From ilyas at MIT.EDU  Mon Nov  6 17:42:42 2006
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Mon, 06 Nov 2006 17:42:42 -0500
Subject: [OWW-SC] web science
Message-ID: <454FBA62.6070404@mit.edu>

http://science.slashdot.org/article.pl?sid=06/11/02/1832240

"Since its inception, the World Wide Web has changed the ways scientists
communicate, collaborate, and educate. There is, however, a growing
realization among many researchers that a clear research agenda aimed at
understanding the current, evolving, and potential Web is needed. If we
want to model the Web; if we want to understand the architectural
principles that have provided for its growth; and if we want to be sure
that it supports the basic social values of trustworthiness, privacy,
and respect for social boundaries, then we must chart out a research
agenda that targets the Web as a primary focus of attention."

http://www.webscience.org/


From jasonk at MIT.EDU  Tue Nov  7 00:58:32 2006
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 7 Nov 2006 00:58:32 -0500
Subject: [OWW-SC] SC meeting on Thursday (11/9)
Message-ID: <7c085c480611062158t3ceb87bfo4e82f83324d6987@mail.gmail.com>

hey folks,

Just a reminder that the steering committee meeting will be this
Thursday -- from noon-1pm in 32-262.  If you would like to call into
the meeting please send me an email.

You can add items to the agenda here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting

Thanks,
jason


From endy at MIT.EDU  Tue Nov  7 12:50:45 2006
From: endy at MIT.EDU (Drew Endy)
Date: Tue, 7 Nov 2006 12:50:45 -0500
Subject: [OWW-SC] Fwd: OWW DNA ligation and nature methods article...
References: <1BFC6DAE48E6D4478BDFF41C012CD31101161AD5@uk-lif-lexc02.crwin.crnet.org>
Message-ID: <3E13DD74-23C2-4336-9482-E53182FB3C52@mit.edu>

OWW SC,

I wanted to send this along to the OWW SC and my guess is that many  
of the people emailed below haven't had time to respond, and it  
provides a interesting use case.

Best,
Drew

Begin forwarded message:

