From ilyas at MIT.EDU  Thu Feb  1 16:04:23 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Thu, 01 Feb 2007 16:04:23 -0500
Subject: [OWW-Discuss] Does anyone have any tips on keeping your lab
 book on	OWW?
In-Reply-To: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>
References: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>
Message-ID: <45C255D7.6010403@mit.edu>

I don't have a formal notebook but when I edit my notes on the wiki, I
usually just keep the page on edit, hit Show preview occasionally and
then Save page at the end.

Ilya


John Cumbers wrote:
> 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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss


From ilyas at MIT.EDU  Thu Feb  1 17:10:09 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Thu, 01 Feb 2007 17:10:09 -0500
Subject: [OWW-Discuss] [OWW-SC]  WYSIWYG editor for Firefox
In-Reply-To: <cfd758050701311813q22c4c31ag8bcac72cb54958df@mail.gmail.com>
References: <2b0cb7a10701311716h1bab5900hd3c25aedde3553ed@mail.gmail.com>
	<cfd758050701311813q22c4c31ag8bcac72cb54958df@mail.gmail.com>
Message-ID: <45C26541.5070704@mit.edu>

FYI, I have a collection of links to WYSIWYG editors which may be
suitable for Mediawiki:
http://openwetware.org/wiki/User:Ilya/OpenWetWare#Editors

Ilya

John Cumbers wrote:
> 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 <mailto: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 <mailto: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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc


From johncumbers at gmail.com  Thu Feb  1 18:01:55 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 1 Feb 2007 18:01:55 -0500
Subject: [OWW-Discuss] [OWW-SC] WYSIWYG editor for Firefox
In-Reply-To: <45C26541.5070704@mit.edu>
References: <2b0cb7a10701311716h1bab5900hd3c25aedde3553ed@mail.gmail.com>
	<cfd758050701311813q22c4c31ag8bcac72cb54958df@mail.gmail.com>
	<45C26541.5070704@mit.edu>
Message-ID: <cfd758050702011501l9066406y474cb820bbc5ea37@mail.gmail.com>

I do agree that WYSIWYG would be better to encourage new users to OWW,
perhaps we could put some OWW funds behind one of these that we like to help
develop it further (I've not checked them out yet, so maybe one is great
already).
cheers,
John

On 2/1/07, Ilya Sytchev <ilyas at mit.edu> wrote:
>
> FYI, I have a collection of links to WYSIWYG editors which may be
> suitable for Mediawiki:
> http://openwetware.org/wiki/User:Ilya/OpenWetWare#Editors
>
> Ilya
>
> John Cumbers wrote:
> > 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 <mailto: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 <mailto: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
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
> _______________________________________________
> 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 bcanton at MIT.EDU  Mon Feb  5 11:32:59 2007
From: bcanton at MIT.EDU (Barry Canton)
Date: Mon, 5 Feb 2007 11:32:59 -0500
Subject: [OWW-Discuss] Does anyone have any tips on keeping your lab
	book on OWW?
In-Reply-To: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>
References: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>
Message-ID: <52c0d2160702050832g3f7f65c2n6c084724d95d3fac@mail.gmail.com>

Hi John, I keep my lab notebook on a mediawiki installation (private
because I try to organize the rest of my life on it too:)).  Right
now, I just have a page for each day, where each day is a subpage of
each month which is a subpage of each year to aid navigation.

So currently, my lab notebook is organized chronologically.  I've been
thinking that since my lab notebook is a website, that I should really
organize it by project and just add dates at each particular step of
the project.  The reason being that when reading over a project it is
much easier if that project is described on one page or a set of pages
rather than distributed over a set of chronologically ordered pages
that aren't necessarily consecutive.  We are much more likely to ask -
"How did I do project X?" than to ask -  "What did I do in November
2004?".  If each project is annotated with the dates I did particular
actions, I can always search to find out what I did on a given day if
need be.  I accept that you could organize by date and then search for
all instances of "Project X" but that seems like a more awkward
approach assuming that you normally want to read about a project than
about a set of dates.

Seems to me the reason for organizing things chronologically is that
it is the only easy solution if you are using paper or even a word
document for you lab notebook.  Otherwise it seems somewhat inferior
to the notebook organized by project.

