From await at genetics.med.harvard.edu  Sun Mar  2 15:20:03 2008
From: await at genetics.med.harvard.edu (Alexander Wait Zaranek)
Date: Sun, 2 Mar 2008 15:20:03 -0500
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <8b89c0c0802261715v7c54fa70l12b7419e960f9303@mail.gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>
	<200802261703.53571.kanzure@gmail.com>
	<8b89c0c0802261715v7c54fa70l12b7419e960f9303@mail.gmail.com>
Message-ID: <8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>

On Tue, Feb 26, 2008 at 8:15 PM, Alexander Wait Zaranek
<await at genetics.med.harvard.edu> wrote:
> On Tue, Feb 26, 2008 at 6:03 PM, Bryan Bishop <kanzure at gmail.com> wrote:
>  >  Encourage people to set up servers and backups
>  >  of the wiki all over the place, with central aggregation nodes to make
>  >  sure all of the updates are propagated.
>  >
>  actually, i wanted to offer to do this last steering committee
>  meeting.  Anyone else doing it already?   We could also run a mysql
>  slave so edits were up to the minute and not just a dump.  Setup a
>  dedicated virtual machine on one of our clusters?   I'd love to see it
>  happen...
>
"Feb. 28, 2008. OpenWetWare.org sustained a database failure on Feb.
28, but is back online. We're deeply sorry for any inconvenience this
may have caused. We'll update the community on what we've done to
recover and add more reliability to our procedures and infrastructure.
Documents edited or created in www.OpenWetWare.org on Feb 28 between
4:00 AM EST to 7:00 PM EST will need to be updated or re-entered."

So, it's never ideal to work on master-slave replication *after* a
database failure but there's no time like the present.    There's a
bunch of talented freelance admins around the Church lab that could
help with this.  And we have the bandwidth/infrastructure too.

How can we help?
Sasha


From bill.altmail at gmail.com  Sun Mar  2 16:32:35 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 2 Mar 2008 16:32:35 -0500
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>
	<200802261703.53571.kanzure@gmail.com>
	<8b89c0c0802261715v7c54fa70l12b7419e960f9303@mail.gmail.com>
	<8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
Message-ID: <26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>

I'd be glad to discuss options tomorrow (Monday).

There's a split between the way a wiki can be exported and the way the
database is managed. Since we currently use MySQL 4 with a single server,
there are some limitations on what we can do, yet there are options re:
replication we've not explored.  The  MediaWiki  server also affords more
options we can look at as well.

It turned out that we did have a little bit of luck in that the backup
provided by our hosting company, Rackspace, was only a binary file backup
and not a mysql dump. The backup file images for the database were in good
shape. This can be a problem: this binary backup can result in database
corruption since the size of some of the files is so large that there are
seconds or more of time between the start and end of the file copy within
which transactions being written to the file can result in an inconsistent
backup image. This is an optional service we didn't know Rackspace hadn't
enabled  when we moved to our current server.

I immediately deployed a script I've used before, automysqlbackup.sh, as
soon as the database was stable. This script is reliably creating static sql
backups on a nightly basis. We're also enabling the binary log option to
allow for intra-day incremental backup in addition to the nightly full
database backup. This means that we'll be able to reload and be up and
running in minutes the next time. I know this is little solace to people who
lose information; we still want to maximize the amount of data that can be
recovered, hopefully to the point of losing no data.

At the MediaWiki level, we externally back up all of the wiki pages in the
database on a nightly basis. This is a disconnected backup from the SQL
dump. This didn't help us since the backup takes place around midnight,
before the Rackspace backup we reloaded from.

Using the Mediawiki API, we can do incremental exports of all new pages on a
regular basis. This would allow us to recover the MediaWiki application
level pages via a simple import via a special page. The nice thing about the
API is that it can be run on a remote system, thus allowing us to provide
for a constant auto-import of the pages into another server. It's not clear
how we would manage the process of rolling the wiki onto a remote system for
operational purposes. But we would never lose the contents of the database
up until the time it went down. To implement this, we need to write a script
that uses the mediawiki api. I'll be glad to provide details to anyone
interested in working with me to do this. I can provide bindings in Python,
Perl, C#, or PHP for this.

We currently have a full backup of all of the images and attachments
uploaded. None were lost last week. But the database records pointing to
them are only current as of around 4:00 AM on the 28th. Since these files
are in a set of well-known directories, rsync can work the same way the page
collection works. I'll have this set up today on an MIT system. We can sync
on an hourly basis to keep the images up to date.

We have no problem with the performance of Rackspace in this situation. They
responded to our request within 15 minutes. Since we had to reload all of
the databases for the private wikis in addition to the main wiki (the MySQL
INNODB tables use a single large binary file shared by all databases), I
also needed to do full backups of all of the other databases, load in the
4:00 AM database image, then load in the backups to get them back to the
10:00 PM state they were in. We didn't lose data in any applications except
for the main OpenWetWare wiki.

Because we use OpenID for access control on all of the private wiki's, they
were inaccessible until the main wiki came back up.

The blog was completely disconnected from the OpenWetWare database. Because
of this, there was no effect on it at all except for the need to swap in the
new database image and then refresh it with the 10:00 PM info when it the
database server was re-enabled.

Let's see what we can do to improve the system. As I mentioned, I'm open to
suggestions but we're already hard at work hardening the system. I'm not
saying this to appear disinterested in external assistance; we need to do
what we know we can immediately.

Thanks.

Bill Flanagan


On Sun, Mar 2, 2008 at 3:20 PM, Alexander Wait Zaranek <
await at genetics.med.harvard.edu> wrote:

> On Tue, Feb 26, 2008 at 8:15 PM, Alexander Wait Zaranek
> <await at genetics.med.harvard.edu> wrote:
> > On Tue, Feb 26, 2008 at 6:03 PM, Bryan Bishop <kanzure at gmail.com> wrote:
> >  >  Encourage people to set up servers and backups
> >  >  of the wiki all over the place, with central aggregation nodes to
> make
> >  >  sure all of the updates are propagated.
> >  >
> >  actually, i wanted to offer to do this last steering committee
> >  meeting.  Anyone else doing it already?   We could also run a mysql
> >  slave so edits were up to the minute and not just a dump.  Setup a
> >  dedicated virtual machine on one of our clusters?   I'd love to see it
> >  happen...
> >
> "Feb. 28, 2008. OpenWetWare.org sustained a database failure on Feb.
> 28, but is back online. We're deeply sorry for any inconvenience this
> may have caused. We'll update the community on what we've done to
> recover and add more reliability to our procedures and infrastructure.
> Documents edited or created in www.OpenWetWare.org on Feb 28 between
> 4:00 AM EST to 7:00 PM EST will need to be updated or re-entered."
>
> So, it's never ideal to work on master-slave replication *after* a
> database failure but there's no time like the present.    There's a
> bunch of talented freelance admins around the Church lab that could
> help with this.  And we have the bandwidth/infrastructure too.
>
> How can we help?
> Sasha
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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From bill.altmail at gmail.com  Sun Mar  2 16:32:35 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 2 Mar 2008 16:32:35 -0500
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>
	<200802261703.53571.kanzure@gmail.com>
	<8b89c0c0802261715v7c54fa70l12b7419e960f9303@mail.gmail.com>
	<8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
Message-ID: <26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>

I'd be glad to discuss options tomorrow (Monday).

There's a split between the way a wiki can be exported and the way the
database is managed. Since we currently use MySQL 4 with a single server,
there are some limitations on what we can do, yet there are options re:
replication we've not explored.  The  MediaWiki  server also affords more
options we can look at as well.

It turned out that we did have a little bit of luck in that the backup
provided by our hosting company, Rackspace, was only a binary file backup
and not a mysql dump. The backup file images for the database were in good
shape. This can be a problem: this binary backup can result in database
corruption since the size of some of the files is so large that there are
seconds or more of time between the start and end of the file copy within
which transactions being written to the file can result in an inconsistent
backup image. This is an optional service we didn't know Rackspace hadn't
enabled  when we moved to our current server.