> From: "James Hadfield" <James.Hadfield at cancer.org.uk>
> Date: November 1, 2006 11:50:13 AM EST
> To: <endy at mit.edu>, <tk at csail.mit.edu>,  
> <pamela_silver at hms.harvard.edu>, <rshetty at mit.edu>, <nkuldell at mit.edu>
> Subject: OWW DNA ligation and nature methods article...
>
> Dear All,
>     I am writing to you as I want to reference the DNA ligation  
> protocol in the Nature methods article I am putting together  
> (http://openwetware.org/wiki/Jamesh008:nature_methods_article). See  
> the email I sent to Sri below for more detail.
>     Basically I would like to exchange my DNA ligation 'consensus'  
> protocol (http://openwetware.org/wiki/ 
> Jamesh008:consensus_DNA_ligation_protocol) for the DNA ligation  
> protocol on the front page (http://openwetware.org/wiki/ 
> DNA_Ligation). It has been written to the 'consensus' protocol  
> style I think will work best and as described in the NM article. It  
> is different from the current DNA ligation protocol and you are all  
> involved in creating that or the lab specific ones. As such I would  
> very much like your input.
>     Get back to me if you have questions or better still. Edit the  
> article and consensus protocol pages (http://openwetware.org/wiki/ 
> User:Jamesh008).
>     James.
>
> James Hadfield
> CRI Genomics Core
>
> Cancer Research UK
> Cambridge Research Institute
> Robinson Way, Cambridge CB2 0RE
> Tel: +44 (0)1223 404250
> Fax: +44 (0)1223 404208
> Mob: +44(0)7879 844167
> email: james.hadfield at cancer.org.uk
>
> -----Original Message-----
>
> From: James Hadfield
>
> Sent: 30 October 2006 11:59
>
> To: 'Sri Kosuri'; 'OpenWetWare Admin'
>
> Subject: FW: Decision on presubmission inquiry NMETH-PI03027
>
> Dear Sri,
>
> Please pass this message on to the OWW steering committee. I have a  
> couple of specific questions I would like the steering committee to  
> answer at the bottom.
>
> I have been very happy to contribute to OWW. I first came across  
> the site when I wanted to get a template for Nature Methods:  
> methods articles to use in our lab as a standard protocol format.  
> Nature declined citing copyright reasons.
>
> OWW will be the standard in my lab and I am doing my best to  
> convince the CRI management on the ease and usefulness of the Wiki  
> approach. It may be that we host something internally rather than  
> on OWW (I know there are discussions ongoing within OWW about  
> private wikis).
>
> I have been looking at what I termed a 'consensus protocol' as the  
> standard protocol for a new scientist to use. See http:// 
> openwetware.org/wiki/Jamesh008:consensus_protocol for more info.  
> This is something I will certainly be working on formalising over  
> the next weeks and months.
>
> While thinking about this I made a presubmission enquiry to Nature  
> Methods about OWW, specifically protocols and consensus protocols  
> and they have asked me to write a brief correspondence article.  
> When I made the enquiry I made it quite clear to the editor that  
> although this was going to be written by me it would also be co- 
> written and edited by the OWW community. They have accepted this as  
> OK. I have started with an abstract but as this is a brief  
> correspondence there will not be an abstract, just the article  
> http://openwetware.org/wiki/Jamesh008:nature_methods_article.
>
> I would like to submit this by the middle of November.
>
>
> Questions:
>
> Is the steering committee happy for me to proceed?
>
> Is authorship OK?
>
> Is the format OK?
>
> Is the submission date OK?
>
> I suggested that three OWW steering committee members 'sign off'  
> the article as ready to submit. Perhaps it would be easier to get  
> people to add comments to the discussion page before November 10th  
> with a provisional submission date of November 17th?
>
> Consensus protocols would really need an editor. I would suggest  
> the editor is self nominated. They would be responsible for  
> updating the protocol and authorising general edits?
>
>
>
> I hope this is a very good way of advertising OWW to a more general  
> audience. Perhaps you (we) should think a bit more about how to  
> show the labs on the front page before lots more people sign up.
>
> James.
>
> PS: please add me to the steering committee.
>
> James Hadfield
>
> CRI Genomics Core
>
>
> Cancer Research UK
>
> Cambridge Research Institute
>
> Robinson Way, Cambridge CB2 0RE
>
> Tel: +44 (0)1223 404250
>
> Fax: +44 (0)1223 404208
>
> Mob: +44(0)7879 844167
>
> email: james.hadfield at cancer.org.uk
>
> -----Original Message-----
>
> From: v.kiermer at natureny.com [mailto:v.kiermer at natureny.com]
>
> Sent: 27 October 2006 20:55
>
> To: James Hadfield
>
> Subject: Decision on presubmission inquiry NMETH-PI03027
>
> 27th Oct 2006
>
>
>
> Dear Mr Hadfield,
>
>
> Thank you for your inquiry about submitting your manuscript  
> entitled "OpenWetWare Protocols: an open-access online protocol  
> resource for everyone." to Nature Methods. The topic you propose to  
> discuss is potentially an important resource for the community and  
> our readership in particular. As such, it could be suitable for our  
> Correspondence section.
>
> We will be happy to consider for publication a brief Correspondence  
> (no more than 400 words).
>
> Of course, it is very difficult to make a definitive judgment about  
> any manuscript based only on the limited information available in a  
> presubmission inquiry. Therefore I am sure you will understand that  
> we cannot make any specific promises until we have read it in its  
> entirety.
>
>
> Again, thank you for your interest in Nature Methods, and I look  
> forward to reading your manuscript.
>
>
> Sincerely,
>
>
> Veronique Kiermer, PhD
>
> Editor
>
> Nature Methods
>
>
>
>
> This email has been sent through the NPG Manuscript Tracking System  
> NY-610A-NPG&MTS.