I'd love to hear if anyone has any experience with, or comments on, this idea.

Thanks,

Barry

On 1/31/07, John Cumbers <johncumbers at gmail.com> wrote:
> 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
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


-- 
Barry Canton
Endy Lab
Biological Engineering Division
Massachusetts Institute of Technology

Tel.:(617) 899 6062
Email1: bcanton at mit.edu
Email2: bcanton at gmail.com


From johncumbers at gmail.com  Mon Feb  5 14:19:42 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 5 Feb 2007 14:19:42 -0500
Subject: [OWW-Discuss] Does anyone have any tips on keeping your lab
	book on OWW?
In-Reply-To: <52c0d2160702050832g3f7f65c2n6c084724d95d3fac@mail.gmail.com>
References: <cfd758050701311814ia94701en5471051b3ba8264a@mail.gmail.com>
	<52c0d2160702050832g3f7f65c2n6c084724d95d3fac@mail.gmail.com>
Message-ID: <cfd758050702051119o67dee320i898af60c01e621a0@mail.gmail.com>

some good arguments, I can see why date-order is a little out-dated. (boom
boom)
John


On 2/5/07, Barry Canton <bcanton at mit.edu> wrote:
>
> Hi John, I keep my lab notebook on a mediawiki installation (private
> because I try to organize the rest of my life on it too:)).  Right
> now, I just have a page for each day, where each day is a subpage of
> each month which is a subpage of each year to aid navigation.
>
> So currently, my lab notebook is organized chronologically.  I've been
> thinking that since my lab notebook is a website, that I should really
> organize it by project and just add dates at each particular step of
> the project.  The reason being that when reading over a project it is
> much easier if that project is described on one page or a set of pages
> rather than distributed over a set of chronologically ordered pages
> that aren't necessarily consecutive.  We are much more likely to ask -
> "How did I do project X?" than to ask -  "What did I do in November
> 2004?".  If each project is annotated with the dates I did particular
> actions, I can always search to find out what I did on a given day if
> need be.  I accept that you could organize by date and then search for
> all instances of "Project X" but that seems like a more awkward
> approach assuming that you normally want to read about a project than
> about a set of dates.
>
> Seems to me the reason for organizing things chronologically is that
> it is the only easy solution if you are using paper or even a word
> document for you lab notebook.  Otherwise it seems somewhat inferior
> to the notebook organized by project.
>
> I'd love to hear if anyone has any experience with, or comments on, this
> idea.
>
> Thanks,
>
> Barry
>
> On 1/31/07, John Cumbers <johncumbers at gmail.com> wrote:
> > 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
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> >
>
>
> --
> Barry Canton
> Endy Lab
> Biological Engineering Division
> Massachusetts Institute of Technology
>
> Tel.:(617) 899 6062
> Email1: bcanton at mit.edu
> Email2: bcanton at gmail.com
>



-- 
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 jasonk at MIT.EDU  Tue Feb  6 19:28:58 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 6 Feb 2007 19:28:58 -0500
Subject: [OWW-Discuss] OpenID
Message-ID: <7c085c480702061628n3b7852e3meed4163ee793eeb6@mail.gmail.com>

yro.slashdot.org/yro/07/02/06/2152214.shtml

More groups (incl. MS) are using the OpenID format, this could help
solve the problem of unique author IDs.  OWW has adopted it, if a few
publishers would follow suit maybe we could have legitimate online
scientific identities.

jason


From ilyas at MIT.EDU  Fri Feb  9 17:29:14 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Fri, 09 Feb 2007 17:29:14 -0500
Subject: [OWW-Discuss] OpenID
In-Reply-To: <7c085c480702061628n3b7852e3meed4163ee793eeb6@mail.gmail.com>
References: <7c085c480702061628n3b7852e3meed4163ee793eeb6@mail.gmail.com>
Message-ID: <45CCF5BA.2060300@mit.edu>

Here's an easy way to have a unique ID:
http://dig.csail.mit.edu/breadcrumbs/node/71

Ilya

Jason Kelly wrote:
> yro.slashdot.org/yro/07/02/06/2152214.shtml
> 
> More groups (incl. MS) are using the OpenID format, this could help
> solve the problem of unique author IDs.  OWW has adopted it, if a few
> publishers would follow suit maybe we could have legitimate online
> scientific identities.
> 
> jason
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss


From jasonk at MIT.EDU  Tue Feb 13 11:36:43 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 13 Feb 2007 11:36:43 -0500
Subject: [OWW-Discuss] 'Biology goes open source' (forbes)
Message-ID: <7c085c480702130836p6a93cc35r4db84f61fe1abca3@mail.gmail.com>

"Novartis, the Basel, Switzerland, drug giant, has helped uncover
which of the 20,000 genes identified by the Human Genome Project are
likely to be associated with diabetes. But rather than hoard this
information, as drug firms have traditionally done, it is making it
available for free on the World Wide Web."

http://www.forbes.com/2007/02/12/novartis-genes-diabetes-research-biz-cz_mh_0212novartis.html?partner=rss

also covered on Slashdot:
http://science.slashdot.org/science/07/02/12/1932221.shtml

it's a start anyway,
jason


From jasonk at MIT.EDU  Thu Feb 15 16:49:45 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 15 Feb 2007 16:49:45 -0500
Subject: [OWW-Discuss] Microsoft says OWW is anarchic :)
Message-ID: <7c085c480702151349qa6d87eay71790a1c91ab68f8@mail.gmail.com>

"Also OpenWetWare, a wiki, captures how experiments and done and
shares this information with others, though it's quite anarchic."
- Tony Hey, VP for tech computing at MS

http://blogs.nature.com/wp/nascent/2007/02/tony_hey_visits_nature_1.html

Hope he doesn't realize MS gave us $ ;)
jason

p.s Nature Network Boston has been joined by London and now lives at:
http://network.nature.com/
(though doesn't look like the features have changed much outside of
forums being added).


From johncumbers at gmail.com  Thu Feb 15 17:18:26 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 15 Feb 2007 17:18:26 -0500
Subject: [OWW-Discuss] Key biology databases go wiki (about time too!)
Message-ID: <cfd758050702151418h4ebf6fbbq6a2973759d4947a2@mail.gmail.com>

News

*Nature* *445*, 691 (15 February 2007) | doi:10.1038/445691a; Published
online 14 February 2007
Key biology databases go wiki

Jim Giles
Top of page<http://www.nature.com/nature/journal/v445/n7129/full/445691a.html#top>
Abstract

Collaborative approach aims to keep pace with discoveries.

Barend Mons's first objective would be ambitious enough for most people: to
meld some of the most important biomedical databases into a single
information resource. But that's just the beginning. Mons, a
bioinformatician at the Erasmus Medical Centre in Rotterdam, the
Netherlands, also wants to apply the Wikipedia philosophy. He's inviting the
whole research community to help update a vast store of interlinked data. If
he and his colleagues can pull it off ? and even the project's advocates are
not sure they can ? they could transform the databases that are central to
the work of many life scientists.

A test version of the project, provisionally dubbed Wiki for Professionals (
http://www.wikiprofessional.info), is due to launch in the next month. It
already contains data from key sources, such as protein information from
Swiss-Prot and gene descriptions from Gene Ontology. Over the past year,
Mons's team has woven together these and other archives to create what, from
a user's point of view, seems to be a single database. The page on the
muscular-dystrophy protein dystrophin, for example, contains data from
Swiss-Prot together with links to disease information from the US National
Library of Medicine, as well as explanatory text. Links to relevant
publications in PubMed are also available.

Existing databases interlink to an extent, although the new resource is more
comprehensive. But the next stage is the really radical bit. Biomedical
research produces hundreds of thousands of papers a year, overwhelming
database curators. To clear this bottleneck, Mons and his colleagues are
allowing anyone to edit the entries, modifying and adding text and links as
new work is published.
[image: Key biology databases go wiki]

A. PASIEKA/SPL

Protein databases could be transformed by extra features.

That's an attractive proposition, say database administrators. Michael
Ashburner, a geneticist at the University of Cambridge, UK, helps run
FlyBase, a collection of gene data on the model organism *Drosophila
melanogaster*. The database receives around US$4 million a year from the US
National Institutes of Health and employs up to five full-time curators, but
still can't keep up with the relevant literature, says Ashburner, who is
working with Mons on the new project. "We have a list of around 12 journals
that we try to cover. Even that's tough."