I immediately deployed a script I've used before, automysqlbackup.sh, as
soon as the database was stable. This script is reliably creating static sql
backups on a nightly basis. We're also enabling the binary log option to
allow for intra-day incremental backup in addition to the nightly full
database backup. This means that we'll be able to reload and be up and
running in minutes the next time. I know this is little solace to people who
lose information; we still want to maximize the amount of data that can be
recovered, hopefully to the point of losing no data.

At the MediaWiki level, we externally back up all of the wiki pages in the
database on a nightly basis. This is a disconnected backup from the SQL
dump. This didn't help us since the backup takes place around midnight,
before the Rackspace backup we reloaded from.

Using the Mediawiki API, we can do incremental exports of all new pages on a
regular basis. This would allow us to recover the MediaWiki application
level pages via a simple import via a special page. The nice thing about the
API is that it can be run on a remote system, thus allowing us to provide
for a constant auto-import of the pages into another server. It's not clear
how we would manage the process of rolling the wiki onto a remote system for
operational purposes. But we would never lose the contents of the database
up until the time it went down. To implement this, we need to write a script
that uses the mediawiki api. I'll be glad to provide details to anyone
interested in working with me to do this. I can provide bindings in Python,
Perl, C#, or PHP for this.

We currently have a full backup of all of the images and attachments
uploaded. None were lost last week. But the database records pointing to
them are only current as of around 4:00 AM on the 28th. Since these files
are in a set of well-known directories, rsync can work the same way the page
collection works. I'll have this set up today on an MIT system. We can sync
on an hourly basis to keep the images up to date.

We have no problem with the performance of Rackspace in this situation. They
responded to our request within 15 minutes. Since we had to reload all of
the databases for the private wikis in addition to the main wiki (the MySQL
INNODB tables use a single large binary file shared by all databases), I
also needed to do full backups of all of the other databases, load in the
4:00 AM database image, then load in the backups to get them back to the
10:00 PM state they were in. We didn't lose data in any applications except
for the main OpenWetWare wiki.

Because we use OpenID for access control on all of the private wiki's, they
were inaccessible until the main wiki came back up.

The blog was completely disconnected from the OpenWetWare database. Because
of this, there was no effect on it at all except for the need to swap in the
new database image and then refresh it with the 10:00 PM info when it the
database server was re-enabled.

Let's see what we can do to improve the system. As I mentioned, I'm open to
suggestions but we're already hard at work hardening the system. I'm not
saying this to appear disinterested in external assistance; we need to do
what we know we can immediately.

Thanks.

Bill Flanagan


On Sun, Mar 2, 2008 at 3:20 PM, Alexander Wait Zaranek <
await at genetics.med.harvard.edu> wrote:

> On Tue, Feb 26, 2008 at 8:15 PM, Alexander Wait Zaranek
> <await at genetics.med.harvard.edu> wrote:
> > On Tue, Feb 26, 2008 at 6:03 PM, Bryan Bishop <kanzure at gmail.com> wrote:
> >  >  Encourage people to set up servers and backups
> >  >  of the wiki all over the place, with central aggregation nodes to
> make
> >  >  sure all of the updates are propagated.
> >  >
> >  actually, i wanted to offer to do this last steering committee
> >  meeting.  Anyone else doing it already?   We could also run a mysql
> >  slave so edits were up to the minute and not just a dump.  Setup a
> >  dedicated virtual machine on one of our clusters?   I'd love to see it
> >  happen...
> >
> "Feb. 28, 2008. OpenWetWare.org sustained a database failure on Feb.
> 28, but is back online. We're deeply sorry for any inconvenience this
> may have caused. We'll update the community on what we've done to
> recover and add more reliability to our procedures and infrastructure.
> Documents edited or created in www.OpenWetWare.org on Feb 28 between
> 4:00 AM EST to 7:00 PM EST will need to be updated or re-entered."
>
> So, it's never ideal to work on master-slave replication *after* a
> database failure but there's no time like the present.    There's a
> bunch of talented freelance admins around the Church lab that could
> help with this.  And we have the bandwidth/infrastructure too.
>
> How can we help?
> Sasha
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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From kanzure at gmail.com  Sun Mar  2 17:21:23 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Sun, 2 Mar 2008 16:21:23 -0600
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>
	<8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
	<26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>
Message-ID: <200803021621.23740.kanzure@gmail.com>

Bill, may I have a link to a backup gzip of OWW?

- Bryan
________________________________________
Bryan Bishop
http://heybryan.org/


From bill.altmail at gmail.com  Sun Mar  2 17:32:16 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 2 Mar 2008 17:32:16 -0500
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <200803021621.23740.kanzure@gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>
	<8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>
	<26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>
	<200803021621.23740.kanzure@gmail.com>
Message-ID: <26428aaa0803021432u6c119bd6v3271ccdc54634628@mail.gmail.com>

I'm not the right person to ask. I'd suggest asking Lorrie or the board.

Thanks.

B.


On Sun, Mar 2, 2008 at 5:21 PM, Bryan Bishop <kanzure at gmail.com> wrote:

> Bill, may I have a link to a backup gzip of OWW?
>
> - Bryan
> ________________________________________
> Bryan Bishop
> http://heybryan.org/
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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From ilyas at MIT.EDU  Mon Mar  3 14:32:50 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Mon, 03 Mar 2008 14:32:50 -0500
Subject: [OWW-Discuss] Why $0.00 Is the Future of Business
In-Reply-To: <26428aaa0803021432u6c119bd6v3271ccdc54634628@mail.gmail.com>
References: <87ve4by8w7.fsf@nitsua.mit.edu>	<8b89c0c0803021220h38bed8f0ud9778ea5dcb5f07a@mail.gmail.com>	<26428aaa0803021332i5dea43c7r546cdefb9387dc79@mail.gmail.com>	<200803021621.23740.kanzure@gmail.com>
	<26428aaa0803021432u6c119bd6v3271ccdc54634628@mail.gmail.com>
Message-ID: <47CC5262.2020801@mit.edu>

Bryan,

You can get a dump of all the pages (with their histories) from here: 
http://openwetware.org/wiki/OpenWetWare:Data_dumps.  We don't yet 
provide a way to obtain the uploaded files in bulk.

Ilya


Bill F wrote:
> I'm not the right person to ask. I'd suggest asking Lorrie or the board.
> 
> Thanks.
> 
> B.
> 
> 
> On Sun, Mar 2, 2008 at 5:21 PM, Bryan Bishop <kanzure at gmail.com 
> <mailto:kanzure at gmail.com>> wrote:
> 
>     Bill, may I have a link to a backup gzip of OWW?
> 
>     - Bryan
>     ________________________________________
>     Bryan Bishop
>     http://heybryan.org/
>     _______________________________________________
>     OpenWetWare Discussion Mailing List
>     discuss at openwetware.org <mailto:discuss at openwetware.org>
>     http://mailman.mit.edu/mailman/listinfo/oww-discuss
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss


From austin at csail.mit.edu  Tue Mar  4 11:54:07 2008
From: austin at csail.mit.edu (Austin Che)
Date: Tue, 04 Mar 2008 11:54:07 -0500
Subject: [OWW-Discuss] methods
Message-ID: <87tzjmwhu8.fsf@nitsua.mit.edu>


    Opportunity for OWW to get into publishing methods?
    
Where did the scientific method go?	pp28 - 29
Michela Noseda and Gary R McLean
doi:10.1038/nbt0108-28
http://ealerts.nature.com/cgi-bin24/DM/y/eiZ50SprR70HjC0Bk2S0EG

Response to Where did the scientific method go?	p29
doi:10.1038/nbt0108-29a
http://ealerts.nature.com/cgi-bin24/DM/y/eiZ50SprR70HjC0Bk2T0EH

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


From tk at csail.mit.edu  Fri Mar  7 13:05:01 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Fri, 7 Mar 2008 13:05:01 -0500
Subject: [OWW-Discuss] You know open source publishing has made it when the
	Wall Street Journal is on board
Message-ID: <ddf67656a7f44a354a36b87f3ad0845d@csail.mit.edu>

http://online.wsj.com/article/SB120486540450119149.html



From austin at csail.mit.edu  Sun Mar  9 10:48:03 2008
From: austin at csail.mit.edu (Austin Che)
Date: Sun, 09 Mar 2008 10:48:03 -0400
Subject: [OWW-Discuss] [Oww-Feedback] Contact us. (from Gunther
	Eysenbach)
In-Reply-To: <20080309124645.B7A613D20A0@mail.openwetware.org> (OpenWetWare
	Feedback Form on OpenWetWare's message of "Sun,
	9 Mar 2008 08:46:45 -0400 (EDT)")
References: <20080309124645.B7A613D20A0@mail.openwetware.org>
Message-ID: <87tzjglzrw.fsf@nitsua.mit.edu>


    Gunther, this looks like a great idea! We've definitely had people
    who had problems with reviewers when trying to cite pages on the
    wiki. The site mentions that it can generate a doi for a page on
    request, which is what we've been talking about for a while. It
    mentions this feature is available to "premium members." What does
    this entail?
    