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From tk at csail.mit.edu  Tue Nov  7 13:04:21 2006
From: tk at csail.mit.edu (Tom Knight)
Date: Tue, 7 Nov 2006 13:04:21 -0500
Subject: [OWW-SC] Why we must replace Genbank
Message-ID: <cdd1fe3841d17046fc0fa88fda3c95ef@csail.mit.edu>

You can't even include the important references in new sequence 
submissions!!

Begin forwarded message:

> From: gb-admin at ncbi.nlm.nih.gov
> Date: November 7, 2006 12:21:07 PM EST
> To: tk at mit.edu
> Subject: GenBank EF036510-EF036511
>
> Dear Dr. Knight:
>
> As per your correspondence:
>
>> I notice that the references have been deleted from this entry.  The
>> references give important information about the source and utility of
>> this construct, and should be included, in my opinion.
>
> REFERENCES on GenBank entries should be directly about the provided
> nucleotide sequence and include at least one of the submitting authors.
> Therefore, these references were removed from your submissions.
>
> Thank you for your understanding in this matter.
>
>
> Sincerely,
>
> Susan Schafer PhD
> The GenBank Submissions Staff
> Bethesda, Maryland USA
> *******************************************************************
> (301) 496-2475
> (301) 480-2918 fax
> gb-admin at ncbi.nlm.nih.gov (for replies/updates to records in GenBank)
> info at ncbi.nlm.nih.gov     (for general questions regarding GenBank)
> *******************************************************************
>
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From jasonk at MIT.EDU  Thu Nov  9 09:49:23 2006
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 9 Nov 2006 09:49:23 -0500
Subject: [OWW-SC] Some quick reading before the meeting
Message-ID: <7c085c480611090649p66be97b5pcf8d9994ec98b132@mail.gmail.com>

Take a look at the Nature Methods article before the meeting if you have time:
http://openwetware.org/wiki/Jamesh008:nature_methods_article

we'll be discussing it a little during the meeting.

thanks,
jason


From jennyn at MIT.EDU  Thu Nov  9 20:32:21 2006
From: jennyn at MIT.EDU (Jenny Nguyen)
Date: Thu, 9 Nov 2006 20:32:21 -0500
Subject: [OWW-SC] OWW People Directory
Message-ID: <cf36c28d0611091732t585f81f7n56a925305aafd286@mail.gmail.com>

I've started a discussion for implementing a directory. It's plain and
basic, but it should start a discussion on how we can best make a directory
on OWW for users to post basic information about themselves, a link to their
userpage, areas of expertise, etc. This could help users find collaborators,
labs for post-doc, their soulmate, etc.

http://www.openwetware.org/wiki/OpenWetWare:Information_management/Directory

Jenny
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From johncumbers at gmail.com  Thu Nov  9 22:18:53 2006
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 9 Nov 2006 22:18:53 -0500
Subject: [OWW-SC] OWW People Directory
In-Reply-To: <cf36c28d0611091732t585f81f7n56a925305aafd286@mail.gmail.com>
References: <cf36c28d0611091732t585f81f7n56a925305aafd286@mail.gmail.com>
Message-ID: <cfd758050611091918i2bf5971exbc63a637414cc086@mail.gmail.com>

Sorry to have totally missed the meeting, I filtered it into the wrong
folder ..   I like the directory idea, I wonder if there are other wiki's
trying to implement similar ideas as this that have found other solutions?
cheers,
john

On 11/9/06, Jenny Nguyen <jennyn at mit.edu> wrote:
>
> I've started a discussion for implementing a directory. It's plain and
> basic, but it should start a discussion on how we can best make a directory
> on OWW for users to post basic information about themselves, a link to their
> userpage, areas of expertise, etc. This could help users find collaborators,
> labs for post-doc, their soulmate, etc.
>
>
> http://www.openwetware.org/wiki/OpenWetWare:Information_management/Directory
>
> Jenny
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
>