Anyone motivated to register can curate Wiki for Professionals. Visitors to
the dystrophin entry, for example, can update almost any of the information
on the page, such as statements about the role of the protein in disease.
Users can also start new pages, and from later this year will be given the
option of creating pages for themselves, with links to relevant
publications. A final function, and the one that most excites Mons, is the
availability of text-mining software. This will allow users to probe links
between proteins, genes and disease that may be revealed only by comparing a
large number of papers and other data.

"Mons is a visionary," says Amos Bairoch at the Swiss Institute of
Bioinformatics in Geneva, a collaborator on the project and the creator of
Swiss-Prot. "This will be a revolution."

This will be a revolution.

Yet realizing the vision will be difficult. Top of the list of challenges is
persuading the community to get involved. Adding one's own data is likely to
be the biggest motivator ? Bairoch and Ashburner say they get several calls
a week asking for updates to databases, usually from researchers who want
their own papers added. Whether this will be enough to keep the database
fresh remains to be seen, given that employers and funders tend not to value
updating information highly.

 ADVERTISEMENT
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Wiki for Professionals will also have to ensure that additions don't just
reflect individual researchers' pet theories. Mons hopes scientists will
adopt entries relevant to their work and use automated systems to alert them
to changes, which they can then amend if necessary. The original data in
Swiss-Prot and other databases will also be protected.

The resource has been set up by Knewco, a scientific computing company based
in Rockville, Maryland, and co-founded by Mons. The firm raised around $2
million in private funding to pay for the initial effort, and says basic
access will be free. Revenue will be generated by charging drug firms and
other users for premium services, such as the option to run a private
version of the system incorporating proprietary data.9999999


-- 
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 jasonk at MIT.EDU  Thu Feb 15 21:06:14 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 15 Feb 2007 21:06:14 -0500
Subject: [OWW-Discuss] Fwd: Key biology databases go wiki (about time too!)
In-Reply-To: <cfd758050702151418h4ebf6fbbq6a2973759d4947a2@mail.gmail.com>
References: <cfd758050702151418h4ebf6fbbq6a2973759d4947a2@mail.gmail.com>
Message-ID: <7c085c480702151806p35f406d4v15f75bbb63a50118@mail.gmail.com>

It's a company doing this, so I wonder if the source for the tools will be
released for re-use -- take a look at the flash demo if you have a chance,
looks like this is definitely built on mediawiki.  And it looks pretty cool
in general.

http://www.wikiprofessional.info

Does anyone know if they will have to release their changes to the Mediawiki
source per the GNU license in this case?  Austin, I remember that you said
extensions didn't have to be released, but changes to the source would?

interesting stuff, I hope it turns out well.
jason

---------- Forwarded message ----------
From: John Cumbers <johncumbers at gmail.com>
Date: Feb 15, 2007 5:18 PM
Subject: [OWW-Discuss] Key biology databases go wiki (about time too!)
To: discuss at openwetware.org

News

*Nature* *445*, 691 (15 February 2007) | doi:10.1038/445691a; Published
online 14 February 2007
Key biology databases go wiki

Jim Giles
Top of page<http://www.nature.com/nature/journal/v445/n7129/full/445691a.html#top>
Abstract

Collaborative approach aims to keep pace with discoveries.

Barend Mons's first objective would be ambitious enough for most people: to
meld some of the most important biomedical databases into a single
information resource. But that's just the beginning. Mons, a
bioinformatician at the Erasmus Medical Centre in Rotterdam, the
Netherlands, also wants to apply the Wikipedia philosophy. He's inviting the
whole research community to help update a vast store of interlinked data. If
he and his colleagues can pull it off ? and even the project's advocates are
not sure they can ? they could transform the databases that are central to
the work of many life scientists.

A test version of the project, provisionally dubbed Wiki for
Professionals (http://www.wikiprofessional.info
), is due to launch in the next month. It already contains data from key
sources, such as protein information from Swiss-Prot and gene descriptions
from Gene Ontology. Over the past year, Mons's team has woven together these
and other archives to create what, from a user's point of view, seems to be
a single database. The page on the muscular-dystrophy protein dystrophin,
for example, contains data from Swiss-Prot together with links to disease
information from the US National Library of Medicine, as well as explanatory
text. Links to relevant publications in PubMed are also available.

