degree sign are so common that I
>>> think they deserve special attention.  I don't have a clear idea of
>>> what to do, but this feature (for me) does not help. It's easier to
>>> type &mu; and &deg;
>>>
>>>
>>>
>>>
>>>
>>> On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
>>>
>>>> We've added a feature to help displaying special characters and
>>>> character string to OpenWetWare documents. If you've used this
>>>> feature in Wikipedia, it now works exactly the same in OpenWetWare.
>>>>
>>>> When you edit any page or choose to download a new file,
>>>> OpenWetWare will now display a list of characters and tags at the
>>>> base of the page. By clicking on any of these characters or tags,
>>>> the ascii code will be inserted into the page being edited at the
>>>> current cursor location.
>>>>
>>>> The range of special sequences includes the following:
>>>>
>>>> MediaWiki Markup
>>>> Greek
>>>> Cyrillic
>>>> Other special characters.
>>>>
>>>> All of the current special tags supported by OpenWetWare will be
>>>> included in the list.
>>>>
>>>> If there are special vocabularies or character sets anyone wants
>>>> add to this list, please consult with me. We can add them quickly.
>>>>
>>>> Thanks.
>>>>
>>>> Bill Flanagan
>>>> OpenWetWare.org
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>> _______________________________________________
>> 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



From bill.altmail at gmail.com  Tue Nov 13 00:40:26 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 13 Nov 2007 00:40:26 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>
Message-ID: <26428aaa0711122140n6d6433c6ubae572504b20912c@mail.gmail.com>

I changed the tabs to use 'talk' rather than discussion.

I never liked it either. But the standard from Wikipedia has been to
call 'talk' 'discussion'. If we're not concerned with that, there's no
harm making things more consistent.

These references can be changed back if there's a problem.

References to 'discussion' within page text still may need to manually
changed. But the tabs  now say 'talk'.

Let me know what ou all think of this.





On Nov 13, 2007 12:01 AM, Tom Knight <tk at csail.mit.edu> wrote:
> I added some comments.  Has anyone else noticed that the way to get
> to a talk page is to click on the "discussion" link at the top of the
> page?  I find this rather unnecessarily confusing.  The name of one
> or the other should be changed.
>
>
>
> On Nov 12, 2007, at 8:10 PM, Reshma Shetty wrote:
>
> > Bill and I've modified the set of characters available at the
> > bottom further.
> >
> > We've stripped out many of the symbols and have added some that are
> > particularly relevant to biological research like those for
> > concentration, volume and temperature.  (This is in keeping with what
> > Tom was suggesting.)
> >
> > Check out any edit page or modify the list at
> > http://openwetware.org/wiki/MediaWiki:Edittools
> > (Thanks Bill!)
> >
> > Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools
> >
> > -Reshma
> >
> > On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
> >> Entering the HTML tag for those characters works. The character
> >> tags for
> >> them are as follows:
> >>
> >>     Mu: &micro;
> >>     Degree: &deg;
> >>
> >> This is a little better than the use of the table at the bottom of
> >> the form.
> >>
> >> An alternative that isn't any shorter than the above expression
> >> would be by
> >> using an extension I modified:
> >>
> >>     {{deg:}} or {{mu:}}
> >>
> >> I've enabled this via an extension in beta. It's pretty clumsy.
> >> Using this
> >> method, we can add any tags of interest. But it's pretty ugly.
> >>
> >> The curly braces tell the parser this is a parser extension, while
> >> the ":"
> >> is present to allow arguments to be appended.
> >>
> >> It's possible to make this more compact if needed, but this is what's
> >> immediately possible,
> >>
> >> We can directly augment the parser if needed if you need a more
> >> compact way
> >> to label either of them.
> >>
> >> If anyone else has suggestions, let me know.
> >>
> >>
> >>
> >>
> >> On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
> >>> On our pages, the micro (mu) and degree sign are so common that I
> >>> think they deserve special attention.  I don't have a clear idea of
> >>> what to do, but this feature (for me) does not help. It's easier to
> >>> type &mu; and &deg;
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
> >>>
> >>>> We've added a feature to help displaying special characters and
> >>>> character string to OpenWetWare documents. If you've used this
> >>>> feature in Wikipedia, it now works exactly the same in OpenWetWare.
> >>>>
> >>>> When you edit any page or choose to download a new file,
> >>>> OpenWetWare will now display a list of characters and tags at the
> >>>> base of the page. By clicking on any of these characters or tags,
> >>>> the ascii code will be inserted into the page being edited at the
> >>>> current cursor location.
> >>>>
> >>>> The range of special sequences includes the following:
> >>>>
> >>>> MediaWiki Markup
> >>>> Greek
> >>>> Cyrillic
> >>>> Other special characters.
> >>>>
> >>>> All of the current special tags supported by OpenWetWare will be
> >>>> included in the list.
> >>>>
> >>>> If there are special vocabularies or character sets anyone wants
> >>>> add to this list, please consult with me. We can add them quickly.
> >>>>
> >>>> Thanks.
> >>>>
> >>>> Bill Flanagan
> >>>> OpenWetWare.org
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>
> >>
> >> _______________________________________________
> >> OpenWetWare Steering Committee Mailing List
> >> sc at openwetware.org
> >> http://mailman.mit.edu/mailman/listinfo/oww-sc
> >>
> >>
>
>


From bill.altmail at gmail.com  Tue Nov 13 00:50:01 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 13 Nov 2007 00:50:01 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <001801c825b4$d2c5ab90$785102b0$@edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<90F71C58-E257-4C12-A2F3-DCCE45300051@csail.mit.edu>
	<001801c825b4$d2c5ab90$785102b0$@edu>
Message-ID: <26428aaa0711122150o2060032dy8f074be12cf79f7f@mail.gmail.com>

Steve,

Please let me know what you think about the way 'talk' feels. As I
mentioned earlier, we can change it back in a flash. I thought it
would be good to try it out rather than imagine what it would be like.

As far as the nature of commenting on a page, Wikipedia has been
pushing for a more structured buletin-board-like format for them. I
haven't seen a date for the inclusion of the current solution, 'liquid
threads' (I think...).

Threaded discussions make a lot of sense for containing a conversation
between users. There are several different gorum applicaions with deep
links to MediaWiki. Let me see how the linking re: talk/discussion
pages are implemented. If any make sense (and actually add value),
I'll let you folks know. I'll let you know even if they don't make
sense for that matter.

I personally find any well-commented web page a bit confusing. You
have to hunt for data. One advantage is that at least all of the
comments are full-text indexed. Presumably this is one of the features
that is making the implementation of the native threaded discussions
within MediaWiki complicated.


Thanks.

Bill.