-- 
John Cumbers,  Graduate Student in Computational Biology
Brown University, Ecology and Evolutionary Biology, Box G-W
80 Waterman Street, Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
UK to USA: 0207 617 7824
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From martin_jambon at emailuser.net  Thu Nov  9 22:48:57 2006
From: martin_jambon at emailuser.net (Martin Jambon)
Date: Thu, 9 Nov 2006 19:48:57 -0800 (PST)
Subject: [OWW-SC] OWW People Directory
In-Reply-To: <cfd758050611091918i2bf5971exbc63a637414cc086@mail.gmail.com>
References: <cf36c28d0611091732t585f81f7n56a925305aafd286@mail.gmail.com>
	<cfd758050611091918i2bf5971exbc63a637414cc086@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0611091944270.3152@droopy>

I hesitated, but I think I should post it. http://people.wink.com is a 
brand new service by wink.com which allows you to search through linkedin, 
myspace and bebo profiles. Maybe more in the future.

Maybe if there was a way of storing user's profiles on one of those sites, 
then you would automatically benefit from the search engine.


Martin

On Thu, 9 Nov 2006, John Cumbers wrote:

> Sorry to have totally missed the meeting, I filtered it into the wrong
> folder ..   I like the directory idea, I wonder if there are other wiki's
> trying to implement similar ideas as this that have found other solutions?
> cheers,
> john
>
> On 11/9/06, Jenny Nguyen <jennyn at mit.edu> wrote:
>> 
>> I've started a discussion for implementing a directory. It's plain and
>> basic, but it should start a discussion on how we can best make a directory
>> on OWW for users to post basic information about themselves, a link to 
>> their
>> userpage, areas of expertise, etc. This could help users find 
>> collaborators,
>> labs for post-doc, their soulmate, etc.
>> 
>> 
>> http://www.openwetware.org/wiki/OpenWetWare:Information_management/Directory
>> 
>> Jenny
>> 
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>> 
>> 
>> 
>
>
> -- 
> John Cumbers,  Graduate Student in Computational Biology
> Brown University, Ecology and Evolutionary Biology, Box G-W
> 80 Waterman Street, Providence, Rhode Island, 02912, USA
> Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
> UK to USA: 0207 617 7824
>

--
Martin Jambon, PhD
http://martin.jambon.free.fr

                    Ce message est confidentiel. Merci !
                    This message is confidential. Thanks!



From jasonk at MIT.EDU  Fri Nov 10 12:09:02 2006
From: jasonk at MIT.EDU (Jason Kelly)
Date: Fri, 10 Nov 2006 12:09:02 -0500
Subject: [OWW-SC] meeting notes, discussions
Message-ID: <7c085c480611100909y1a73ee70haea48f56f6c9727@mail.gmail.com>

Hi SC,

Just wanted to point out there are a few wiki pages posted to follow
up on discussions we had at the meeting.  Please contribute to those,
particularly folks whose opinions we missed at the meeting yesterday:

Should we have editors/curators listed by name for (some) protocols?:
http://openwetware.org/wiki/OpenWetWare:Information_management/Protocol_curators

Should we have an OWW directory to aid finding collaborators / how do
we implement it?
http://openwetware.org/wiki/OpenWetWare:Information_management/Directory

Thanks!
jason

p.s.
meeting notes (thanks jenny!) posted here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_November_2006

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


From johncumbers at gmail.com  Fri Nov 10 13:22:54 2006
From: johncumbers at gmail.com (John Cumbers)
Date: Fri, 10 Nov 2006 13:22:54 -0500
Subject: [OWW-SC] OWW People Directory
In-Reply-To: <Pine.LNX.4.64.0611091944270.3152@droopy>
References: <cf36c28d0611091732t585f81f7n56a925305aafd286@mail.gmail.com>
	<cfd758050611091918i2bf5971exbc63a637414cc086@mail.gmail.com>
	<Pine.LNX.4.64.0611091944270.3152@droopy>
Message-ID: <cfd758050611101022k62bda0f6odd4c8e663783a5e8@mail.gmail.com>

Yeah, I sort of think that trying to do it through the wiki would be trying
to reinvent the wheel, it is quite easy to embed another page inside the
wiki, e.g do our social network through linkedin/wink and then embed it in a
page on OWW, the only trouble is the more we outsource to other websites,
the less control we have as a community and the more passwords people have
to type in...
John