Existing databases interlink to an extent, although the new resource is more
comprehensive. But the next stage is the really radical bit. Biomedical
research produces hundreds of thousands of papers a year, overwhelming
database curators. To clear this bottleneck, Mons and his colleagues are
allowing anyone to edit the entries, modifying and adding text and links as
new work is published.
[image: Key biology databases go wiki]

A. PASIEKA/SPL

Protein databases could be transformed by extra features.

That's an attractive proposition, say database administrators. Michael
Ashburner, a geneticist at the University of Cambridge, UK, helps run
FlyBase, a collection of gene data on the model organism *Drosophila
melanogaster*. The database receives around US$4 million a year from the US
National Institutes of Health and employs up to five full-time curators, but
still can't keep up with the relevant literature, says Ashburner, who is
working with Mons on the new project. "We have a list of around 12 journals
that we try to cover. Even that's tough."

Anyone motivated to register can curate Wiki for Professionals. Visitors to
the dystrophin entry, for example, can update almost any of the information
on the page, such as statements about the role of the protein in disease.
Users can also start new pages, and from later this year will be given the
option of creating pages for themselves, with links to relevant
publications. A final function, and the one that most excites Mons, is the
availability of text-mining software. This will allow users to probe links
between proteins, genes and disease that may be revealed only by comparing a
large number of papers and other data.

"Mons is a visionary," says Amos Bairoch at the Swiss Institute of
Bioinformatics in Geneva, a collaborator on the project and the creator of
Swiss-Prot. "This will be a revolution."

This will be a revolution.

Yet realizing the vision will be difficult. Top of the list of challenges is
persuading the community to get involved. Adding one's own data is likely to
be the biggest motivator ? Bairoch and Ashburner say they get several calls
a week asking for updates to databases, usually from researchers who want
their own papers added. Whether this will be enough to keep the database
fresh remains to be seen, given that employers and funders tend not to value
updating information highly.

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Wiki for Professionals will also have to ensure that additions don't just
reflect individual researchers' pet theories. Mons hopes scientists will
adopt entries relevant to their work and use automated systems to alert them
to changes, which they can then amend if necessary. The original data in
Swiss-Prot and other databases will also be protected.

The resource has been set up by Knewco, a scientific computing company based
in Rockville, Maryland, and co-founded by Mons. The firm raised around $2
million in private funding to pay for the initial effort, and says basic
access will be free. Revenue will be generated by charging drug firms and
other users for premium services, such as the option to run a private
version of the system incorporating proprietary data.9999999


-- 
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
_______________________________________________
OpenWetWare Discussion Mailing List
discuss at openwetware.org
http://mailman.mit.edu/mailman/listinfo/oww-discuss
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From amallet at MIT.EDU  Fri Feb 16 15:01:44 2007
From: amallet at MIT.EDU (Alex Mallet)
Date: Fri, 16 Feb 2007 15:01:44 -0500
Subject: [OWW-Discuss] Microsoft says OWW is anarchic :)
In-Reply-To: <7c085c480702151349qa6d87eay71790a1c91ab68f8@mail.gmail.com>
References: <7c085c480702151349qa6d87eay71790a1c91ab68f8@mail.gmail.com>
Message-ID: <20070216150144.2ajlqtm2lfk0skow@webmail.mit.edu>

Because, you know, at MS, there's absolutely no anarchy. Just drones 
marching in
perfect lockstep ;-)

-Alex.

> "Also OpenWetWare, a wiki, captures how experiments and done and
> shares this information with others, though it's quite anarchic."
> - Tony Hey, VP for tech computing at MS
>
> http://blogs.nature.com/wp/nascent/2007/02/tony_hey_visits_nature_1.html
>
> Hope he doesn't realize MS gave us $ ;)
> jason
>
> p.s Nature Network Boston has been joined by London and now lives at:
> http://network.nature.com/
> (though doesn't look like the features have changed much outside of
> forums being added).
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>




From ilyas at MIT.EDU  Thu Feb 22 14:15:58 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Thu, 22 Feb 2007 14:15:58 -0500
Subject: [OWW-Discuss] Wikipedia now a top site, thanks to Google
Message-ID: <45DDEBEE.90707@mit.edu>

http://education.zdnet.com/?p=865
http://www.technewsworld.com/story/UtCaXe53zvhuiK/Google-Paves-Way-for-Wikipedia-Breakthrough.xhtml

"In January, Wikipedia first appeared on comScore's top 10 hottest 
properties on the Web with 42.9 million unique visitors. That is thanks 
in large part to Google -- Wikipedia's page designs are optimized to be 
picked up by the search giant, which often lists a Wikipedia entry among 
the top five results for a term search."