On Nov 13, 2007 12:19 AM, Steven J. Koch <sjkoch at unm.edu> wrote:
> I remember that being confusing to me when I signed up on OWW earlier this
> year.  I was a newbie to wikis at the time, but I think OWW will be dealing
> with newbies for a long time, so it is important to consider.  A downside of
> changing the name is that newbies may have edited Wikipedia first (which I
> think also has the confusing talk/discussion naming).  The fact that OWW was
> "the same" as Wikipedia was a big plus at the beginning (and also now).
>
> A related confusion is that on OWW it's often not clear whether to put edits
> on the talk or the main article page.  In Wikipedia, it's usually more clear
> given that most of the pages are encyclopedia articles.  Whereas on OWW it
> seems like the main point of an article is often a discussion in the first
> place (such as brainstorming ideas).  Or, in the case of grading, I don't
> like to use the Talk: page, because I have a bunch of little comments, so I
> use a little hack template that's like adding comment bubbles in a PDF or
> Word.  (See this for an example:
> http://openwetware.org/wiki/Physics307L:People/Knockel/formal).  I think in
> my entire Physics307L class, we haven't used the Talk: page ever.
>
> OK, not sure if I have a productive suggestion buried in those comments, but
> I do agree with TK's post and think it may be a real barrier to edits for
> new people.
>
> --S
>
>
> -----Original Message-----
> From: oww-sc-bounces at mit.edu [mailto:oww-sc-bounces at mit.edu] On Behalf Of
> Tom Knight
> Sent: Monday, November 12, 2007 10:02 PM
> To: Reshma Shetty
> Cc: Steering Committee
> Subject: Re: [OWW-SC] EditTools helper enabled (Greek characters, etc).
>
> I added some comments.  Has anyone else noticed that the way to get
> to a talk page is to click on the "discussion" link at the top of the
> page?  I find this rather unnecessarily confusing.  The name of one
> or the other should be changed.
>
>
> On Nov 12, 2007, at 8:10 PM, Reshma Shetty wrote:
>
> > Bill and I've modified the set of characters available at the
> > bottom further.
> >
> > We've stripped out many of the symbols and have added some that are
> > particularly relevant to biological research like those for
> > concentration, volume and temperature.  (This is in keeping with what
> > Tom was suggesting.)
> >
> > Check out any edit page or modify the list at
> > http://openwetware.org/wiki/MediaWiki:Edittools
> > (Thanks Bill!)
> >
> > Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools
> >
> > -Reshma
> >
> > On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
> >> Entering the HTML tag for those characters works. The character
> >> tags for
> >> them are as follows:
> >>
> >>     Mu: &micro;
> >>     Degree: &deg;
> >>
> >> This is a little better than the use of the table at the bottom of
> >> the form.
> >>
> >> An alternative that isn't any shorter than the above expression
> >> would be by
> >> using an extension I modified:
> >>
> >>     {{deg:}} or {{mu:}}
> >>
> >> I've enabled this via an extension in beta. It's pretty clumsy.
> >> Using this
> >> method, we can add any tags of interest. But it's pretty ugly.
> >>
> >> The curly braces tell the parser this is a parser extension, while
> >> the ":"
> >> is present to allow arguments to be appended.
> >>
> >> It's possible to make this more compact if needed, but this is what's
> >> immediately possible,
> >>
> >> We can directly augment the parser if needed if you need a more
> >> compact way
> >> to label either of them.
> >>
> >> If anyone else has suggestions, let me know.
> >>
> >>
> >>
> >>
> >> On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
> >>> On our pages, the micro (mu) and degree sign are so common that I
> >>> think they deserve special attention.  I don't have a clear idea of
> >>> what to do, but this feature (for me) does not help. It's easier to
> >>> type &mu; and &deg;
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
> >>>
> >>>> We've added a feature to help displaying special characters and
> >>>> character string to OpenWetWare documents. If you've used this
> >>>> feature in Wikipedia, it now works exactly the same in OpenWetWare.
> >>>>
> >>>> When you edit any page or choose to download a new file,
> >>>> OpenWetWare will now display a list of characters and tags at the
> >>>> base of the page. By clicking on any of these characters or tags,
> >>>> the ascii code will be inserted into the page being edited at the
> >>>> current cursor location.
> >>>>
> >>>> The range of special sequences includes the following:
> >>>>
> >>>> MediaWiki Markup
> >>>> Greek
> >>>> Cyrillic
> >>>> Other special characters.
> >>>>
> >>>> All of the current special tags supported by OpenWetWare will be
> >>>> included in the list.
> >>>>
> >>>> If there are special vocabularies or character sets anyone wants
> >>>> add to this list, please consult with me. We can add them quickly.
> >>>>
> >>>> Thanks.
> >>>>
> >>>> Bill Flanagan
> >>>> OpenWetWare.org
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> 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
> >>>
> >>
> >>
> >> _______________________________________________
> >> 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
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>


From bill.altmail at gmail.com  Tue Nov 13 09:52:32 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 13 Nov 2007 09:52:32 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
Message-ID: <26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>

I've rewritten the MagicLink handler that was on beta.openwetware.org
to be a standard MediaWiki extension. It's now installed on
http://www.openwetware.org. The extension, OWWMagicLink.php, is
invoked using a hook in the MediaWiki parser. I'm in the process of
converting the entries to the new format.

Once all of the keyword and expressions we have discussed are
implemented, I'll add a new Special page similar to the one used to
edit system messages to allow OWW admins to add and modify the
supported entries. I'm completing the move of the Genbank support
today.

I'll provide a full list of the current supported entries when I
finish adding them to the server today.

I've incuded a few shortcuts for frequently requested symbols as well:

degc: ?C
degf: ?F
mu: ?
lambda:?

These symbols may be awkward to use. The benefit is in not having to
use the panel at the base of the page to enter symbols.

I've  also added an entry for PDB lookup:

PDB 1234

Let's play it by ear. If these don't work, we can remove them. My goal
is to make as many as possible editable by OWW members rather than
programmable.

B.

On Nov 12, 2007 8:10 PM, Reshma Shetty <rshetty at mit.edu> wrote:
> Bill and I've modified the set of characters available at the bottom further.
>
> We've stripped out many of the symbols and have added some that are
> particularly relevant to biological research like those for
> concentration, volume and temperature.  (This is in keeping with what
> Tom was suggesting.)
>
> Check out any edit page or modify the list at
> http://openwetware.org/wiki/MediaWiki:Edittools
> (Thanks Bill!)
>
> Leave comments at http://openwetware.org/wiki/MediaWiki_talk:Edittools
>
> -Reshma
>
>
> On Nov 10, 2007 7:59 PM, Bill F <bill.altmail at gmail.com> wrote:
> > Entering the HTML tag for those characters works. The character tags for
> > them are as follows:
> >
> >     Mu: &micro;
> >     Degree: &deg;
> >
> > This is a little better than the use of the table at the bottom of the form.
> >
> > An alternative that isn't any shorter than the above expression would be by
> > using an extension I modified:
> >
> >     {{deg:}} or {{mu:}}
> >
> > I've enabled this via an extension in beta. It's pretty clumsy. Using this
> > method, we can add any tags of interest. But it's pretty ugly.
> >
> > The curly braces tell the parser this is a parser extension, while the ":"
> > is present to allow arguments to be appended.
> >
> > It's possible to make this more compact if needed, but this is what's
> > immediately possible,
> >
> > We can directly augment the parser if needed if you need a more compact way
> > to label either of them.
> >
> > If anyone else has suggestions, let me know.
> >
> >
> >
> >
> > On Nov 10, 2007 5:01 PM, Tom Knight < tk at csail.mit.edu> wrote:
> > > On our pages, the micro (mu) and degree sign are so common that I
> > > think they deserve special attention.  I don't have a clear idea of
> > > what to do, but this feature (for me) does not help. It's easier to
> > > type &mu; and &deg;
> > >
> > >
> > >
> > >
> > >
> > > On Nov 10, 2007, at 4:23 PM, Bill Flanagan wrote:
> > >
> > > > We've added a feature to help displaying special characters and
> > > > character string to OpenWetWare documents. If you've used this
> > > > feature in Wikipedia, it now works exactly the same in OpenWetWare.
> > > >
> > > > When you edit any page or choose to download a new file,
> > > > OpenWetWare will now display a list of characters and tags at the
> > > > base of the page. By clicking on any of these characters or tags,
> > > > the ascii code will be inserted into the page being edited at the
> > > > current cursor location.
> > > >
> > > > The range of special sequences includes the following:
> > > >
> > > > MediaWiki Markup
> > > > Greek
> > > > Cyrillic
> > > > Other special characters.
> > > >
> > > > All of the current special tags supported by OpenWetWare will be
> > > > included in the list.
> > > >
> > > > If there are special vocabularies or character sets anyone wants
> > > > add to this list, please consult with me. We can add them quickly.
> > > >
> > > > Thanks.
> > > >
> > > > Bill Flanagan
> > > > OpenWetWare.org
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> > _______________________________________________
>
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
> >
> >
>



From austin at csail.mit.edu  Tue Nov 13 10:45:11 2007
From: austin at csail.mit.edu (Austin Che)
Date: Tue, 13 Nov 2007 10:45:11 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	(Bill F.'s message of "Tue, 13 Nov 2007 09:52:32 -0500")
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
Message-ID: <87k5omkv3s.fsf@nitsua.mit.edu>


> I've incuded a few shortcuts for frequently requested symbols as well:
>
> degc: ?C
> degf: ?F
> mu: ?
> lambda:?
>
> These symbols may be awkward to use. The benefit is in not having to
> use the panel at the base of the page to enter symbols.