On 11/9/06, Martin Jambon <martin_jambon at emailuser.net> wrote:
>
> I hesitated, but I think I should post it. http://people.wink.com is a
> brand new service by wink.com which allows you to search through linkedin,
> myspace and bebo profiles. Maybe more in the future.
>
> Maybe if there was a way of storing user's profiles on one of those sites,
> then you would automatically benefit from the search engine.
>
>
> Martin
>
> On Thu, 9 Nov 2006, John Cumbers wrote:
>
> > Sorry to have totally missed the meeting, I filtered it into the wrong
> > folder ..   I like the directory idea, I wonder if there are other
> wiki's
> > trying to implement similar ideas as this that have found other
> solutions?
> > cheers,
> > john
> >
> > On 11/9/06, Jenny Nguyen <jennyn at mit.edu> wrote:
> >>
> >> I've started a discussion for implementing a directory. It's plain and
> >> basic, but it should start a discussion on how we can best make a
> directory
> >> on OWW for users to post basic information about themselves, a link to
> >> their
> >> userpage, areas of expertise, etc. This could help users find
> >> collaborators,
> >> labs for post-doc, their soulmate, etc.
> >>
> >>
> >>
> http://www.openwetware.org/wiki/OpenWetWare:Information_management/Directory
> >>
> >> Jenny
> >>
> >> _______________________________________________
> >> OpenWetWare Steering Committee Mailing List
> >> sc at openwetware.org
> >> http://mailman.mit.edu/mailman/listinfo/oww-sc
> >>
> >>
> >>
> >
> >
> > --
> > John Cumbers,  Graduate Student in Computational Biology
> > Brown University, Ecology and Evolutionary Biology, Box G-W
> > 80 Waterman Street, Providence, Rhode Island, 02912, USA
> > Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
> > UK to USA: 0207 617 7824
> >
>
> --
> Martin Jambon, PhD
> http://martin.jambon.free.fr
>
>                     Ce message est confidentiel. Merci !
>                     This message is confidential. Thanks!
>
>


-- 
John Cumbers,  Graduate Student in Computational Biology
Brown University, Ecology and Evolutionary Biology, Box G-W
80 Waterman Street, Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
UK to USA: 0207 617 7824
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From johncumbers at gmail.com  Mon Nov 13 01:12:04 2006
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 13 Nov 2006 01:12:04 -0500
Subject: [OWW-SC] http://openwetware.org/wiki/Reddit
Message-ID: <cfd758050611122212k25e0fb82s21d866a4f8da0a5f@mail.gmail.com>

Hi People,

We've (myself, Julius and Jason) been experimenting with Reddit at:
http://openwetware.org/wiki/Reddit.  The idea would be to link from the main
page of oww, and possibly have the top few links scraped and appearing on
the main page of oww.   The guys at reddit have set this up for us to see
how it goes.  You have to log into reddit as a separate account at the
moment, if this works, then we could look at combining the log-ins.

 A couple of issues:
1. If you comment then you see ads.  We could ask for this to be removed,
but not sure how well it would go down.  We should think about a sustainable
model for the future if we decide to go with this.
2. Do we want to become a "slashdot  for synthetic biology"?  Or should we
just limit the postings to pages on OWW?  I think we should see how it
evolves rather than limit content right away.
3. should we put it on the front page as a link, or as the headlines?
4.  We could not have it embedded into OWW  e.g:  http://oww.reddit.com/

cheers,
John




-- 
John Cumbers,  Graduate Student in Computational Biology
Brown University, Ecology and Evolutionary Biology, Box G-W
80 Waterman Street, Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
UK to USA: 0207 617 7824
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From austin at csail.mit.edu  Mon Nov 13 09:35:29 2006
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 13 Nov 2006 09:35:29 -0500
Subject: [OWW-SC] http://openwetware.org/wiki/Reddit
In-Reply-To: <cfd758050611122212k25e0fb82s21d866a4f8da0a5f@mail.gmail.com>
	(John Cumbers's message of "Mon, 13 Nov 2006 01:12:04 -0500")
References: <cfd758050611122212k25e0fb82s21d866a4f8da0a5f@mail.gmail.com>
Message-ID: <87psbrifda.fsf@nitsua.mit.edu>


> how it goes.  You have to log into reddit as a separate account at the
> moment, if this works, then we could look at combining the log-ins.

