From jasonk at MIT.EDU  Thu Jan 18 09:43:31 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 18 Jan 2007 09:43:31 -0500
Subject: [OWW-Discuss] digg-like site for post publication review
Message-ID: <7c085c480701180643j774dfc6dge8e512339712b9ae@mail.gmail.com>

http://www.scientificdebate.com/

Looks like it was started pretty recently, probably worth keeping an
eye on.  Would be great if it takes off.

jason


From jasonk at MIT.EDU  Tue Jan 23 13:23:38 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 23 Jan 2007 13:23:38 -0500
Subject: [OWW-Discuss] Interesting presentation on open science
Message-ID: <7c085c480701231023g66f67df6l5c11585a923e5c09@mail.gmail.com>

http://showme.physics.drexel.edu/share/BlogConfBradleyJan07/BlogConfBradleyJan07.html

Jean-Claude Bradley at Drexel who runs the UsefulChem wiki talks about
using a wiki for their primary lab notebook, among other things (incl
OWW).

jason


From johncumbers at gmail.com  Tue Jan 23 20:47:22 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 24 Jan 2007 09:47:22 +0800
Subject: [OWW-Discuss] Interesting presentation on open science
In-Reply-To: <7c085c480701231023g66f67df6l5c11585a923e5c09@mail.gmail.com>
References: <7c085c480701231023g66f67df6l5c11585a923e5c09@mail.gmail.com>
Message-ID: <cfd758050701231747m6c17528dk188b9f49396910ce@mail.gmail.com>

That's really good Jason,
I always feel that I'm doing things in the most time-consuming way when I;m
doing my lab notebook on the wiki, or when I'm adding detailed info,
(e.gusing math ml to write the microlitre sign looks nice, but seems
pointless).  What I'd like to hear are people's top 3 tips for writing your
lab book on oww and your top 3 tips for productivity (i.e  quick elegant
ways of doing things that don't suck up all your time clicking save and edit
again...)
any ideas?

John

On 1/24/07, Jason Kelly <jasonk at mit.edu> wrote:
>
>
> http://showme.physics.drexel.edu/share/BlogConfBradleyJan07/BlogConfBradleyJan07.html
>
> Jean-Claude Bradley at Drexel who runs the UsefulChem wiki talks about
> using a wiki for their primary lab notebook, among other things (incl
> OWW).
>
> jason
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>



-- 
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 ilyas at MIT.EDU  Thu Jan 25 01:33:15 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Thu, 25 Jan 2007 01:33:15 -0500
Subject: [OWW-Discuss] Idea of Paid Entries Roils Wikipedia
Message-ID: <45B84F2B.3060409@mit.edu>

http://hosted.ap.org/dynamic/stories/W/WIKIPEDIA_PAID_ENTRIES


From jasonk at MIT.EDU  Thu Jan 25 19:38:35 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 25 Jan 2007 19:38:35 -0500
Subject: [OWW-Discuss] Wiley / Elsevier stepping up anti-OA publishing
	efforts
Message-ID: <7c085c480701251638x45308aadk59b2373a08f312e1@mail.gmail.com>

Looks like some of the established journals are getting a little
concerned about open access for scientific publications.  Nature.com
is reporting how Wiley and Elsevier (among others) have hired a PR
firm to help them argue against the PLoS crowd.

"We're like any firm under siege," says Barbara Meredith, a
vice-president at the organization. "It's common to hire a PR firm
when you're under siege."

Nature Article:
http://www.nature.com/news/2007/070122/full/445347a.html

Slashdot post:
http://science.slashdot.org/science/07/01/25/2155223.shtml

looks like things are heating up.
jason


From jasonk at MIT.EDU  Thu Jan 25 20:45:53 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 25 Jan 2007 20:45:53 -0500
Subject: [OWW-Discuss] Interesting presentation on open science
In-Reply-To: <cfd758050701231747m6c17528dk188b9f49396910ce@mail.gmail.com>
References: <7c085c480701231023g66f67df6l5c11585a923e5c09@mail.gmail.com>
	<cfd758050701231747m6c17528dk188b9f49396910ce@mail.gmail.com>
Message-ID: <7c085c480701251745j411fc737qdf061d5832fb613c@mail.gmail.com>

Well if you haven't seen it there's a tutorial here for using the
Calender extension to set up a lab notebook, it autogenerates all the
page names for you with dates which saves you some trouble:

http://openwetware.org/wiki/Help:Notebook

jason


On 1/23/07, John Cumbers <johncumbers at gmail.com> wrote:
> That's really good Jason,
> I always feel that I'm doing things in the most time-consuming way when I;m
> doing my lab notebook on the wiki, or when I'm adding detailed info, (e.g
> using math ml to write the microlitre sign looks nice, but seems pointless).
>  What I'd like to hear are people's top 3 tips for writing your lab book on
> oww and your top 3 tips for productivity ( i.e  quick elegant ways of doing
> things that don't suck up all your time clicking save and edit again...)
> any ideas?
>
> John
>
>
> On 1/24/07, Jason Kelly <jasonk at mit.edu> wrote:
> >
> >
> http://showme.physics.drexel.edu/share/BlogConfBradleyJan07/BlogConfBradleyJan07.html
> >
> > Jean-Claude Bradley at Drexel who runs the UsefulChem wiki talks about
> > using a wiki for their primary lab notebook, among other things (incl
> > OWW).
> >
> > jason
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
>
>
>
> --
>  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