    I don't like this approach of having random text to mean something
    else just to save typing. If the extension is ever uninstalled or
    for anyone who gets a data dump, they'll have a bunch of macros
    without knowing what those macros should be expanded to. It's the
    same with interwiki links. We have a perfectly good unique way of
    referring to pages on the web and replace it with a site-specific
    way of naming. Adding a layer of indirection means that to really
    get all the content on a page, not only do you need the text of
    the page, you need the interwiki link table. With these
    'shortcuts', not only will you need the page text, you need the
    extensions installed on the site.
    
    I would prefer that as much of the fancy stuff be client-side or
    that the translation be saved directly to the page. I also don't
    like the panels at the bottom of the page because they seem to far
    away from the edit box. Alternatives include putting it on the
    right or left of the text box or perhaps the best would be to pop
    it up over the text box when some shortcut key/button is
    pressed. Or maybe a right click should bring up a list of items.

-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899



From julius at younglucks.com  Tue Nov 13 10:56:47 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Tue, 13 Nov 2007 10:56:47 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <87k5omkv3s.fsf@nitsua.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	<87k5omkv3s.fsf@nitsua.mit.edu>
Message-ID: <2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>

>
>> I've incuded a few shortcuts for frequently requested symbols as  
>> well:
>>
>> degc: ?C
>> degf: ?F
>> mu: ?
>> lambda:?
>>
>> These symbols may be awkward to use. The benefit is in not having to
>> use the panel at the base of the page to enter symbols.
>
>     I don't like this approach of having random text to mean something
>     else just to save typing. If the extension is ever uninstalled or
>     for anyone who gets a data dump, they'll have a bunch of macros
>     without knowing what those macros should be expanded to. It's the
>     same with interwiki links. We have a perfectly good unique way of
>     referring to pages on the web and replace it with a site-specific
>     way of naming. Adding a layer of indirection means that to really
>     get all the content on a page, not only do you need the text of
>     the page, you need the interwiki link table. With these
>     'shortcuts', not only will you need the page text, you need the
>     extensions installed on the site.

I agree with Austin here.  I worked on a small project for OLPC to  
grab slices of wikipedia content once, and it was painful to have to  
do the translation of special syntax, especially templates.  The  
current system also makes it a lot harder to implement client-side  
'preview'  functionality as part of an off-line editor useful for lab  
notebooks, etc.

Julius


From bill.altmail at gmail.com  Tue Nov 13 13:05:12 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 13 Nov 2007 13:05:12 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	<87k5omkv3s.fsf@nitsua.mit.edu>
	<2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>
Message-ID: <26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>

As I said in my message, I am not advocating, I'm just looking into
how we can do it.

I agree re: Wikipedia's implementation of MediaWiki; it's almost
impossible to represent text from there in other systems because of
complex style sheets and their byzantine templating system. I don't
want to add to the complexity for the sake of complexity. Take a look
at any of the more well-edited pages on Wikipedia. They're thick with
nested templates that are incredibly hard to unwind.

Part of the reason Wikipedia has this problem is because of the
article review process. A relatively small number of editors police
all the documents in their domain, reformatting them to  use the
templates they design, independent in many cases of other similar
templates in the system.

The reason I've put forward the linking syntax is because it's
literally part of MediaWiki already and in use today. In most cases,
the tags used are legible even if not displayed with the extension.

I'm trying to respond to as many people as possible in doing what I've
done so far. We can add and delete these capablities to make it work
well for all.

I do appreciate all of the comments. I'm doing my best to internalize
all of them as I work.


B.



On Nov 13, 2007 10:56 AM, Julius B. Lucks <julius at younglucks.com> wrote:
> >
> >> I've incuded a few shortcuts for frequently requested symbols as
> >> well:
> >>
> >> degc: ?C
> >> degf: ?F
> >> mu: ?
> >> lambda:?
> >>
> >> These symbols may be awkward to use. The benefit is in not having to
> >> use the panel at the base of the page to enter symbols.
> >
> >     I don't like this approach of having random text to mean something
> >     else just to save typing. If the extension is ever uninstalled or
> >     for anyone who gets a data dump, they'll have a bunch of macros
> >     without knowing what those macros should be expanded to. It's the
> >     same with interwiki links. We have a perfectly good unique way of
> >     referring to pages on the web and replace it with a site-specific
> >     way of naming. Adding a layer of indirection means that to really
> >     get all the content on a page, not only do you need the text of
> >     the page, you need the interwiki link table. With these
> >     'shortcuts', not only will you need the page text, you need the
> >     extensions installed on the site.
>
> I agree with Austin here.  I worked on a small project for OLPC to
> grab slices of wikipedia content once, and it was painful to have to
> do the translation of special syntax, especially templates.  The
> current system also makes it a lot harder to implement client-side
> 'preview'  functionality as part of an off-line editor useful for lab
> notebooks, etc.
>
> Julius
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>



From austin at csail.mit.edu  Tue Nov 13 13:16:29 2007
From: austin at csail.mit.edu (Austin Che)
Date: Tue, 13 Nov 2007 13:16:29 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>
	(Bill F.'s message of "Tue, 13 Nov 2007 13:05:12 -0500")
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	<87k5omkv3s.fsf@nitsua.mit.edu>
	<2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>
	<26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>
Message-ID: <87mytij9j6.fsf@nitsua.mit.edu>


    I think we should look seriously again at getting a wysiwyg editor
    for the wiki up. Not only would this make it prettier/easier to
    edit, but many of these issues could be solved if we have an
    intermediate layer between the user and the wiki. I have no
    problem with having people click a button or type degc or whatever
    as long as the intermediate editor translates that to something
    universal before it saves it to the page. It can then do the
    reverse conversion when the user edits the page again.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From jasonk at MIT.EDU  Tue Nov 13 13:21:52 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 13 Nov 2007 13:21:52 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <87mytij9j6.fsf@nitsua.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	<87k5omkv3s.fsf@nitsua.mit.edu>
	<2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>
	<26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>
	<87mytij9j6.fsf@nitsua.mit.edu>
Message-ID: <7c085c480711131021nd305e8duf9cd9d5940d4b1c4@mail.gmail.com>

Couldn't agree more with this.  Not having a WYSIWYG editor is the #1
barrier to contribution on the site in my opinion.  I wasn't sure if
anything available was good enough though, has anyone tried any of the
available ones for mediawiki?

thanks,
jason

On Nov 13, 2007 1:16 PM, Austin Che <austin at csail.mit.edu> wrote:
>
>     I think we should look seriously again at getting a wysiwyg editor
>     for the wiki up. Not only would this make it prettier/easier to
>     edit, but many of these issues could be solved if we have an
>     intermediate layer between the user and the wiki. I have no
>     problem with having people click a button or type degc or whatever
>     as long as the intermediate editor translates that to something
>     universal before it saves it to the page. It can then do the
>     reverse conversion when the user edits the page again.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
>
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>


From jennytnguyen at gmail.com  Tue Nov 13 13:53:53 2007
From: jennytnguyen at gmail.com (Jenny Nguyen)
Date: Tue, 13 Nov 2007 12:53:53 -0600
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <87mytij9j6.fsf@nitsua.mit.edu>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>
	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>
	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>
	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>
	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>
	<87k5omkv3s.fsf@nitsua.mit.edu>
	<2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>
	<26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>
	<87mytij9j6.fsf@nitsua.mit.edu>
Message-ID: <cf36c28d0711131053v4f974c8cmb281ff7692cd919a@mail.gmail.com>

I agree with Austin in getting a wysiwyg editor. Less intimidating code =
more users editing.