> Regarding your section "Cite this page", please consider to recommend
> use of WebCite (http://www.webcitation.org) to archive the pages
> before they are cited. URLs and the content changes. Taking a snapshot
> with WebCite ensures not only long-term digital preservation, but also
> that readers who access cited material still see exactly the same
> version as the citing author.
>
> The more elgant solution would be to add (as described on
> http://www.webcitation.org/archive) a dynamic link to the left
> sidebar, saying "Cite this page!", linking to
> http://www.webcitation.org/archive?url=openwetware.org/wiki/THISURL&title=TITLE_OF_PAGE&author=AUTHORS&date=TODAY&source=OA+Librarian&subject=SUBJECT
>
> (plug in the variables as appropiate).
>
> This will link to the archiving form, which will ultimately also give
> citing authors a citation suggestion, including the WebCite ID.

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


From jasonk at MIT.EDU  Mon Mar 10 10:13:03 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 10 Mar 2008 10:13:03 -0400
Subject: [OWW-Discuss] reminder: SC meeting TH (3/13) at Noon-1pm EST
Message-ID: <7c085c480803100713ld47317ct6bf8246296daac4d@mail.gmail.com>

hey SC,

Reminder that the Steering Committee meeting is this TH (3/13) at Noon
EST. Number is 617-452-5208 or you can join the chat.  Anyone is
welcome to call in, new folks encouraged!

Also, as a reminder, if you have a nomination for the SC coordinator
spot, please send it to me.

Chairs fill in your reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_March_2008

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

lots of items on the agenda this month, should be a good meeting :)

Thanks!
jason


From jasonk at MIT.EDU  Mon Mar 10 10:13:03 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 10 Mar 2008 10:13:03 -0400
Subject: [OWW-Discuss] reminder: SC meeting TH (3/13) at Noon-1pm EST
Message-ID: <7c085c480803100713ld47317ct6bf8246296daac4d@mail.gmail.com>

hey SC,

Reminder that the Steering Committee meeting is this TH (3/13) at Noon
EST. Number is 617-452-5208 or you can join the chat.  Anyone is
welcome to call in, new folks encouraged!

Also, as a reminder, if you have a nomination for the SC coordinator
spot, please send it to me.

Chairs fill in your reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_March_2008

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

lots of items on the agenda this month, should be a good meeting :)

Thanks!
jason


From wjf42 at MIT.EDU  Mon Mar 10 17:33:55 2008
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Mon, 10 Mar 2008 17:33:55 -0400
Subject: [OWW-Discuss] Giving OWW search a haircut.
Message-ID: <26428aaa0803101433r690e8bfanb1e9264c904e21e5@mail.gmail.com>

I've removed two of the three buttons from the sidebar search, "Go" and
"Search from here". These buttons seem to get in the way of search. I didn't
do this unilaterally. Several people have requested this and I finally got
around to it.

Nothing is final. If anyone has ideas on how to make search better, let me
know. We're always open to trying things out.

Thanks.

Bill Flanagan
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From enobarber at gmail.com  Tue Mar 11 15:18:51 2008
From: enobarber at gmail.com (Reid Williams)
Date: Tue, 11 Mar 2008 12:18:51 -0700
Subject: [OWW-Discuss] TalkShoe for recorded conference calls
Message-ID: <B1CFDF4B-8127-4E78-9E05-E1B32FD8075C@gmail.com>

Http://www.talkshoe.com let's you host, join live, or listen to  
recorded conference calls. Might be good for SC meetings or community  
discussions that warrant more than wiki comments or text chats.


-reid


From rvidal at openwetware.org  Tue Mar 11 20:23:39 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Tue, 11 Mar 2008 20:23:39 -0400
Subject: [OWW-Discuss] Genome Projector
Message-ID: <213fc43b0803111723t25f980a1v5b76538859943766@mail.gmail.com>

This looks pretty interesting. Using the Google Maps API as a zooming tool.
http://www.g-language.org/GenomeProjector/

-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From rvidal at openwetware.org  Wed Mar 12 00:45:30 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Wed, 12 Mar 2008 00:45:30 -0400
Subject: [OWW-Discuss] Genome Projector
Message-ID: <213fc43b0803112145q5f268ee4od829302b40805bd0@mail.gmail.com>

This looks pretty interesting. It uses the Google Maps API as a zooming tool
for bacterial genomic maps (320 genomes available)
http://www.g-language.org/GenomeProjector/


-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From dan.bolser at gmail.com  Wed Mar 12 07:21:43 2008
From: dan.bolser at gmail.com (dan.bolser@gmail.com)
Date: Wed, 12 Mar 2008 11:21:43 +0000
Subject: [OWW-Discuss] dan.bolser has invited you to Spokeo
Message-ID: <47d7bcc7a6ff_47881c1766dabf0842839@mongrel2.tmail>

Hi discuss at openwetware.org,<br/><br/> 

dan.bolser at gmail.com has invited you to Spokeo,
which finds your friends' updates across the Web.

On average, Spokeo finds 87 friends across 30 different social
networks. See what Spokeo can find for you now!

Click http://www.spokeo.com/public/join?c=6ac90f0c2cccd369b0ca1177e3324d8ca6a9c356 to accept your invitation.



-----
This invitation was sent with dan.bolser's approval.
If you wish to opt out of all future emails, go to http://www.spokeo.com/optout?c=d495256575751525349

Copyright (c) 2008 Spokeo, Inc. All rights reserved.
1685 Plymouth Street #200, Mountain View, CA 94043
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From dan.bolser at gmail.com  Wed Mar 12 07:23:20 2008
From: dan.bolser at gmail.com (dan.bolser@gmail.com)
Date: Wed, 12 Mar 2008 11:23:20 +0000
Subject: [OWW-Discuss] dan.bolser has invited you to Spokeo
Message-ID: <47d7bd288afab_47881c1766dabf08881b4@mongrel2.tmail>

Hi oww-discuss at mit.edu,<br/><br/> 

dan.bolser at gmail.com has invited you to Spokeo,
which finds your friends' updates across the Web.

On average, Spokeo finds 87 friends across 30 different social
networks. See what Spokeo can find for you now!

Click http://www.spokeo.com/public/join?c=4da5ea20fdbe418710ad376cdd5e6715e6b0d7b9 to accept your invitation.



-----
This invitation was sent with dan.bolser's approval.
If you wish to opt out of all future emails, go to http://www.spokeo.com/optout?c=o495256575753494949

Copyright (c) 2008 Spokeo, Inc. All rights reserved.
1685 Plymouth Street #200, Mountain View, CA 94043
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From jasonk at MIT.EDU  Wed Mar 12 09:54:21 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Wed, 12 Mar 2008 09:54:21 -0400
Subject: [OWW-Discuss] blogs discussion / SC meeting tomorrow.
Message-ID: <7c085c480803120654q1b4fdb9bk4fb5250ccdc7cc2e@mail.gmail.com>

One of the topics for the next SC meeting is "what's the point of the
OWW blogs?"  We started these as an undirected experiment a bit back,
and as a community we need to decide what we're trying to accomplish.
Why should we encourage scientists to use OWW blogs rather than just
host their own blog on blogger?  Is there a larger mission?  Should we
continue using resources to support the blogs?