    Can you check if they support/plan to support/can support OpenID?
    If they do, then we can have single login as OWW now supports
    OpenID via the URL of your user page
    e.g. http://openwetware.org/wiki/User:NAME
    
> A couple of issues:
> 1. If you comment then you see ads.  We could ask for this to be removed,
> but not sure how well it would go down.  We should think about a sustainable
> model for the future if we decide to go with this.
> 2. Do we want to become a "slashdot  for synthetic biology"?  Or should we
> just limit the postings to pages on OWW?  I think we should see how it
> evolves rather than limit content right away.
    
    There's already a slashdot for synthetic biology at taqdot.org
    
> 3. should we put it on the front page as a link, or as the headlines?

    Headlines.
    
> 4.  We could not have it embedded into OWW  e.g:  http://oww.reddit.com/

    I'd rather have it embedded.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From lucks at fas.harvard.edu  Mon Nov 13 09:58:30 2006
From: lucks at fas.harvard.edu (Julius Lucks)
Date: Mon, 13 Nov 2006 09:58:30 -0500
Subject: [OWW-SC] http://openwetware.org/wiki/Reddit
In-Reply-To: <87psbrifda.fsf@nitsua.mit.edu>
References: <cfd758050611122212k25e0fb82s21d866a4f8da0a5f@mail.gmail.com>
	<87psbrifda.fsf@nitsua.mit.edu>
Message-ID: <8E0763A9-48A1-4D6F-8207-CB63C1CA8021@fas.harvard.edu>

I will check on the OpenID support.  I am with John in thinking we  
should see how the OWW community decides to use it.  That said, some  
good example usage and maybe a highlight blurb about suggested usage  
will go a long way in shaping how the community views the service.

Cheers,

Julius

-----------------------------------------------------
http://openwetware.org/wiki/User:Lucks
-----------------------------------------------------



On Nov 13, 2006, at 9:35 AM, Austin Che wrote:

>
>> how it goes.  You have to log into reddit as a separate account at  
>> the
>> moment, if this works, then we could look at combining the log-ins.
>
>     Can you check if they support/plan to support/can support OpenID?
>     If they do, then we can have single login as OWW now supports
>     OpenID via the URL of your user page
>     e.g. http://openwetware.org/wiki/User:NAME
>
>> A couple of issues:
>> 1. If you comment then you see ads.  We could ask for this to be  
>> removed,
>> but not sure how well it would go down.  We should think about a  
>> sustainable
>> model for the future if we decide to go with this.
>> 2. Do we want to become a "slashdot  for synthetic biology"?  Or  
>> should we
>> just limit the postings to pages on OWW?  I think we should see  
>> how it
>> evolves rather than limit content right away.
>
>     There's already a slashdot for synthetic biology at taqdot.org
>
>> 3. should we put it on the front page as a link, or as the headlines?
>
>     Headlines.
>
>> 4.  We could not have it embedded into OWW  e.g:  http:// 
>> oww.reddit.com/
>
>     I'd rather have it embedded.
>
> -- 
> 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 rshetty at MIT.EDU  Mon Nov 13 12:15:25 2006
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Mon, 13 Nov 2006 12:15:25 -0500
Subject: [OWW-SC] Fwd: TALK:Friday 11-17-06 Making Tea with Chemists and
	Bioinformatitians
In-Reply-To: <E1GjesH-0003vA-UY@spruce-goose.csail.mit.edu>
References: <E1GjesH-0003vA-UY@spruce-goose.csail.mit.edu>
Message-ID: <6e9f40380611130915r61b2aa7au504ef320bf7a4bc9@mail.gmail.com>

This talk may be of interest based on the abstract below.  It has to
do with capturing information about experiments digitally.