On Nov 13, 2007 12:16 PM, Austin Che <austin at csail.mit.edu> wrote:

>
>    I think we should look seriously again at getting a wysiwyg editor
>    for the wiki up. Not only would this make it prettier/easier to
>    edit, but many of these issues could be solved if we have an
>    intermediate layer between the user and the wiki. I have no
>    problem with having people click a button or type degc or whatever
>    as long as the intermediate editor translates that to something
>    universal before it saves it to the page. It can then do the
>    reverse conversion when the user edits the page again.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
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From ilyas at MIT.EDU  Tue Nov 13 17:39:18 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Tue, 13 Nov 2007 17:39:18 -0500
Subject: [OWW-SC] EditTools helper enabled (Greek characters, etc).
In-Reply-To: <cf36c28d0711131053v4f974c8cmb281ff7692cd919a@mail.gmail.com>
References: <26428aaa0711101323r3a513a34rd0c70e65a4fba260@mail.gmail.com>	<D6402528-E675-4187-83CF-789242DDDEEC@csail.mit.edu>	<26428aaa0711101659i30eb6e19nd000659afe1b427@mail.gmail.com>	<6e9f40380711121710i4cbfb253rb7cb6f3152188028@mail.gmail.com>	<26428aaa0711130652k5cde37f5la0b7a17222b32a55@mail.gmail.com>	<87k5omkv3s.fsf@nitsua.mit.edu>	<2DF7611B-AAB5-430D-AE37-806E807F2B5F@younglucks.com>	<26428aaa0711131005x55a9856au47ccceb1b30fa62d@mail.gmail.com>	<87mytij9j6.fsf@nitsua.mit.edu>
	<cf36c28d0711131053v4f974c8cmb281ff7692cd919a@mail.gmail.com>
Message-ID: <473A2796.4050602@mit.edu>

Here are some links to info about WYSIWYG editors and MediaWiki:

http://www.mediawiki.org/wiki/WYSIWYG_editor
http://www.mediawiki.org/wiki/Extension:Wikiwyg

Also, using character entities (like &#176; and &deg;) is a standard way 
to include special characters in web pages: 
http://www.w3.org/TR/html401/sgml/entities.html

Ilya

Jenny Nguyen wrote:
> I agree with Austin in getting a wysiwyg editor. Less intimidating code 
> = more users editing.
> 
> On Nov 13, 2007 12:16 PM, Austin Che <austin at csail.mit.edu 
> <mailto:austin at csail.mit.edu>> wrote:
> 
> 
>        I think we should look seriously again at getting a wysiwyg editor
>        for the wiki up. Not only would this make it prettier/easier to
>        edit, but many of these issues could be solved if we have an
>        intermediate layer between the user and the wiki. I have no
>        problem with having people click a button or type degc or whatever
>        as long as the intermediate editor translates that to something
>        universal before it saves it to the page. It can then do the
>        reverse conversion when the user edits the page again.
> 
>     --
>     Austin Che           <austin at csail.mit.edu
>     <mailto:austin at csail.mit.edu>>          (617)253-5899
>     _______________________________________________
>     OpenWetWare Steering Committee Mailing List
>     sc at openwetware.org <mailto:sc at openwetware.org>
>     http://mailman.mit.edu/mailman/listinfo/oww-sc
>     <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


From jasonk at MIT.EDU  Wed Nov 14 02:07:49 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Wed, 14 Nov 2007 02:07:49 -0500
Subject: [OWW-SC] November SC meeting notes
Message-ID: <7c085c480711132307h748bc243r355ac4e7266e5b88@mail.gmail.com>

Hi SC,

Thanks everyone for calling in to the meeting last week.  For those
who couldn't make it,
notes are here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_November_2007

action list here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_actions

Also, thanks to folks for providing email feedback on new extensions
as Bill is trying stuff out.  Your comments really help make sure we
keep providing tools that are relevant to the community.

thanks!
jason


From bill.altmail at gmail.com  Wed Nov 14 18:20:53 2007
From: bill.altmail at gmail.com (Bill F)
Date: Wed, 14 Nov 2007 18:20:53 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
Message-ID: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>

I've installed a copy of OpenWetWare's data onto a preliminary version
of the FCKEdit OpenSource development team's HTML editor/Wikitext
editor.

This work is NOT a sanctioned activity by the MediaWiki team. The
project is run by the FCKEdit folks.

Their original integration was not good. With little to no support
from the MediaWiki developers, they've already created a great set of
features.

Here's a pointer to OWW running with FCKEdit:

http://www.openwetware.org/fck

It looks pretty useful. But there are a slew of problems with it that
need to be fixed. Even with this caveat, this is as close to a bona
fide WYSIWYG editor for MediaWiki as anyone has done to date.

This site is a separate database. Any changes made to it will be held
in this and not the main database.

The HTML table editor built into it is very good. Images are a bit
complicated at this point.


From jennytnguyen at gmail.com  Wed Nov 14 18:30:10 2007
From: jennytnguyen at gmail.com (Jenny Nguyen)
Date: Wed, 14 Nov 2007 17:30:10 -0600
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
Message-ID: <cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>

That so sooooo cooool!!! I love this! Although I do admit, after typing in
wiki-code for so long, converting to a completely wysiwyg format is a little
difficult. It does make the wikicode look strangely formatted too, but I'm
sure these type of bugs can be tweeked.

Niiiice work Bill. That is really neat.


On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:

> I've installed a copy of OpenWetWare's data onto a preliminary version
> of the FCKEdit OpenSource development team's HTML editor/Wikitext
> editor.
>
> This work is NOT a sanctioned activity by the MediaWiki team. The
> project is run by the FCKEdit folks.
>
> Their original integration was not good. With little to no support
> from the MediaWiki developers, they've already created a great set of
> features.
>
> Here's a pointer to OWW running with FCKEdit:
>
> http://www.openwetware.org/fck
>
> It looks pretty useful. But there are a slew of problems with it that
> need to be fixed. Even with this caveat, this is as close to a bona
> fide WYSIWYG editor for MediaWiki as anyone has done to date.
>
> This site is a separate database. Any changes made to it will be held
> in this and not the main database.
>
> The HTML table editor built into it is very good. Images are a bit
> complicated at this point.
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
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From bill.altmail at gmail.com  Wed Nov 14 18:34:42 2007
From: bill.altmail at gmail.com (Bill F)
Date: Wed, 14 Nov 2007 18:34:42 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
	<cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
Message-ID: <26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>

You can switch back and forth between the two formats. Also, you can
tag pages or individual sections/namespaces to use this as the default
editor. Although not done yet, you could also allow it to be set as a
user preference.




On Nov 14, 2007 6:30 PM, Jenny Nguyen <jennytnguyen at gmail.com> wrote:
> That so sooooo cooool!!! I love this! Although I do admit, after typing in
> wiki-code for so long, converting to a completely wysiwyg format is a little
> difficult. It does make the wikicode look strangely formatted too, but I'm
> sure these type of bugs can be tweeked.
>
> Niiiice work Bill. That is really neat.
>
>
>
>
> On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:
> >
> >
> >
> > I've installed a copy of OpenWetWare's data onto a preliminary version
> > of the FCKEdit OpenSource development team's HTML editor/Wikitext
> > editor.
> >
> > This work is NOT a sanctioned activity by the MediaWiki team. The
> > project is run by the FCKEdit folks.
> >
> > Their original integration was not good. With little to no support
> > from the MediaWiki developers, they've already created a great set of
> > features.
> >
> > Here's a pointer to OWW running with FCKEdit:
> >
> > http://www.openwetware.org/fck
> >
> > It looks pretty useful. But there are a slew of problems with it that
> > need to be fixed. Even with this caveat, this is as close to a bona
> > fide WYSIWYG editor for MediaWiki as anyone has done to date.
> >
> > This site is a separate database. Any changes made to it will be held
> > in this and not the main database.
> >
> > The HTML table editor built into it is very good. Images are a bit
> > complicated at this point.
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
> >
>
>


From austin at csail.mit.edu  Thu Nov 15 10:50:09 2007
From: austin at csail.mit.edu (Austin Che)
Date: Thu, 15 Nov 2007 10:50:09 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>
	(Bill F.'s message of "Wed, 14 Nov 2007 18:34:42 -0500")
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
	<cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
	<26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>
Message-ID: <877ikjh5ji.fsf@nitsua.mit.edu>


    I agree this is great. And there is a preference option under
    editing to turn on/off the rich text editing and the rich editor
    tab for using it in some namespaces. I see no reason not to turn
    it on by default immediately and let whoever wants to disable it
    manually do so. Only by making it the default will we be able to
    find and iron out all the bugs with it.

    Also, I think the one remaining absolutely critical feature for an
    editor is auto-save. This would probably be a separate extension
    but I would like to see something like the following:     
    When the page is closed without saving (I think javascript can
    detect page close as some websites pop up bunch of things on page
    close), the edited text should automatically be sent to the server
    via an ajax request and stored in a separate table. Upon the next
    time I try to edit the same page if an unsaved edit is there, it
    should either ask me what I want to do or bring up a box with my
    previous edits so I can choose whether I want to restore it. 
    