I started a page here to seed discussion before the SC meeting
tomorrow (@ Noon EST, 617-452-5208).  There are some links to other
info sources there, too, please read/add/edit.

http://openwetware.org/wiki/OpenWetWare:Blogs

Please post comments to the list or on the wiki page!

thanks,
jason

p.s.
chairs add reports here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_March_2008

add items to for next SC meeting here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting


From austin at csail.mit.edu  Wed Mar 12 14:25:17 2008
From: austin at csail.mit.edu (Austin Che)
Date: Wed, 12 Mar 2008 14:25:17 -0400
Subject: [OWW-Discuss] OWW SC jabber group
Message-ID: <87bq5jiyuq.fsf@nitsua.mit.edu>


    There's a group called "OWW SC" on jabber now. All users that log
    in to jabber will automatically get this group and the members in
    that group on their buddy list. I think this is a pretty good way
    for new people to find help or to communicate with sc people. If
    you want to be part of the group, let me know.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From ilyas at MIT.EDU  Thu Mar 13 16:18:45 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Thu, 13 Mar 2008 16:18:45 -0400
Subject: [OWW-Discuss] OWW SC jabber group
In-Reply-To: <87bq5jiyuq.fsf@nitsua.mit.edu>
References: <87bq5jiyuq.fsf@nitsua.mit.edu>
Message-ID: <47D98C25.1030600@mit.edu>

This is a great alternative to the "lounge" chat room.

Austin Che wrote:
>     There's a group called "OWW SC" on jabber now. All users that log
>     in to jabber will automatically get this group and the members in
>     that group on their buddy list. I think this is a pretty good way
>     for new people to find help or to communicate with sc people. If
>     you want to be part of the group, let me know.
>     


From ilyas at MIT.EDU  Fri Mar 14 18:13:19 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Fri, 14 Mar 2008 18:13:19 -0400
Subject: [OWW-Discuss] dan.bolser has invited you to Spokeo
In-Reply-To: <47d7bcc7a6ff_47881c1766dabf0842839@mongrel2.tmail>
References: <47d7bcc7a6ff_47881c1766dabf0842839@mongrel2.tmail>
Message-ID: <47DAF87F.1050701@mit.edu>

"Spokeo is a hyper-aggregator that syndicates blogs, photos, and videos 
from social networks and web feeds."
http://en.wikipedia.org/wiki/Spokeo

I've just tried it and it looks pretty cool. It's a kind of a feed 
reader for social networks and sites with social network components.  I 
think this is an example of integration that Google's OpenSocial API is 
supposed to enable.  It would be interesting to figure out if/how it 
could be leveraged by OWW.


dan.bolser at gmail.com wrote:
> Hi discuss at openwetware.org,
> 
> dan.bolser at gmail.com <mailto:dan.bolser at gmail.com> has invited you to 
> Spokeo,
> which finds your friends' updates across the Web.
> 
> On average, Spokeo finds 87 friends across 30 different social
> networks. See what Spokeo can find for you now!
> 
> Click here to accept your invitation 
> <http://www.spokeo.com/public/join?c=6ac90f0c2cccd369b0ca1177e3324d8ca6a9c356> 
> 
> 
> 
> ------------------------------------------------------------------------
> This invitation was sent with dan.bolser's approval.
> If you wish to opt out of all future emails, click here 
> <http://www.spokeo.com/optout?c=d495256575751525349>.
> 
> Copyright ? 2008 Spokeo, Inc. All rights reserved.
> 1685 Plymouth Street #200, Mountain View, CA 94043
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss


From johncumbers at gmail.com  Sun Mar 16 00:19:43 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Sun, 16 Mar 2008 00:19:43 -0400
Subject: [OWW-Discuss] Genome Projector
In-Reply-To: <213fc43b0803112145q5f268ee4od829302b40805bd0@mail.gmail.com>
References: <213fc43b0803112145q5f268ee4od829302b40805bd0@mail.gmail.com>
Message-ID: <cfd758050803152119nc69328byeead0e7657fea65d@mail.gmail.com>

that's awesome...

On Wed, Mar 12, 2008 at 12:45 AM, Ricardo Vidal <rvidal at openwetware.org>
wrote:

> This looks pretty interesting. It uses the Google Maps API as a zooming
> tool for bacterial genomic maps (320 genomes available)
>
> http://www.g-language.org/GenomeProjector/
>
>
> --
> Ricardo Vidal
> rvidal at gmail.com | http://my.biotechlife.net
> http://www.openwetware.org - Share your Science
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From bill.altmail at gmail.com  Sun Mar 16 14:37:47 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 16 Mar 2008 14:37:47 -0400
Subject: [OWW-Discuss] Monthly development updates posted
Message-ID: <26428aaa0803161137v758c2874sa751f649631d320b@mail.gmail.com>

This still needs to be prioritized but here's what we're working on. Given
the late timing of this month's Board and Steering Committee meeting, most
of the items are already underway. I'll update the items as they're
completed.

Link to page:

http://openwetware.org/wiki/OpenWetWare:Software/Milestones/March_2008

Thanks!

Bill Flanagan
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From skosuri at gmail.com  Mon Mar 17 00:56:34 2008
From: skosuri at gmail.com (Sriram Kosuri)
Date: Mon, 17 Mar 2008 00:56:34 -0400
Subject: [OWW-Discuss] perhaps we should send letter of support?
Message-ID: <2b0cb7a10803162156u48c11de5r108e324db3e54734@mail.gmail.com>

http://www.newscientist.com/article/mg19726473.300-physicists-slam-publishers-over-wikipedia-ban.html
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From austin at csail.mit.edu  Mon Mar 17 11:22:52 2008
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 17 Mar 2008 11:22:52 -0400
Subject: [OWW-Discuss] invitrogen foundation
Message-ID: <87k5k1bcj7.fsf@nitsua.mit.edu>


    Just saw this:
    http://www.invitrogen.com/content.cfm?pageid=12185
    
    Invitrogen apparently has a foundation with money to give for
    "strengthening the pipeline of future life scientists." It is
    explicitly targeted at not-for-profit organizations. Given the
    number of not-for-profit organizations in the life sciences, it
    seems that if OWW made a proposal, there'd be a pretty good chance
    of getting some funding.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From koeris at bu.edu  Mon Mar 17 11:44:04 2008
From: koeris at bu.edu (Koeris, Michael, Sandor)
Date: Mon, 17 Mar 2008 11:44:04 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <87k5k1bcj7.fsf@nitsua.mit.edu>
References: <87k5k1bcj7.fsf@nitsua.mit.edu>
Message-ID: <38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>

I'm all for writing up a proposal, seems like they are looking for K-12
stuff though. Maybe if we play up the global reach, protocol repository
(for CC instructors) and the video lab tours as outreach mechanisms,
we'll stand a good chance.

Mike


Guidelines:
The Invitrogen Foundation is committed to strengthening the pipeline of
future life scientists. Funding and partnership opportunities that
address the following areas of interest will be considered:

    * Life science education for students, beginning at the high school
level
    * Professional development for high school and community college
instructors

------
    * Programs that are broad in scope and reach students and/or
educators from a variety of geographic locations are preferred.
------

    * Special consideration is also given to programs that target groups
traditionally underrepresented in the life sciences, including but not
limited to women and diverse populations

Through outreach and education, the Invitrogen Foundation also seeks to
increase society's understanding of the life sciences and their critical
role in addressing global issues. Programs and initiatives that address
these objectives are preferred:

    * Educating community leaders about the importance of life science,
particularly as it relates to education, economic strength and global
health
    * Activities and initiatives that demonstrate thought leadership
    * Museum and traveling exhibits, community events and public
lectures, that reach a broad, cross-section of the population
    * Special consideration is also given to programs that have a global
dimension 



-----Original Message-----
From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
On Behalf Of Austin Che
Sent: Monday, March 17, 2008 11:23 AM
To: discuss at openwetware.org
Subject: [OWW-Discuss] invitrogen foundation


    Just saw this:
    http://www.invitrogen.com/content.cfm?pageid=12185
    
    Invitrogen apparently has a foundation with money to give for
    "strengthening the pipeline of future life scientists." It is
    explicitly targeted at not-for-profit organizations. Given the
    number of not-for-profit organizations in the life sciences, it
    seems that if OWW made a proposal, there'd be a pretty good chance
    of getting some funding.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899
_______________________________________________
OpenWetWare Discussion Mailing List
discuss at openwetware.org
http://mailman.mit.edu/mailman/listinfo/oww-discuss



From nkuldell at MIT.EDU  Mon Mar 17 11:56:16 2008
From: nkuldell at MIT.EDU (natalie kuldell)
Date: Mon, 17 Mar 2008 11:56:16 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>
References: <87k5k1bcj7.fsf@nitsua.mit.edu>
	<38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>
Message-ID: <p06230908c4044402f964@[10.0.1.197]>

It seems like the goal of their program, at least currently, is to 
promote general scientific literacy.
See:  http://biz.yahoo.com/bw/080221/20080221005076.html?.v=1

I had a talk with the Invitrogen Foundation folks last week and have 
requested info on previously funded applications. That list may give 
a better sense of what kinds of synthetic biology projects stand a 
chance. I'm happy to pass along the information I get back.