-Reshma

---------- Forwarded message ----------
From: CSAIL Event Calendar <eventcalendar at csail.mit.edu>
Date: Nov 13, 2006 11:41 AM
Subject: TALK:Friday 11-17-06 Making Tea with Chemists and Bioinformatitians
To: seminars at csail.mit.edu



Making Tea with Chemists and Bioinformatitians - lessons learned in
designing up close and at a distance
HCI Seminar Series Fall 2006
Speaker: mc schraefel
Speaker Affiliation: University of Southampton
Host: Rob Miller
Host Affiliation: MIT CSAIL

Date: 11-17-2006
Time: 1:30 PM - 2:30 PM
Refreshments: 1:15 PM
Location: Star Seminar Room (32-D463)

In our design methods work with Synthetic Chemists in the Smarttea
project (smarttea.org), we looked at design approaches to help
scientists move from paper lab books to semantic web based digital
experiment capture systems. The result was a novel design method
(called Making Tea) that focuses on designing for highly expert,
idiosyncratic, longitudinal processes.

In the myTea project (mytea.org.uk) we have been able to investigate
how a design method developed in one context can be applied to
another. In this case we wanted to look at applying the Making Tea
method for a design challenge with  with bioinformaticians. The
challenge has been to help them keep a record of their always already
computer-based experiments. WHere the chemists had a lab book and
wanted to go from paper to digital, the bioinformatitians have had no
history of recording their experiments. For them, we learned, it has
been easier to redo an experiment that to keep track of the hundreds
of small files they create working with their web and digital sources.

By re-deploying the Making Tea method in a new context, we have been
able to address the bioinformatition experiment capture problem, and
by this, consider how that method generalizes. But also, due to
unpredicted differences between the two contexts of the two projects,
we learned about additional factors in the design process that we
would recommend need to be taken into account for prepping future
e-Science usability work in particular. This talk reviews the Making
Tea design process as developed in the SmartTea project, and as
applied in the MyTea project. It also presents the lessons learned in
applying the approach in a distributed design environment.

Bio: mc schraefel is a visiting scientist in DIG/CSAIL and is the
first visiting fellow of the new Web Science Research Initiative
(webscience.org) between MIT and the University of Southampton, UK.
She is a Senior Lecturer at the University of Southampton's IAM Group,
School of Electronics and Computer Science. Her research has lately
focused on interaction issues for exploratory search and the semantic
web.
http://www.ecs.soton.ac.uk/~mc
email: mc at csail.mit.edu

Relevant URL(S):
For more information please contact: Rob Miller, x46028, rcm at mit.edu

_______________________________________________
Seminars mailing list
Seminars at lists.csail.mit.edu
https://lists.csail.mit.edu/mailman/listinfo/seminars


From johncumbers at gmail.com  Mon Nov 13 21:19:02 2006
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 13 Nov 2006 21:19:02 -0500
Subject: [OWW-SC] http://openwetware.org/wiki/Reddit
In-Reply-To: <8E0763A9-48A1-4D6F-8207-CB63C1CA8021@fas.harvard.edu>
References: <cfd758050611122212k25e0fb82s21d866a4f8da0a5f@mail.gmail.com>
	<87psbrifda.fsf@nitsua.mit.edu>
	<8E0763A9-48A1-4D6F-8207-CB63C1CA8021@fas.harvard.edu>
Message-ID: <cfd758050611131819r3f82e4baj1e97bdec1731cf4d@mail.gmail.com>

So any thoughts on the ads, or are we okay to go ahead and try it out?  If
we keep it embedded in the wiki and link from the front page, then I think
we would maintain control (e.g if we wanted to change the provider then we
could just change what is embedded there).
any objections?
cheers,
John