With ~150,000 visitors in January, OWW has only 2-3 orders of magnitude 
to go toward the world domination :)

Ilya


From johncumbers at gmail.com  Sun Feb 25 15:37:08 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Sun, 25 Feb 2007 15:37:08 -0500
Subject: [OWW-Discuss] Screencast introducing OpenID
Message-ID: <cfd758050702251237g19c698b4g1334ca4cde2eba@mail.gmail.com>

A good screencast introducing  OpenID, a way to log-in to many websites,
http://simonwillison.net/2006/openid-screencast/

Austin, is this easily implementable for OWW?

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 skosuri at MIT.EDU  Sun Feb 25 16:21:55 2007
From: skosuri at MIT.EDU (Sri Kosuri)
Date: Sun, 25 Feb 2007 16:21:55 -0500
Subject: [OWW-Discuss] Screencast introducing OpenID
In-Reply-To: <cfd758050702251237g19c698b4g1334ca4cde2eba@mail.gmail.com>
References: <cfd758050702251237g19c698b4g1334ca4cde2eba@mail.gmail.com>
Message-ID: <2b0cb7a10702251321p59f0c04cwb06a2daca2e896d7@mail.gmail.com>

Technically, Austin has already implemented OpenID on OWW.  The
private test-bed wikis are using OpenID for verification off the
public OWW site.

Sri

On 2/25/07, John Cumbers <johncumbers at gmail.com> wrote:
> A good screencast introducing  OpenID, a way to log-in to many websites,
> http://simonwillison.net/2006/openid-screencast/
>
> Austin, is this easily implementable for OWW?
>
> 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
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


From johncumbers at gmail.com  Sun Feb 25 17:08:59 2007
From: johncumbers at gmail.com (John Cumbers)
Date: Sun, 25 Feb 2007 17:08:59 -0500
Subject: [OWW-Discuss] Screencast introducing OpenID
In-Reply-To: <2b0cb7a10702251321p59f0c04cwb06a2daca2e896d7@mail.gmail.com>
References: <cfd758050702251237g19c698b4g1334ca4cde2eba@mail.gmail.com>
	<2b0cb7a10702251321p59f0c04cwb06a2daca2e896d7@mail.gmail.com>
Message-ID: <cfd758050702251408x73e494bbg4420012b23e84943@mail.gmail.com>

So to get around the opposition to the reddit adverts, what I want to work
on is an implementation of http://www.pligg.com/ (Digg clone) for OWW, and
hook them together with OpenID (which pligg is about to implement I think
http://www.pligg.com/forum/archive/index.php?t-3600.html)  so you don't have
to log-in twice.

I think we could start it off as just being able to pligg oww pages and see
how it develops.

any thoughts?

cheers,
John


On 2/25/07, Sri Kosuri <skosuri at mit.edu> wrote:
>
> Technically, Austin has already implemented OpenID on OWW.  The
> private test-bed wikis are using OpenID for verification off the
> public OWW site.
>
> Sri
>
> On 2/25/07, John Cumbers < johncumbers at gmail.com> wrote:
> > A good screencast introducing  OpenID, a way to log-in to many websites,
> > http://simonwillison.net/2006/openid-screencast/
> >
> > Austin, is this easily implementable for OWW?
> >
> > 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
> > _______________________________________________
> > 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  Wed Feb 28 23:54:17 2007
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Wed, 28 Feb 2007 23:54:17 -0500
Subject: [OWW-Discuss] alternative workspaces
Message-ID: <45E65C79.8040907@mit.edu>

http://www.businessweek.com/smallbiz/content/feb2007/sb20070226_761145.htm

This article caught my eye because they use a wiki for collaboration:
http://coworking.pbwiki.com/

and there's another example of a virtual collaboration space - in Second 
Life:
http://slurl.com/secondlife/