Natalie



>I'm all for writing up a proposal, seems like they are looking for K-12
>stuff though. Maybe if we play up the global reach, protocol repository
>(for CC instructors) and the video lab tours as outreach mechanisms,
>we'll stand a good chance.
>
>Mike
>
>
>Guidelines:
>The Invitrogen Foundation is committed to strengthening the pipeline of
>future life scientists. Funding and partnership opportunities that
>address the following areas of interest will be considered:
>
>     * Life science education for students, beginning at the high school
>level
>     * Professional development for high school and community college
>instructors
>
>------
>     * Programs that are broad in scope and reach students and/or
>educators from a variety of geographic locations are preferred.
>------
>
>     * Special consideration is also given to programs that target groups
>traditionally underrepresented in the life sciences, including but not
>limited to women and diverse populations
>
>Through outreach and education, the Invitrogen Foundation also seeks to
>increase society's understanding of the life sciences and their critical
>role in addressing global issues. Programs and initiatives that address
>these objectives are preferred:
>
>     * Educating community leaders about the importance of life science,
>particularly as it relates to education, economic strength and global
>health
>     * Activities and initiatives that demonstrate thought leadership
>     * Museum and traveling exhibits, community events and public
>lectures, that reach a broad, cross-section of the population
>     * Special consideration is also given to programs that have a global
>dimension
>
>
>
>-----Original Message-----
>From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
>On Behalf Of Austin Che
>Sent: Monday, March 17, 2008 11:23 AM
>To: discuss at openwetware.org
>Subject: [OWW-Discuss] invitrogen foundation
>
>
>     Just saw this:
>     http://www.invitrogen.com/content.cfm?pageid=12185
>    
>     Invitrogen apparently has a foundation with money to give for
>     "strengthening the pipeline of future life scientists." It is
>     explicitly targeted at not-for-profit organizations. Given the
>     number of not-for-profit organizations in the life sciences, it
>     seems that if OWW made a proposal, there'd be a pretty good chance
>     of getting some funding.
>    
>--
>Austin Che           <austin at csail.mit.edu>          (617)253-5899
>_______________________________________________
>OpenWetWare Discussion Mailing List
>discuss at openwetware.org
>http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>_______________________________________________
>OpenWetWare Discussion Mailing List
>discuss at openwetware.org
>http://mailman.mit.edu/mailman/listinfo/oww-discuss
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From ilyas at MIT.EDU  Mon Mar 17 17:33:00 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Mon, 17 Mar 2008 17:33:00 -0400
Subject: [OWW-Discuss] perhaps we should send letter of support?
In-Reply-To: <2b0cb7a10803162156u48c11de5r108e324db3e54734@mail.gmail.com>
References: <2b0cb7a10803162156u48c11de5r108e324db3e54734@mail.gmail.com>
Message-ID: <47DEE38C.70501@mit.edu>

I think we should find out more details first.  See the comments on this 
blog post: 
http://www.earlham.edu/~peters/fos/2008/03/american-physical-society-v-wikipedia.html


Sriram Kosuri wrote:
> http://www.newscientist.com/article/mg19726473.300-physicists-slam-publishers-over-wikipedia-ban.html
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss


From rvidal at openwetware.org  Mon Mar 17 18:50:57 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Mon, 17 Mar 2008 18:50:57 -0400
Subject: [OWW-Discuss] Publishing for the future of science
Message-ID: <213fc43b0803171550k71cc2f8dg253ce2b7b3c6adcd@mail.gmail.com>

Thought this might be of interest in the scope of publishing @ oww
http://sciencecommons.org/weblog/archives/2008/03/17/publishing-for-the-future-of-science/

no time like the present.

-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From bill.altmail at gmail.com  Mon Mar 17 19:05:47 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 17 Mar 2008 19:05:47 -0400
Subject: [OWW-Discuss] Publishing for the future of science
In-Reply-To: <213fc43b0803171550k71cc2f8dg253ce2b7b3c6adcd@mail.gmail.com>
References: <213fc43b0803171550k71cc2f8dg253ce2b7b3c6adcd@mail.gmail.com>
Message-ID: <26428aaa0803171605i337a61b8heddb59050e3e36e@mail.gmail.com>

I heard the story in NPR and had a similar reaction. PLOS1 getting airplay
is a great level-set for open publishing.



On Mon, Mar 17, 2008 at 6:50 PM, Ricardo Vidal <rvidal at openwetware.org>
wrote:

> Thought this might be of interest in the scope of publishing @ oww
>
> http://sciencecommons.org/weblog/archives/2008/03/17/publishing-for-the-future-of-science/
>
> no time like the present.
>
> --
> Ricardo Vidal
> rvidal at gmail.com | http://my.biotechlife.net
> http://www.openwetware.org - Share your Science
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From rvidal at openwetware.org  Tue Mar 18 23:13:04 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Tue, 18 Mar 2008 23:13:04 -0400
Subject: [OWW-Discuss] WikiPathways
Message-ID: <213fc43b0803182013w7bd8d857sca4e8e3811ef7aef@mail.gmail.com>

Here's a good example of mediawiki put to action for biological pathways

http://www.wikipathways.org/index.php/WikiPathways

Some good ideas to take into consideration from their homepage. Featured
content, use of Google custom search (?), etc.
-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From jasonk at MIT.EDU  Wed Mar 19 00:24:14 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Wed, 19 Mar 2008 00:24:14 -0400
Subject: [OWW-Discuss] March SC meeting notes
Message-ID: <7c085c480803182124v50948127v8b4f8658547cdccb@mail.gmail.com>

Hi SC,

Thanks to those who called in this month.

For those who couldn't make it, notes are here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_March_2008

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

We spent some time at the meeting discussing expansion of the
Etiquette page here:
http://openwetware.org/wiki/Etiquette

As OWW grows and gains more credibility as a platform for scientific
communication, we expect that more folks will be drawn to the site to
post content that might be pseudo scientific / advertising / etc. We
decided to write a clearer statement about some of the norms that make
OWW a scientific community, so we have something down in writing to
share with new members.

I posted a quick draft at the bottom of the etiquette page based on
our discussions at the meeting, please add/edit/clean it up:
http://openwetware.org/wiki/Etiquette

thanks!
jason


From jasonk at MIT.EDU  Wed Mar 19 00:43:14 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Wed, 19 Mar 2008 00:43:14 -0400
Subject: [OWW-Discuss] New OWW Steering Committee coordinator: John Cumbers!
Message-ID: <7c085c480803182143s2925228exab87cc8aceb57d8e@mail.gmail.com>

John Cumbers has been elected as the new SC coordinator!  Congrats
john, may you steward the community well :)

In honor of John's new position, I have added a redirect on the
official SC coord torch page:
http://openwetware.org/wiki/OpenWetWare:SC_coordinator_torch

ah, that's nerdy.