> You can switch back and forth between the two formats. Also, you can
> tag pages or individual sections/namespaces to use this as the default
> editor. Although not done yet, you could also allow it to be set as a
> user preference.
>
> On Nov 14, 2007 6:30 PM, Jenny Nguyen <jennytnguyen at gmail.com> wrote:
>> That so sooooo cooool!!! I love this! Although I do admit, after typing in
>> wiki-code for so long, converting to a completely wysiwyg format is a little
>> difficult. It does make the wikicode look strangely formatted too, but I'm
>> sure these type of bugs can be tweeked.
>>
>> Niiiice work Bill. That is really neat.
>>
>>
>>
>>
>> On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:
>> >
>> >
>> >
>> > I've installed a copy of OpenWetWare's data onto a preliminary version
>> > of the FCKEdit OpenSource development team's HTML editor/Wikitext
>> > editor.
>> >
>> > This work is NOT a sanctioned activity by the MediaWiki team. The
>> > project is run by the FCKEdit folks.
>> >
>> > Their original integration was not good. With little to no support
>> > from the MediaWiki developers, they've already created a great set of
>> > features.
>> >
>> > Here's a pointer to OWW running with FCKEdit:
>> >
>> > http://www.openwetware.org/fck
>> >
>> > It looks pretty useful. But there are a slew of problems with it that
>> > need to be fixed. Even with this caveat, this is as close to a bona
>> > fide WYSIWYG editor for MediaWiki as anyone has done to date.
>> >
>> > This site is a separate database. Any changes made to it will be held
>> > in this and not the main database.
>> >
>> > The HTML table editor built into it is very good. Images are a bit
>> > complicated at this point.

-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From wjf42 at MIT.EDU  Thu Nov 15 11:02:00 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Thu, 15 Nov 2007 11:02:00 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <877ikjh5ji.fsf@nitsua.mit.edu>
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
	<cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
	<26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>
	<877ikjh5ji.fsf@nitsua.mit.edu>
Message-ID: <26428aaa0711150802j65f3d3acr3cc894fb40883b41@mail.gmail.com>

There is a current FCKEditor 'autosave' plugin available. This plugin
sends the entire frame back to the server on a periodic basis. The
server application must take responsibility for then updating a
'persistent cache' with the content.

I'll track it down and load it to see how it works. It's not clear how
well it works with the MediaWiki support. I'll submit a request on the
development wiki site to see what they have to say about it.

Talk about killing 2 birds with one stone...

I'll let you know what I hear.

B.



On Nov 15, 2007 10:50 AM, Austin Che <austin at csail.mit.edu> wrote:
>
>     I agree this is great. And there is a preference option under
>     editing to turn on/off the rich text editing and the rich editor
>     tab for using it in some namespaces. I see no reason not to turn
>     it on by default immediately and let whoever wants to disable it
>     manually do so. Only by making it the default will we be able to
>     find and iron out all the bugs with it.
>
>     Also, I think the one remaining absolutely critical feature for an
>     editor is auto-save. This would probably be a separate extension
>     but I would like to see something like the following:
>     When the page is closed without saving (I think javascript can
>     detect page close as some websites pop up bunch of things on page
>     close), the edited text should automatically be sent to the server
>     via an ajax request and stored in a separate table. Upon the next
>     time I try to edit the same page if an unsaved edit is there, it
>     should either ask me what I want to do or bring up a box with my
>     previous edits so I can choose whether I want to restore it.
>
>
> > You can switch back and forth between the two formats. Also, you can
> > tag pages or individual sections/namespaces to use this as the default
> > editor. Although not done yet, you could also allow it to be set as a
> > user preference.
> >
> > On Nov 14, 2007 6:30 PM, Jenny Nguyen <jennytnguyen at gmail.com> wrote:
> >> That so sooooo cooool!!! I love this! Although I do admit, after typing in
> >> wiki-code for so long, converting to a completely wysiwyg format is a little
> >> difficult. It does make the wikicode look strangely formatted too, but I'm
> >> sure these type of bugs can be tweeked.
> >>
> >> Niiiice work Bill. That is really neat.
> >>
> >>
> >>
> >>
> >> On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:
> >> >
> >> >
> >> >
> >> > I've installed a copy of OpenWetWare's data onto a preliminary version
> >> > of the FCKEdit OpenSource development team's HTML editor/Wikitext
> >> > editor.
> >> >
> >> > This work is NOT a sanctioned activity by the MediaWiki team. The
> >> > project is run by the FCKEdit folks.
> >> >
> >> > Their original integration was not good. With little to no support
> >> > from the MediaWiki developers, they've already created a great set of
> >> > features.
> >> >
> >> > Here's a pointer to OWW running with FCKEdit:
> >> >
> >> > http://www.openwetware.org/fck
> >> >
> >> > It looks pretty useful. But there are a slew of problems with it that
> >> > need to be fixed. Even with this caveat, this is as close to a bona
> >> > fide WYSIWYG editor for MediaWiki as anyone has done to date.
> >> >
> >> > This site is a separate database. Any changes made to it will be held
> >> > in this and not the main database.
> >> >
> >> > The HTML table editor built into it is very good. Images are a bit
> >> > complicated at this point.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>


From macowell at gmail.com  Thu Nov 15 18:54:41 2007
From: macowell at gmail.com (Mackenzie Cowell)
Date: Thu, 15 Nov 2007 18:54:41 -0500
Subject: [OWW-SC] websites with wiki wisdom
Message-ID: <54746a3f0711151554k5c2be5feleaff20ca461eb781@mail.gmail.com>

Hi SC,

I was thinking of posting this in the SC blog, but I decided to just push
them out to you all via email instead.  I've come across three sites that
could be really valuable in imagining how to make OpenWetWare (and igem.org)
better.  Check them out:

UI-patterns.com is a categorized collection of 30 or so user interface
design patterns (recurring solutions to solve common problems) culled from
the best sites around the web.  It provides generalized descriptions and
links to actual instances of solutions to many common website tasks, such as
tags, WYSIWYG editors, autocomplete text areas, pagination, live previews,
table sorting, etc.   Go have a quick look and consider if any could make
OWW better.

Wikipatterns.com "is a toolbox of patterns & anti-patterns, and a guide to
the stages of wiki adoption."  They categorize and describe ~100 common
methods of optimizing how wikis work and are used, similar to
ui-patterns.com.  Here are some interesting entries: Set Window of
Discussion<http://www.wikipatterns.com/display/wikipatterns/Set+Window+of+Discussion>,
IdentityMatters<http://www.wikipatterns.com/display/wikipatterns/IdentityMatters>,
Built-in obsolescence<http://www.wikipatterns.com/display/wikipatterns/Built-in+obsolescence>,
BarnRaising <http://www.wikipatterns.com/display/wikipatterns/BarnRaising>.

Aboutus.org has nothing directly to do with running a wiki.  I'm including
it because it is a stunning example of how mediawiki can be re-themed to
look absolutely great and how the structure of mediawiki URLs can be simple
and logical; for instance, the aboutus.org entry on openwetware is simply
aboutus.org/openwetware.org.

I think these sites are great resources for helping us improve OWW.

mac

-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From rshetty at MIT.EDU  Fri Nov 16 11:36:34 2007
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Fri, 16 Nov 2007 11:36:34 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <26428aaa0711150802j65f3d3acr3cc894fb40883b41@mail.gmail.com>
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
	<cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
	<26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>
	<877ikjh5ji.fsf@nitsua.mit.edu>
	<26428aaa0711150802j65f3d3acr3cc894fb40883b41@mail.gmail.com>
Message-ID: <6e9f40380711160836g20a27cf4y8beb430f3305bb4c@mail.gmail.com>

The FCKEditor still seems quite buggy to me.  In just playing around
with it for a few minutes, I found

1) It is incompatible with the recent edit tools extension that places
commonly used characters below the edit window.  (Not a major issue.)

2) Formulas didn't seem to work.  See
http://www.openwetware.org/fck/index.php/Sandbox

3) It seems to be incompatible with Biblio?

So I'd be nervous about deploying this site-wide by default without
having a handful of steering committee members test it first.  I think
we'd also need to be prepared to invest significant development time
into it to fix bugs.