On 11/13/06, Julius Lucks <lucks at fas.harvard.edu> wrote:
>
> I will check on the OpenID support.  I am with John in thinking we should
> see how the OWW community decides to use it.  That said, some good example
> usage and maybe a highlight blurb about suggested usage will go a long way
> in shaping how the community views the service.
> Cheers,
>
> Julius
>
> -----------------------------------------------------
> http://openwetware.org/wiki/User:Lucks
> -----------------------------------------------------
>
>
>
> On Nov 13, 2006, at 9:35 AM, Austin Che wrote:
>
>
> how it goes.  You have to log into reddit as a separate account at the
> moment, if this works, then we could look at combining the log-ins.
>
>
>     Can you check if they support/plan to support/can support OpenID?
>     If they do, then we can have single login as OWW now supports
>     OpenID via the URL of your user page
>     e.g. http://openwetware.org/wiki/User:NAME
>
> A couple of issues:
> 1. If you comment then you see ads.  We could ask for this to be removed,
> but not sure how well it would go down.  We should think about a
> sustainable
> model for the future if we decide to go with this.
> 2. Do we want to become a "slashdot  for synthetic biology"?  Or should we
> just limit the postings to pages on OWW?  I think we should see how it
> evolves rather than limit content right away.
>
>
>     There's already a slashdot for synthetic biology at taqdot.org
>
> 3. should we put it on the front page as a link, or as the headlines?
>
>
>     Headlines.
>
> 4.  We could not have it embedded into OWW  e.g:  http://oww.reddit.com/
>
>
>     I'd rather have it embedded.
>
> --
> 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
>
>
>


-- 
John Cumbers,  Graduate Student in Computational Biology
Brown University, Ecology and Evolutionary Biology, Box G-W
80 Waterman Street, Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190,  Fax: +1 401 863-2166
UK to USA: 0207 617 7824
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From jennytnguyen at gmail.com  Wed Nov 15 09:57:39 2006
From: jennytnguyen at gmail.com (Jenny Nguyen)
Date: Wed, 15 Nov 2006 09:57:39 -0500
Subject: [OWW-SC] Possible Sticker Design
Message-ID: <cf36c28d0611150657q5986eaednfe97000618b8e11c@mail.gmail.com>

Check it!

http://www.openwetware.org/wiki/OpenWetWare:Design/Sticker#Options_for_sticker

Let me know your thoughts.

Love,
Jenny
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From jasonk at MIT.EDU  Tue Nov 21 02:28:41 2006
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 21 Nov 2006 02:28:41 -0500
Subject: [OWW-SC] Meeting about hiring options
Message-ID: <7c085c480611202328w7ecbd9ebx871b81b18e4c5232@mail.gmail.com>

Hi SC,

As decided at the last SC meeting, we'll be holding a seperate meeting
to talk about hiring someone to work on OWW full/part time using the
money available from the NIH grant.  We'll need to decide what sort
background we're looking for / can reasonably find.  If you're
interested in contributing to the discussion but don't can't make a
meeting, please write me an email with your thoughts.

The possible meeting times (Nov 4/5) are here:
http://openwetware.org/wiki/OpenWetWare:Hiring
(please sign up for any of the time slots you can make, lunch will be provided.)

thanks,
jason

p.s. if you would like to teleconference in, please email me as well.


From jasonk at MIT.EDU  Thu Nov 23 18:18:57 2006
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 23 Nov 2006 18:18:57 -0500
Subject: [OWW-SC] Fwd: Google Alert - "OpenWetWare"
In-Reply-To: <1164297531.2168c1e1f0b09d89.ae8de1@persist.google.com>
References: <1164297531.2168c1e1f0b09d89.ae8de1@persist.google.com>
Message-ID: <7c085c480611231518q4b58b93eg9d2e0349e11926de@mail.gmail.com>

oww in nature.  Happy turkey day!

---------- Forwarded message ----------
From: Google Alerts <googlealerts-noreply at google.com>
Date: Thu, 23 Nov 2006 07:58:51 -0800 (PST)
Subject: Google Alert - "OpenWetWare"
To: jrkelly at gmail.com



Google News Alert for: "OpenWetWare"
   YouTube for test tubes
 Nature.com (subscription) - London,England,UK
 ... OpenWetWare ? a biology website that allows participants to add
and edit content ? has a section devoted to protocols and encourages
the submission of ...

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