As my last demand, I'm going to request that all the SC chairs get in
touch with me and john to give a debrief on their position, and help
brainstorm how to bring in new folks to help them out / replace them.
We used the positions to good end previously to help the SC expand
outside the "MIT crowd".  However, now that there's a close-knit group
of folks who regularly attend SC meetings, I want to make sure we are
still providing opportunities for excited new folks to come in without
feeling overwhelmed.  Any suggestions are welcome on how to do that
better.

thanks!
jason


From johncumbers at gmail.com  Wed Mar 19 17:56:35 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 19 Mar 2008 17:56:35 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <p06230908c4044402f964@10.0.1.197>
References: <87k5k1bcj7.fsf@nitsua.mit.edu>
	<38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>
	<p06230908c4044402f964@10.0.1.197>
Message-ID: <cfd758050803191456i2a4015cfrccfc2db7bb754cc@mail.gmail.com>

I'd be happy to direct a series of protocol videos aimed at high school
students, a la 'nanodrop it like it's hot' :)
cheers,
John

On Mon, Mar 17, 2008 at 11:56 AM, natalie kuldell <nkuldell at mit.edu> wrote:

>  It seems like the goal of their program, at least currently, is to
> promote general scientific literacy.
> See:  http://biz.yahoo.com/bw/080221/20080221005076.html?.v=1
>
> I had a talk with the Invitrogen Foundation folks last week and have
> requested info on previously funded applications. That list may give a
> better sense of what kinds of synthetic biology projects stand a chance. I'm
> happy to pass along the information I get back.
>
> Natalie
>
>
>
> I'm all for writing up a proposal, seems like they are looking for K-12
> stuff though. Maybe if we play up the global reach, protocol repository
> (for CC instructors) and the video lab tours as outreach mechanisms,
> we'll stand a good chance.
>
> Mike
>
>
> Guidelines:
> The Invitrogen Foundation is committed to strengthening the pipeline of
> future life scientists. Funding and partnership opportunities that
> address the following areas of interest will be considered:
>
>     * Life science education for students, beginning at the high school
> level
>     * Professional development for high school and community college
> instructors
>
> ------
>     * Programs that are broad in scope and reach students and/or
> educators from a variety of geographic locations are preferred.
> ------
>
>     * Special consideration is also given to programs that target groups
> traditionally underrepresented in the life sciences, including but not
> limited to women and diverse populations
>
> Through outreach and education, the Invitrogen Foundation also seeks to
> increase society's understanding of the life sciences and their critical
> role in addressing global issues. Programs and initiatives that address
> these objectives are preferred:
>
>     * Educating community leaders about the importance of life science,
> particularly as it relates to education, economic strength and global
> health
>     * Activities and initiatives that demonstrate thought leadership
>     * Museum and traveling exhibits, community events and public
> lectures, that reach a broad, cross-section of the population
>     * Special consideration is also given to programs that have a global
> dimension
>
>
>
> -----Original Message-----
> From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
> On Behalf Of Austin Che
> Sent: Monday, March 17, 2008 11:23 AM
> To: discuss at openwetware.org
> Subject: [OWW-Discuss] invitrogen foundation
>
>
>     Just saw this:
>     http://www.invitrogen.com/content.cfm?pageid=12185
>
>     Invitrogen apparently has a foundation with money to give for
>     "strengthening the pipeline of future life scientists." It is
>     explicitly targeted at not-for-profit organizations. Given the
>     number of not-for-profit organizations in the life sciences, it
>     seems that if OWW made a proposal, there'd be a pretty good chance
>     of getting some funding.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From johncumbers at gmail.com  Wed Mar 19 18:00:27 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 19 Mar 2008 18:00:27 -0400
Subject: [OWW-Discuss] New OWW Steering Committee coordinator: John
	Cumbers!
In-Reply-To: <7c085c480803182143s2925228exab87cc8aceb57d8e@mail.gmail.com>
References: <7c085c480803182143s2925228exab87cc8aceb57d8e@mail.gmail.com>
Message-ID: <cfd758050803191500m590168abm459ddccbd3ed519f@mail.gmail.com>

Thanks Jason,
Yes, please e-mail me if you'd like to get involved, the SC meets once a
month via teleconference and we're looking to include more people.  Please
also mail me if you are an existing chair in need of help, or wanting to
step down from your responsibilities and try another role on the SC, or take
a break.
cheers,
John


On Wed, Mar 19, 2008 at 12:43 AM, Jason Kelly <jasonk at mit.edu> wrote:

> John Cumbers has been elected as the new SC coordinator!  Congrats
> john, may you steward the community well :)
>
> In honor of John's new position, I have added a redirect on the
> official SC coord torch page:
> http://openwetware.org/wiki/OpenWetWare:SC_coordinator_torch
>
> ah, that's nerdy.
>
> As my last demand, I'm going to request that all the SC chairs get in
> touch with me and john to give a debrief on their position, and help
> brainstorm how to bring in new folks to help them out / replace them.
> We used the positions to good end previously to help the SC expand
> outside the "MIT crowd".  However, now that there's a close-knit group
> of folks who regularly attend SC meetings, I want to make sure we are
> still providing opportunities for excited new folks to come in without
> feeling overwhelmed.  Any suggestions are welcome on how to do that
> better.
>
> thanks!
> jason
>



-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From koeris at bu.edu  Thu Mar 20 10:17:31 2008
From: koeris at bu.edu (Michael S. Koeris)
Date: Thu, 20 Mar 2008 10:17:31 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <cfd758050803191456i2a4015cfrccfc2db7bb754cc@mail.gmail.com>
Message-ID: <C407EA3B.A430%koeris@bu.edu>

I think we should also think about what we exactly want the funding to be
used for. I would love to take a look at the previously funded projects.

Best
Mike


On 3/19/08 5:56 PM, "John Cumbers" <johncumbers at gmail.com> wrote:

> I'd be happy to direct a series of protocol videos aimed at high school
> students, a la 'nanodrop it like it's hot' :)
> cheers, 
> John
> 
> On Mon, Mar 17, 2008 at 11:56 AM, natalie kuldell <nkuldell at mit.edu> wrote:
>> It seems like the goal of their program, at least currently, is to promote
>> general scientific literacy.
>> See: http://biz.yahoo.com/bw/080221/20080221005076.html?.v=1
>> 
>> I had a talk with the Invitrogen Foundation folks last week and have
>> requested info on previously funded applications. That list may give a better
>> sense of what kinds of synthetic biology projects stand a chance. I'm happy
>> to pass along the information I get back.
>> 
>> Natalie
>> 
>> 
>> 
>>> I'm all for writing up a proposal, seems like they are looking for K-12
>>> stuff though. Maybe if we play up the global reach, protocol repository
>>> (for CC instructors) and the video lab tours as outreach mechanisms,
>>> we'll stand a good chance.
>>> 
>>> Mike
>>> 
>>> 
>>> Guidelines:
>>> The Invitrogen Foundation is committed to strengthening the pipeline of
>>> future life scientists. Funding and partnership opportunities that
>>> address the following areas of interest will be considered:
>>> 
>>>     * Life science education for students, beginning at the high school
>>> level
>>>     * Professional development for high school and community college
>>> instructors
>>> 
>>> ------
>>>     * Programs that are broad in scope and reach students and/or
>>> educators from a variety of geographic locations are preferred.
>>> ------
>>> 
>>>     * Special consideration is also given to programs that target groups
>>> traditionally underrepresented in the life sciences, including but not
>>> limited to women and diverse populations
>>> 
>>> Through outreach and education, the Invitrogen Foundation also seeks to
>>> increase society's understanding of the life sciences and their critical
>>> role in addressing global issues. Programs and initiatives that address
>>> these objectives are preferred:
>>> 
>>>     * Educating community leaders about the importance of life science,
>>> particularly as it relates to education, economic strength and global
>>> health
>>>     * Activities and initiatives that demonstrate thought leadership
>>>     * Museum and traveling exhibits, community events and public
>>> lectures, that reach a broad, cross-section of the population
>>>     * Special consideration is also given to programs that have a global
>>> dimension
>>> 
>>> 
>>> 
>>> -----Original Message-----
>>> From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
>>> On Behalf Of Austin Che
>>> Sent: Monday, March 17, 2008 11:23 AM
>>> To: discuss at openwetware.org
>>> Subject: [OWW-Discuss] invitrogen foundation
>>> 
>>> 
>>>     Just saw this:
>>>    http://www.invitrogen.com/content.cfm?pageid=12185
>>>    
>>>     Invitrogen apparently has a foundation with money to give for
>>>     "strengthening the pipeline of future life scientists." It is
>>>     explicitly targeted at not-for-profit organizations. Given the
>>>     number of not-for-profit organizations in the life sciences, it
>>>     seems that if OWW made a proposal, there'd be a pretty good chance
>>>     of getting some funding.
>>>    
>>> --
>>> Austin Che          <austin at csail.mit.edu>          (617)253-5899
>>> _______________________________________________
>>> OpenWetWare Discussion Mailing List
>>> discuss at openwetware.org
>>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>>> 
>>> _______________________________________________
>>> OpenWetWare Discussion Mailing List
>>> discuss at openwetware.org
>>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>>> 
>>> 
>>> _______________________________________________
>>> OpenWetWare Discussion Mailing List
>>> discuss at openwetware.org
>>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>>> 
>>> 
>>> 