-Reshma


On Nov 15, 2007 11:02 AM, Bill Flanagan <wjf42 at mit.edu> wrote:
> There is a current FCKEditor 'autosave' plugin available. This plugin
> sends the entire frame back to the server on a periodic basis. The
> server application must take responsibility for then updating a
> 'persistent cache' with the content.
>
> I'll track it down and load it to see how it works. It's not clear how
> well it works with the MediaWiki support. I'll submit a request on the
> development wiki site to see what they have to say about it.
>
> Talk about killing 2 birds with one stone...
>
> I'll let you know what I hear.
>
> B.
>
>
>
>
> On Nov 15, 2007 10:50 AM, Austin Che <austin at csail.mit.edu> wrote:
> >
> >     I agree this is great. And there is a preference option under
> >     editing to turn on/off the rich text editing and the rich editor
> >     tab for using it in some namespaces. I see no reason not to turn
> >     it on by default immediately and let whoever wants to disable it
> >     manually do so. Only by making it the default will we be able to
> >     find and iron out all the bugs with it.
> >
> >     Also, I think the one remaining absolutely critical feature for an
> >     editor is auto-save. This would probably be a separate extension
> >     but I would like to see something like the following:
> >     When the page is closed without saving (I think javascript can
> >     detect page close as some websites pop up bunch of things on page
> >     close), the edited text should automatically be sent to the server
> >     via an ajax request and stored in a separate table. Upon the next
> >     time I try to edit the same page if an unsaved edit is there, it
> >     should either ask me what I want to do or bring up a box with my
> >     previous edits so I can choose whether I want to restore it.
> >
> >
> > > You can switch back and forth between the two formats. Also, you can
> > > tag pages or individual sections/namespaces to use this as the default
> > > editor. Although not done yet, you could also allow it to be set as a
> > > user preference.
> > >
> > > On Nov 14, 2007 6:30 PM, Jenny Nguyen <jennytnguyen at gmail.com> wrote:
> > >> That so sooooo cooool!!! I love this! Although I do admit, after typing in
> > >> wiki-code for so long, converting to a completely wysiwyg format is a little
> > >> difficult. It does make the wikicode look strangely formatted too, but I'm
> > >> sure these type of bugs can be tweeked.
> > >>
> > >> Niiiice work Bill. That is really neat.
> > >>
> > >>
> > >>
> > >>
> > >> On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:
> > >> >
> > >> >
> > >> >
> > >> > I've installed a copy of OpenWetWare's data onto a preliminary version
> > >> > of the FCKEdit OpenSource development team's HTML editor/Wikitext
> > >> > editor.
> > >> >
> > >> > This work is NOT a sanctioned activity by the MediaWiki team. The
> > >> > project is run by the FCKEdit folks.
> > >> >
> > >> > Their original integration was not good. With little to no support
> > >> > from the MediaWiki developers, they've already created a great set of
> > >> > features.
> > >> >
> > >> > Here's a pointer to OWW running with FCKEdit:
> > >> >
> > >> > http://www.openwetware.org/fck
> > >> >
> > >> > It looks pretty useful. But there are a slew of problems with it that
> > >> > need to be fixed. Even with this caveat, this is as close to a bona
> > >> > fide WYSIWYG editor for MediaWiki as anyone has done to date.
> > >> >
> > >> > This site is a separate database. Any changes made to it will be held
> > >> > in this and not the main database.
> > >> >
> > >> > The HTML table editor built into it is very good. Images are a bit
> > >> > complicated at this point.
> >
> > --
> > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> >
> > _______________________________________________
> > 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
>


From julius at younglucks.com  Fri Nov 16 12:24:08 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Fri, 16 Nov 2007 12:24:08 -0500
Subject: [OWW-SC] fyi: wysiwywiki...
In-Reply-To: <6e9f40380711160836g20a27cf4y8beb430f3305bb4c@mail.gmail.com>
References: <26428aaa0711141520u3edf4a88sd77a8a90afa532f9@mail.gmail.com>
	<cf36c28d0711141530n21b06eeas2f1ad8131fe249fd@mail.gmail.com>
	<26428aaa0711141534l808499dpc678bba1a4db4bca@mail.gmail.com>
	<877ikjh5ji.fsf@nitsua.mit.edu>
	<26428aaa0711150802j65f3d3acr3cc894fb40883b41@mail.gmail.com>
	<6e9f40380711160836g20a27cf4y8beb430f3305bb4c@mail.gmail.com>
Message-ID: <5E8D8E56-8254-4B8F-8348-9A69264F1903@younglucks.com>

Though not ideal, some of these issues can be solved 'socially'  
through proper documentation to the effect that we are providing this  
WYSIWYG editor, but some features need manual work arounds for now.   
It seems like it is a good solution for the very basic editing tasks,  
and thereby might enable a significant fraction of the community that  
at present does not edit because of a technology barrier.  More  
advanced editing might have to be done by those willing to learn wiki  
syntax, etc.  Obviously a stop-gap solution while we can work on  
fixes etc.

I still think it is a good idea for a few people to use it  
exclusively for a bit and see what happens.  Maybe they can formalize  
a bug reporting process that OWW users can use to provide feedback  
when it gets rolled out.

Cheers,

Julius


> 2) Formulas didn't seem to work.  See
> http://www.openwetware.org/fck/index.php/Sandbox
>
> 3) It seems to be incompatible with Biblio?
>
> So I'd be nervous about deploying this site-wide by default without
> having a handful of steering committee members test it first.  I think
> we'd also need to be prepared to invest significant development time
> into it to fix bugs.
>
> -Reshma
>
>
> On Nov 15, 2007 11:02 AM, Bill Flanagan <wjf42 at mit.edu> wrote:
>> There is a current FCKEditor 'autosave' plugin available. This plugin
>> sends the entire frame back to the server on a periodic basis. The
>> server application must take responsibility for then updating a
>> 'persistent cache' with the content.
>>
>> I'll track it down and load it to see how it works. It's not clear  
>> how
>> well it works with the MediaWiki support. I'll submit a request on  
>> the
>> development wiki site to see what they have to say about it.
>>
>> Talk about killing 2 birds with one stone...
>>
>> I'll let you know what I hear.
>>
>> B.
>>
>>
>>
>>
>> On Nov 15, 2007 10:50 AM, Austin Che <austin at csail.mit.edu> wrote:
>>>
>>>     I agree this is great. And there is a preference option under
>>>     editing to turn on/off the rich text editing and the rich editor
>>>     tab for using it in some namespaces. I see no reason not to turn
>>>     it on by default immediately and let whoever wants to disable it
>>>     manually do so. Only by making it the default will we be able to
>>>     find and iron out all the bugs with it.
>>>
>>>     Also, I think the one remaining absolutely critical feature  
>>> for an
>>>     editor is auto-save. This would probably be a separate extension
>>>     but I would like to see something like the following:
>>>     When the page is closed without saving (I think javascript can
>>>     detect page close as some websites pop up bunch of things on  
>>> page
>>>     close), the edited text should automatically be sent to the  
>>> server
>>>     via an ajax request and stored in a separate table. Upon the  
>>> next
>>>     time I try to edit the same page if an unsaved edit is there, it
>>>     should either ask me what I want to do or bring up a box with my
>>>     previous edits so I can choose whether I want to restore it.
>>>
>>>
>>>> You can switch back and forth between the two formats. Also, you  
>>>> can
>>>> tag pages or individual sections/namespaces to use this as the  
>>>> default
>>>> editor. Although not done yet, you could also allow it to be set  
>>>> as a
>>>> user preference.
>>>>
>>>> On Nov 14, 2007 6:30 PM, Jenny Nguyen <jennytnguyen at gmail.com>  
>>>> wrote:
>>>>> That so sooooo cooool!!! I love this! Although I do admit,  
>>>>> after typing in
>>>>> wiki-code for so long, converting to a completely wysiwyg  
>>>>> format is a little
>>>>> difficult. It does make the wikicode look strangely formatted  
>>>>> too, but I'm
>>>>> sure these type of bugs can be tweeked.
>>>>>
>>>>> Niiiice work Bill. That is really neat.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Nov 14, 2007 5:20 PM, Bill F <bill.altmail at gmail.com> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> I've installed a copy of OpenWetWare's data onto a preliminary  
>>>>>> version
>>>>>> of the FCKEdit OpenSource development team's HTML editor/Wikitext
>>>>>> editor.
>>>>>>
>>>>>> This work is NOT a sanctioned activity by the MediaWiki team. The
>>>>>> project is run by the FCKEdit folks.
>>>>>>
>>>>>> Their original integration was not good. With little to no  
>>>>>> support
>>>>>> from the MediaWiki developers, they've already created a great  
>>>>>> set of
>>>>>> features.
>>>>>>
>>>>>> Here's a pointer to OWW running with FCKEdit:
>>>>>>
>>>>>> http://www.openwetware.org/fck
>>>>>>
>>>>>> It looks pretty useful. But there are a slew of problems with  
>>>>>> it that
>>>>>> need to be fixed. Even with this caveat, this is as close to a  
>>>>>> bona
>>>>>> fide WYSIWYG editor for MediaWiki as anyone has done to date.
>>>>>>
>>>>>> This site is a separate database. Any changes made to it will  
>>>>>> be held
>>>>>> in this and not the main database.
>>>>>>
>>>>>> The HTML table editor built into it is very good. Images are a  
>>>>>> bit
>>>>>> complicated at this point.
>>>
>>> --
>>> Austin Che           <austin at csail.mit.edu>          (617)253-5899
>>>
>>> _______________________________________________
>>> 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
>>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc



From bill.altmail at gmail.com  Fri Nov 16 19:58:17 2007
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 16 Nov 2007 19:58:17 -0500
Subject: [OWW-SC] 3 character search terms are working again
Message-ID: <26428aaa0711161658x1fc1285eu1f6bfa58463d92cb@mail.gmail.com>

Full-text searches for words less than 4 characters were not working
in OpenWetWare.

I reset the minimal search term length in the database from 4 to 3
characters, rebuilt the full-text index, and restarted the server.

3-character searches are operational again. This problem was
introduced when we moved to a new server.

The change will be applied to all private wikis as well.

Thanks.

Bill Flanagan


From wjf42 at MIT.EDU  Mon Nov 19 18:37:18 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Mon, 19 Nov 2007 18:37:18 -0500
Subject: [OWW-SC] November Development Update
Message-ID: <26428aaa0711191537o5d2ddbc1v29e24dd61de36885@mail.gmail.com>

*
November Development Update
*
There's only so much time in a month, especially when there are 2-3 holidays
in it. I'll do my best to keep updating the individual projects on a regular
basis. If you have specific features that you're looking for that aren't
being worked upon, let me or anyone on the OWW Board of Directors know about
it and we'll do our best to accommodate your request. It may not be
immediate but I assure you that we'll do our best to stay on top of all of
them.

*People*

Julius Lucks (http://openwetware.org/wiki/Julius_B._Lucks) generously
donated his time this month to work with us on a number of development
tasks. We've implemented a way for his project, a new Atom-based API for
Cornell's arXiv archive ( http://www.arxiv.org <http://www.arxiv.com>),  to
be displayable within OpenWetWare. We'll move it to the main server  soon.
Julius has also been very helpful in outlining ways in which we can start
implementing ways to start creating more formal ways in which individuals
and their labs can be connected together.

Steve Koch (http://openwetware.org/wiki/User:Skoch3) continues to help us
develop Lab Notebooks. We are in the middle of implementing prototypes for
various features for the notebooks. He's sent us a number of  requests for
email-enabling wikis that would help both the notebooks and a multitude of
other aspects of OpenWetWare. We'll do our best to get inbound email up and
running. We're constrained by the need to finish off other parts of the
system before moving on to this one. I haven't forgotten it, however!

Cameron Neylon (http://openwetware.org/wiki/User:Cameron_Neylon) visited
with us a few weeks ago. He demonstrated some of the work he's been doing on
lab notebooks. His work is extremely interesting. He's spent a long time
working through the line between structured and unstructured applications
for supporting lab science. We look forward to continuing to collaborate
with him as we move forward.

We also met with Jim Hu from Texas A&M. For those not familiar with his
project, e-Coli Wiki (http://www.ecoliwiki.com), check out his site. We have
a lot to learn from him in the way he has built up his site. He's also
walking the line between a classical "formal" application for curating
genomic information related to e-coli and providing a more fr--form
wiki-based system for allowing others to co-curate. His site features a very
nice integration with gbrowser
(http://www.gmod.org/wiki/index.php/GBrowse<http://www.gmod.org/wiki/index.php/GBrowse>),
among many other tools. We look forward to finding ways to work with his
site.

Here at MIT, Ilya Sytchev (http://www.openwetware.org/wiki/Ilya_Sytchev)
continues to amaze me with his ability to predict the future. He told me to
wait at least a few months before upgrading to Leopard on my Mac. It's not a
bad upgrade. The problem is the amount of time one needs to spend fixing
problems when so few others have had to contend with them already.
Installing developer tools on Friday really can make the rest of the weekend
disappear. The moral is never to lse your 'tar' executable.  And never doubt
Ilya! Ilya's keen eye can find a problem in OWW from 300 yards. My continued
thanks to him for his vigilance.


*Magic Links and Printable Labels
*
I'm still in the process of moving the "magic links" to the main server as
well as providing label printing support. I'll keep you posted on both of
these topics. The mention of using a bar-code scanner generated a good deal
of email traffic. I'm still working on the implementation of the label
printing. I created a new extension to handle the extended "Magic Links" (
http://www.mediawiki.org/wiki/Markup_spec/BNF/Magic_links). We chose to wait
until we move to the next release of MediaWiki to roll it out on the main
OpenWetWare server. The original version was implemented directly in the OWW
MediaWiki core and was intended for test. Expect to see it on the main
system soon.


*GUI Editor
*
A GUI editor, based on the Javascript-based FCKEditor HTML editor
http://www.fckeditor.net/, was experimented with this month. There are a LOT
of details still to be handled before this meets the needs of everyone. In
the short term, I have it deployed on an OWW copy. Our initial enthusiasm
for it was quelled by some of the more daunting usability and stability
problems present with it. But we're still working with the FCKEditor team to
see how much it will take to get to the point where it's no longer "not
quite ready for prime time". It's a great project.


*November Milestones
*
Although we're still centered upon improving lab notebooks, there are
several other items we're working on. I was tardy on posting the November
update but it can be found here:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007<http://openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007><http://openwetware.org/wiki/OpenWetWare:Software/Milestones/November_2007>
*
This is where you can find all of the monthly status/milestone summaries:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Milestones<http://openwetware.org/wiki/OpenWetWare:Software/Milestones>
*

*Extensions
*
I've also cleaned up documentation on extensions. All of the extensions are
now linked into the main Extensions page which can be found here:

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions<http://openwetware.org/wiki/OpenWetWare:Software/Extensions>
*
For each extension, there's currently a main page. My goal is to write and
document lab-centric examples for each extension. Anyone who wants to add
these should feel free to do so. Currently, extension pages are named as
follows
*

http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions/<http://openwetware.org/wiki/OpenWetWare:Software/Extensions/>
                      <Extension name or Type>
*
Demos for each extension will also be present. They will be located directly
below the name/type in a document, Demo. As an example, the full path of the
RSS extension (XFeeds) demo document is

*
http://www.openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS/Demo<http://openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS/Demo>
*
If you don't see a demo for an extension and would like to add to the docs
or create a document for it, please feel free to do so.

All active extension pages are now connected together as a single category.
The category page is located here:

*
http://www.openwetware.org/wiki/Category:Extensions<http://openwetware.org/wiki/Category:Extensions>
*
I'll eventually add additional categories to improve discovery. I've
imported  the original doc  pages for some of the non-OWW-developed
extensions so people can find them. It may be more appropriate to link to
some of these pages in general, but I wanted to allow the text to be
searchable from within OpenWetWare.

One other note. You can also find out about all of the current OWW
extensions by checking the Special:Version page here:

*               http://www.openwetware.org/wiki/Special:Version
<http://openwetware.org/wiki/Special:Version>

*This is the "official" source of what is and is not running on the server.
This is a list of all currently active extensions published by the MediaWiki
server. if it's not there, it ain't runnin!

*
Semantic Wiki
*
We're just starting to work with Semantic Wiki. This isn't just an extension
but a way of ordering all of the information contained within OWW. The jury
is still out as to how we'll use it. I'll keep all of you posted as we
figure out exactly where it fits in. For more information, check out the
following:*

**               http://www.semwiki.org/*
*

"OpenWetWare Developers" blog
*
This and other OpenWetWare development messages will be posted inside
OpenWetWare as well as on the new "OpenWetWare Developers" blog. I intend to
publish there on a regular basis. it can be found here:

*              http://blog.openwetware.org/developers
*
Thanks and Happy Thanksgiving.