From goderisa at cs.man.ac.uk  Sat Jan 27 07:01:08 2007
From: goderisa at cs.man.ac.uk (Antoon Goderis)
Date: Sat, 27 Jan 2007 12:01:08 +0000 (GMT)
Subject: [OWW-Discuss] Talk on semantic e-science at Harvard, Wed January 31,
	4pm
Message-ID: <Pine.GSO.4.42.0701271154400.23247-100000@phoebus>


http://iic.harvard.edu/event12.php

Antoon
http://openwetware.org/wiki/User:AntoonGoderis
--

Sense and Sensibility: Adding meaning to metadata for manageable
middleware

Prof. Carole Goble, University of Manchester, UK

Abstract

It is a truth universally acknowledged that a grid application in
possession of good middleware, must be in want of meaningful metadata.

We have seen a variety of projects and programmes of activity thathave
promoted systematic approaches to describing, linking and sharing
metadata, particularly through the use of community-wide terminologies or
ontologies. Life Sciences have led the way. The founding of the USA.s
National Centre for BioMedical Ontology (http://www.bioontology.org) is an
example. The Semantic Web has given distributed information management a
technical impetus, and once again the Life Sciences are pioneers.
Meanwhile, the Semantic Grid initiative attempts to marry the two
technical efforts of Grid Middleware and Web-wide Information Management
to generally support better metadata (and data) management for Science
applications and the infrastructure that underpins them. Again, early
examples such as myGrid are found in the Life Sciences. Recent work on a
Semantic Open Grid Service Architecture (S-OGSA) lays the foundation for a
systematic yet lightweight approach to deploying semantics into new and
legacy Grid middleware.

In this talk I will share my experiences of applying Semantic Web and
ontology based approaches to represent and classify metadata and discuss
the Semantic Grid using the S-OGSA as an illustration. I.ll also take the
opportunity to voice some concerns and raise some challenges that we have
to overcome, not many of which are technical.





From skosuri at MIT.EDU  Wed Jan 31 20:16:00 2007
From: skosuri at MIT.EDU (Sri Kosuri)
Date: Wed, 31 Jan 2007 20:16:00 -0500
Subject: [OWW-Discuss] WYSIWYG editor for Firefox
Message-ID: <2b0cb7a10701311716h1bab5900hd3c25aedde3553ed@mail.gmail.com>

The following page describes a browser plugin for Firefox that makes
wikicode more WYSIWYG.

http://en.wikipedia.org/wiki/User:Cacycle/wikEd

It's a super simple installation process and probably would be pretty decent
for beginners.  Installation instructions can be found here:
http://en.wikipedia.org/wiki/User:Cacycle/wikEd#Complete_version

I wonder if we could make this a default option for new users.  It
definitely makes it easier for novices to edit.

Sri
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From johncumbers at gmail.com  Wed Jan 31 21:13:27 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 31 Jan 2007 21:13:27 -0500
Subject: [OWW-Discuss] WYSIWYG editor for Firefox
In-Reply-To: <2b0cb7a10701311716h1bab5900hd3c25aedde3553ed@mail.gmail.com>
References: <2b0cb7a10701311716h1bab5900hd3c25aedde3553ed@mail.gmail.com>
Message-ID: <cfd758050701311813q22c4c31ag8bcac72cb54958df@mail.gmail.com>

I'm not actually sure that it makes it easier though, I suppose that large
list of buttons looks more like MS Word which most people are used to, to me
I found it a bit daunting.. I've just started using
http://www.wikispaces.com/ for organising a co-op that I'm in, this has a
simple but good WYSIWYG  editor in it and editing is much nicer than
wikimedia, mainly cause you don't have to keep re-saving all the time.

Perhaps we could try the extension out on new users and see what they think,
or old users who have had trouble editing...
cheers,
John



On 1/31/07, Sri Kosuri <skosuri at mit.edu> wrote:
>
> The following page describes a browser plugin for Firefox that makes
> wikicode more WYSIWYG.
>
> http://en.wikipedia.org/wiki/User:Cacycle/wikEd
>
> It's a super simple installation process and probably would be pretty
> decent for beginners.  Installation instructions can be found here:
> http://en.wikipedia.org/wiki/User:Cacycle/wikEd#Complete_version
>
> I wonder if we could make this a default option for new users.  It
> definitely makes it easier for novices to edit.
>
> Sri
>
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
>


-- 
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  Wed Jan 31 21:14:24 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 31 Jan 2007 21:14:24 -0500
Subject: [OWW-Discuss] Does anyone have any tips on keeping your lab book on
	OWW?
Message-ID: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>

Does anyone have any tips on keeping your lab book on OWW?  If typing notes
into a page, do you keep one page on edit and keep saving?  Do you use an
external editor?   Do you write in wordpad and then paste into the wiki?
Any tips appreciated, I've tried all the above and each one is a little
painful in its own way..
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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