Bill Flanagan.
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From jasonk at MIT.EDU  Mon Nov 26 13:13:13 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 26 Nov 2007 13:13:13 -0500
Subject: [OWW-SC] Letter of support for E-science initiative
Message-ID: <7c085c480711261013md7b0148id0004e8a9b18cbfb@mail.gmail.com>

Hi SC,

Cameron Neylon is writing a grant to support 2-3 meetings about open
science over three years, including travel costs, and provide funds
for exchange visits.

You can read more about it at his OWW blog here:
http://blog.openwetware.org/scienceintheopen/2007/11/22/e-science-for-open-science-an-epsrc-research-network-proposal/

Also, you can see the (in progress) grant draft here
http://docs.google.com/Doc?id=dhs5x5kr_559gqg6x7


He asked "What I would like from the community is an expression of
interest, specifically the committment to write a letter of support
saying you would like to be involved."  I personally think it would be
great to have more opportunities to meet face-to-face and discuss all
the open science projects going on.

I'll volunteer to write up a letter of support from the OWW SC,
assuming that's OK with folks.  Please write me / the list an email if
you think this is a bad idea for some reason.

Thanks!
jason

p.s. I'll send out a draft of the letter when it's finished.


From julius at younglucks.com  Mon Nov 26 13:41:44 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Mon, 26 Nov 2007 13:41:44 -0500
Subject: [OWW-SC] Letter of support for E-science initiative
In-Reply-To: <7c085c480711261013md7b0148id0004e8a9b18cbfb@mail.gmail.com>
References: <7c085c480711261013md7b0148id0004e8a9b18cbfb@mail.gmail.com>
Message-ID: <5FD47C31-ACD9-4DA3-A304-4B85C02F463A@younglucks.com>

I think this is a great idea and am happy to sign the letter,

Julius

Please Reply to julius at younglucks.com

On Nov 26, 2007, at 1:13 PM, "Jason Kelly" <jasonk at mit.edu> wrote:

> Hi SC,
>
> Cameron Neylon is writing a grant to support 2-3 meetings about open
> science over three years, including travel costs, and provide funds
> for exchange visits.
>
> You can read more about it at his OWW blog here:
> http://blog.openwetware.org/scienceintheopen/2007/11/22/e-science-for-open-science-an-epsrc-research-network-proposal/
>
> Also, you can see the (in progress) grant draft here
> http://docs.google.com/Doc?id=dhs5x5kr_559gqg6x7
>
>
> He asked "What I would like from the community is an expression of
> interest, specifically the committment to write a letter of support
> saying you would like to be involved."  I personally think it would be
> great to have more opportunities to meet face-to-face and discuss all
> the open science projects going on.
>
> I'll volunteer to write up a letter of support from the OWW SC,
> assuming that's OK with folks.  Please write me / the list an email if
> you think this is a bad idea for some reason.
>
> Thanks!
> jason
>
> p.s. I'll send out a draft of the letter when it's finished.
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc


From hoatlinm at ohsu.edu  Mon Nov 26 14:06:13 2007
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 Nov 2007 13:06:13 -0600
Subject: [OWW-SC] Letter of support for E-science initiative
In-Reply-To: <7c085c480711261013md7b0148id0004e8a9b18cbfb@mail.gmail.com>
References: <7c085c480711261013md7b0148id0004e8a9b18cbfb@mail.gmail.com>
Message-ID: <FA8668ED-773E-4E8B-9AAE-154D3EDC20C9@ohsu.edu>

Great idea!


Sent from ZaZen

On Nov 26, 2007, at 12:13 PM, "Jason Kelly" <jasonk at mit.edu> wrote:

> Hi SC,
>
> Cameron Neylon is writing a grant to support 2-3 meetings about open
> science over three years, including travel costs, and provide funds
> for exchange visits.
>
> You can read more about it at his OWW blog here:
> http://blog.openwetware.org/scienceintheopen/2007/11/22/e-science-for-open-science-an-epsrc-research-network-proposal/
>
> Also, you can see the (in progress) grant draft here
> http://docs.google.com/Doc?id=dhs5x5kr_559gqg6x7
>
>
> He asked "What I would like from the community is an expression of
> interest, specifically the committment to write a letter of support
> saying you would like to be involved."  I personally think it would be
> great to have more opportunities to meet face-to-face and discuss all
> the open science projects going on.
>
> I'll volunteer to write up a letter of support from the OWW SC,
> assuming that's OK with folks.  Please write me / the list an email if
> you think this is a bad idea for some reason.
>
> Thanks!
> jason
>
> p.s. I'll send out a draft of the letter when it's finished.
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc


From jasonk at MIT.EDU  Tue Nov 27 08:44:17 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 27 Nov 2007 08:44:17 -0500
Subject: [OWW-SC] letter of support
Message-ID: <7c085c480711270544x42232903v2ef8c34dedda50a8@mail.gmail.com>

Hi SC,

Attached is our letter of support for Cameron Neylon's proposal.
Thanks to those who offered to sign, but I just ended up putting "The
OWW SC" as the signature since Cameron needs this by later today.  Let
me know if there are any problems with the letter.

Thanks!
jason
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From julius at younglucks.com  Wed Nov 28 10:55:12 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 28 Nov 2007 10:55:12 -0500
Subject: [OWW-SC] 'Publishing' on Pre-print services like arXiv.org
Message-ID: <65BAF402-A32B-422C-BE0F-CDD219BC5EBB@younglucks.com>

Hi SC,

Following up on last month's meeting, I would like to gather your  
ideas on how the OWW community might like to use a pre-print service  
such as arXiv.org or Nature Proceedings to 'publish' content  
originally created on OWW.

My first impression was that these pre-print services could be used  
as a stepping-stone towards more traditional publication - i.e. an  
article would be written with the OWW wiki, and when sufficiently  
polished, sent off to arXiv as an official pre-print.  This would  
provide a citeable uri for that version of the document, and would be  
used as the basis to notify the community of the polished work, as  
well as submit to a traditional peer-reviewed journal (if the authors  
desire).

In discussing this at the last SC meeting, Barry mentioned a very  
interesting possibility of posting non-article content such as lab  
protocols or reagent lists up on a pre-print archive.  I would like  
to brainstorm with you possible uses of pre-print archives.  In  
particular:

* Would you consider using a pre-print archive as a way to turn a  
wiki document into a journal article (wiki -> pre-print -> paper)?
** If so, are you ready to try this out, or do you know of anyone  
that is ready?  I would like to walk whoever is ready through the  
process with them and see how it goes.  I can also facilitate  
submission to arXiv.org's quantitative biology section if that is  
necessary.

* What other types of documents do you imagine posting on a pre-print  
archive?  (protocols, reagent lists, etc.)
** For each type of document, it would be great to know why the wiki  
page is insufficient for your purposes.  For example, Barry mentioned  
that reviewers were hesitant to honor a wiki link as a citeable  
document.

* What is the best way to ask the OWW community outside the SC these  
questions?

I would appreciate ALL of your comments.  I think arXiv.org is  
already prepared to handle traditional journal-article-like  
submissions, but might be more hesitant for other types of  
submissions.  I would like to get a list of ideas to before I discuss  
this with them.

Thanks for your help,

Cheers,

Julius


------------------------------------------------------------------------ 
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------ 
----------------



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From jasonk at MIT.EDU  Fri Nov 30 08:40:39 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Fri, 30 Nov 2007 08:40:39 -0500
Subject: [OWW-SC] December SC Meeting TH 12/6 @ Noon EST
Message-ID: <7c085c480711300540j617ea39dsf499d5810eb191ff@mail.gmail.com>

hey SC,

Reminder that the SC meeting is coming up on the 1st TH of the month
(12/6) at Noon EST.

Chairs fill in your reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_December_2007

Please add items to the agenda:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting

Or take a look at action list from last month for left over to-do items.
http://openwetware.org/wiki/OpenWetWare:Steering_committee_actions

Number is 617-452-5208, and austin can send out details for people using sip.

Thanks!
jason