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From macowell at gmail.com  Thu Mar 20 13:27:10 2008
From: macowell at gmail.com (Mackenzie Cowell)
Date: Thu, 20 Mar 2008 13:27:10 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <cfd758050803191456i2a4015cfrccfc2db7bb754cc@mail.gmail.com>
References: <87k5k1bcj7.fsf@nitsua.mit.edu>
	<38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>
	<p06230908c4044402f964@10.0.1.197>
	<cfd758050803191456i2a4015cfrccfc2db7bb754cc@mail.gmail.com>
Message-ID: <54746a3f0803201027i3e2cc74ch9231cda5e9cec454@mail.gmail.com>

Boo.  From: http://www.invitrogen.com/content.cfm?pageid=12186

Media is specifically not funded. See bold:

"Due to IRS regulations and Invitrogen's funding priorities, The Invitrogen
Foundation will not support the following:

   - Individuals and for-profit organizations
   - Political organizations, campaigns, and activities
   - Fraternal/labor/veteran's organizations and activities
   - Religious organizations or groups whose activities are primarily
   sectarian in purpose
   - Organizations that discriminate on the basis of race, color, sex,
   sexual orientation, marital status, religion, age, national origin,
   veteran's status, or disability
   - Fund-raising activities
   - Capital or building campaigns, including new construction and
   renovation of facilities
   - *Media (e.g., radio, TV, film, web-cast) productions (except Public
   Broadcasting)*
   - Sponsored research
   - Basic or clinical research projects, such as epidemiological
   studies, clinical trials, or other pharmaceutical studies
   - Meetings, conferences, symposia or workshops unrelated to advancing
   the life sciences
   - Unrestricted general support or ongoing operating support
   - Fellowship/tuition support for a specific individual
   - Debt reduction
   - Beauty or talent contests
   - Advertising
   - Festivals and parades

In some cases, Invitrogen may consider funding the following activities as
they relate to advancing the life sciences:

   - Dinners
   - Galas
   - Capital campaigns
   - Building campaigns"



On Wed, Mar 19, 2008 at 5:56 PM, John Cumbers <johncumbers at gmail.com> wrote:

> I'd be happy to direct a series of protocol videos aimed at high school
> students, a la 'nanodrop it like it's hot' :)
> cheers,
> John
>
>
> On Mon, Mar 17, 2008 at 11:56 AM, natalie kuldell <nkuldell at mit.edu>
> wrote:
>
> >  It seems like the goal of their program, at least currently, is to
> > promote general scientific literacy.
> > See:  http://biz.yahoo.com/bw/080221/20080221005076.html?.v=1
> >
> > I had a talk with the Invitrogen Foundation folks last week and have
> > requested info on previously funded applications. That list may give a
> > better sense of what kinds of synthetic biology projects stand a chance. I'm
> > happy to pass along the information I get back.
> >
> > Natalie
> >
> >
> >
> > I'm all for writing up a proposal, seems like they are looking for K-12
> > stuff though. Maybe if we play up the global reach, protocol repository
> > (for CC instructors) and the video lab tours as outreach mechanisms,
> > we'll stand a good chance.
> >
> > Mike
> >
> >
> > Guidelines:
> > The Invitrogen Foundation is committed to strengthening the pipeline of
> > future life scientists. Funding and partnership opportunities that
> > address the following areas of interest will be considered:
> >
> >     * Life science education for students, beginning at the high school
> > level
> >     * Professional development for high school and community college
> > instructors
> >
> > ------
> >     * Programs that are broad in scope and reach students and/or
> > educators from a variety of geographic locations are preferred.
> > ------
> >
> >     * Special consideration is also given to programs that target groups
> > traditionally underrepresented in the life sciences, including but not
> > limited to women and diverse populations
> >
> > Through outreach and education, the Invitrogen Foundation also seeks to
> > increase society's understanding of the life sciences and their critical
> > role in addressing global issues. Programs and initiatives that address
> > these objectives are preferred:
> >
> >     * Educating community leaders about the importance of life science,
> > particularly as it relates to education, economic strength and global
> > health
> >     * Activities and initiatives that demonstrate thought leadership
> >     * Museum and traveling exhibits, community events and public
> > lectures, that reach a broad, cross-section of the population
> >     * Special consideration is also given to programs that have a global
> > dimension
> >
> >
> >
> > -----Original Message-----
> > From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
> > On Behalf Of Austin Che
> > Sent: Monday, March 17, 2008 11:23 AM
> > To: discuss at openwetware.org
> > Subject: [OWW-Discuss] invitrogen foundation
> >
> >
> >     Just saw this:
> >     http://www.invitrogen.com/content.cfm?pageid=12185
> >
> >     Invitrogen apparently has a foundation with money to give for
> >     "strengthening the pipeline of future life scientists." It is
> >     explicitly targeted at not-for-profit organizations. Given the
> >     number of not-for-profit organizations in the life sciences, it
> >     seems that if OWW made a proposal, there'd be a pretty good chance
> >     of getting some funding.
> >
> > --
> > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> >
> >
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> >
>
>
> --
> John Cumbers, Graduate Student
> Molecular Biology, Cell Biology, and Biochemistry
> Biology and Medicine, Brown University, Box G-W
> Providence, Rhode Island, 02912, USA
> Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824
>
> Delivery address: Brown University (EEB) Biomed Stock Room
> 34 OLIVE ST, Providence, RI 02912
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From johncumbers at gmail.com  Thu Mar 20 13:30:58 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 20 Mar 2008 13:30:58 -0400
Subject: [OWW-Discuss] invitrogen foundation
In-Reply-To: <54746a3f0803201027i3e2cc74ch9231cda5e9cec454@mail.gmail.com>
References: <87k5k1bcj7.fsf@nitsua.mit.edu>
	<38ACE5B2FDD7B14E913A09CA4685E88805B2A605@ENG-EXCHANGE1.ad.bu.edu>
	<p06230908c4044402f964@10.0.1.197>
	<cfd758050803191456i2a4015cfrccfc2db7bb754cc@mail.gmail.com>
	<54746a3f0803201027i3e2cc74ch9231cda5e9cec454@mail.gmail.com>
Message-ID: <cfd758050803201030j637904fbgb4b0b7802514a6b@mail.gmail.com>

I'd say that Youtube counts as a public broadcast...

On Thu, Mar 20, 2008 at 1:27 PM, Mackenzie Cowell <macowell at gmail.com>
wrote:

> Boo.  From: http://www.invitrogen.com/content.cfm?pageid=12186
>
> Media is specifically not funded. See bold:
>
> "Due to IRS regulations and Invitrogen's funding priorities, The
> Invitrogen Foundation will not support the following:
>
>    - Individuals and for-profit organizations
>    - Political organizations, campaigns, and activities
>    - Fraternal/labor/veteran's organizations and activities
>    - Religious organizations or groups whose activities are primarily
>    sectarian in purpose
>    - Organizations that discriminate on the basis of race, color, sex,
>    sexual orientation, marital status, religion, age, national origin,
>    veteran's status, or disability
>    - Fund-raising activities
>    - Capital or building campaigns, including new construction and
>    renovation of facilities
>    - *Media (e.g., radio, TV, film, web-cast) productions (except
>    Public Broadcasting)*
>    - Sponsored research
>    - Basic or clinical research projects, such as epidemiological
>    studies, clinical trials, or other pharmaceutical studies
>    - Meetings, conferences, symposia or workshops unrelated to
>    advancing the life sciences
>    - Unrestricted general support or ongoing operating support
>    - Fellowship/tuition support for a specific individual
>    - Debt reduction
>    - Beauty or talent contests
>    - Advertising
>    - Festivals and parades
>
> In some cases, Invitrogen may consider funding the following activities as
> they relate to advancing the life sciences:
>
>    - Dinners
>    - Galas
>    - Capital campaigns
>    - Building campaigns"
>
>
>
> On Wed, Mar 19, 2008 at 5:56 PM, John Cumbers <johncumbers at gmail.com>
> wrote:
>
> > I'd be happy to direct a series of protocol videos aimed at high school
> > students, a la 'nanodrop it like it's hot' :)
> > cheers,
> > John
> >
> >
> > On Mon, Mar 17, 2008 at 11:56 AM, natalie kuldell <nkuldell at mit.edu>
> > wrote:
> >
> > >  It seems like the goal of their program, at least currently, is to
> > > promote general scientific literacy.
> > > See:  http://biz.yahoo.com/bw/080221/20080221005076.html?.v=1
> > >
> > > I had a talk with the Invitrogen Foundation folks last week and have
> > > requested info on previously funded applications. That list may give a
> > > better sense of what kinds of synthetic biology projects stand a chance. I'm
> > > happy to pass along the information I get back.
> > >
> > > Natalie
> > >
> > >
> > >
> > > I'm all for writing up a proposal, seems like they are looking for
> > > K-12
> > > stuff though. Maybe if we play up the global reach, protocol
> > > repository
> > > (for CC instructors) and the video lab tours as outreach mechanisms,
> > > we'll stand a good chance.
> > >
> > > Mike
> > >
> > >
> > > Guidelines:
> > > The Invitrogen Foundation is committed to strengthening the pipeline
> > > of
> > > future life scientists. Funding and partnership opportunities that
> > > address the following areas of interest will be considered:
> > >
> > >     * Life science education for students, beginning at the high
> > > school
> > > level
> > >     * Professional development for high school and community college
> > > instructors
> > >
> > > ------
> > >     * Programs that are broad in scope and reach students and/or
> > > educators from a variety of geographic locations are preferred.
> > > ------
> > >
> > >     * Special consideration is also given to programs that target
> > > groups
> > > traditionally underrepresented in the life sciences, including but not
> > > limited to women and diverse populations
> > >
> > > Through outreach and education, the Invitrogen Foundation also seeks
> > > to
> > > increase society's understanding of the life sciences and their
> > > critical
> > > role in addressing global issues. Programs and initiatives that
> > > address
> > > these objectives are preferred:
> > >
> > >     * Educating community leaders about the importance of life
> > > science,
> > > particularly as it relates to education, economic strength and global
> > > health
> > >     * Activities and initiatives that demonstrate thought leadership
> > >     * Museum and traveling exhibits, community events and public
> > > lectures, that reach a broad, cross-section of the population
> > >     * Special consideration is also given to programs that have a
> > > global
> > > dimension
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu]
> > > On Behalf Of Austin Che
> > > Sent: Monday, March 17, 2008 11:23 AM
> > > To: discuss at openwetware.org
> > > Subject: [OWW-Discuss] invitrogen foundation
> > >
> > >
> > >     Just saw this:
> > >     http://www.invitrogen.com/content.cfm?pageid=12185
> > >
> > >     Invitrogen apparently has a foundation with money to give for
> > >     "strengthening the pipeline of future life scientists." It is
> > >     explicitly targeted at not-for-profit organizations. Given the
> > >     number of not-for-profit organizations in the life sciences, it
> > >     seems that if OWW made a proposal, there'd be a pretty good chance
> > >     of getting some funding.
> > >
> > > --
> > > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> > > _______________________________________________
> > > OpenWetWare Discussion Mailing List
> > > discuss at openwetware.org
> > > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> > >
> > > _______________________________________________
> > > OpenWetWare Discussion Mailing List
> > > discuss at openwetware.org
> > > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> > >
> > >
> > >
> > > _______________________________________________
> > > OpenWetWare Discussion Mailing List
> > > discuss at openwetware.org
> > > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> > >
> > >
> >
> >
> > --
> > John Cumbers, Graduate Student
> > Molecular Biology, Cell Biology, and Biochemistry
> > Biology and Medicine, Brown University, Box G-W
> > Providence, Rhode Island, 02912, USA
> > Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824
> >
> > Delivery address: Brown University (EEB) Biomed Stock Room
> > 34 OLIVE ST, Providence, RI 02912
> >
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> >
>
>
> --
> Mac Cowell
> iGEM Coordinator
> igem.org
> 231.313.9062
>



-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From bill.altmail at gmail.com  Fri Mar 21 07:28:11 2008
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 21 Mar 2008 07:28:11 -0400
Subject: [OWW-Discuss] MIT Scratch
Message-ID: <26428aaa0803210428y5ad00d63v88a20b9746f248d1@mail.gmail.com>

This is an example of the kind of apps kids are creating using a MIT open
source educational project called Scratch:

http://scratch.mit.edu/projects/Jacobo/62911

Scratch is a drag-and drop desktop programming application. It's a sort of
"mash up for tyros".

What impressed me is how fast kids can learn to manipulate the programming
language to build pretty compelling applications. It's very similar to the
first Lego Mindstorms programming model.

For $32, you can buy a 'scratchboard', a bright yellow USB I/O device that
is intrinsically supported by the language. The board has 4 input lines
(each with a wire and alligator clip and a yellow wire), a slider
potentiometer, a light sensor, and a noise sensor.

Jacob's Alien DNA application is funny. But this environment could be used
for simple simulations in a classroom environment. The ridiculously low
entry price, compelling look of the output apps (which are designed to be
shared via the web), and the dead-simple programming model are impressive.

One cool part of the system is that anyone can reprogram another model they
download with Scratch. One 'seed' production can lead to dozens of
mutations.

We may be a lot closer to "M13 Cart" and "T7 Goes Wild" than anyone thinks.
Don't worry about the biohackers. It may be the teen-bopper scratches that
have the last laugh.

B.
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From johncumbers at gmail.com  Fri Mar 21 11:20:42 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Fri, 21 Mar 2008 11:20:42 -0400
Subject: [OWW-Discuss] What previously underrecognized sport or pastime
	should be included in the Olympic Games?
Message-ID: <cfd758050803210820qfa17268ke7f0cab55545fd2b@mail.gmail.com>

*What previously underrecognized sport or pastime should be included in the
Olympic Games?*

The contestants are given a bag of spinach and asked to isolate the DNA,
purify the ribulose-1,5-bisphosphate carboxylase, and separate the rRNA from
the mRNA. This would be a timed trial with certain as-yet-undetermined
constraints, but leaning towards the low-tech.
from: http://www.nature.com/nature/journal/v422/n6932/full/422567a.html

Are you thinking what I'm thinking?

-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From bill.altmail at gmail.com  Fri Mar 21 15:05:26 2008
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 21 Mar 2008 15:05:26 -0400
Subject: [OWW-Discuss] What previously underrecognized sport or pastime
	should be included in the Olympic Games?
In-Reply-To: <cfd758050803210820qfa17268ke7f0cab55545fd2b@mail.gmail.com>
References: <cfd758050803210820qfa17268ke7f0cab55545fd2b@mail.gmail.com>
Message-ID: <26428aaa0803211205v213f8322r49c926572bcc08d@mail.gmail.com>

Up close and personal: Alan Charning, UK PostDoc. World renowned pipette
pro. His presence on any team is enough to titrate fear in the hearts of his
opponents. Merely having him at the lab bench has propelled the austere labs
of Cambridge into a force to be reckoned with in the global pro-am wetlab
circuit.

When not pushing copious quantities of fluids through ridiculously thin
tubes, Alan likes to relax in his training lab in the Outer Hebrides. Where
sheep once trod, now Alan's legendary training regimen is conducted with a
host of experts flown in from the four corners of the globe. Swimming 2
miles every day, pumping through massive volumes of treacle syrup to
increase training friction, performing hundreds of arm rep lifts per day,
and consuming the highlights of the world's literature cell biology output
well into the night makes for little time for his wife, Brit, and their son,
Watson, and daughter, Sabine.

As he prepares for his date with destiny this summer in Beijing, Alan
understand the  kind of expectations physicists, chemists, and biologists
have heaped upon him. The bust of Cavendish that sits on his desk and the
picture of Fleming on the wall remind him of the titans who preceded him.
Little did they know that one day, endorsement deals with Van Heusen,
Dockers, and VWR Scientific would one day be the prizes of their
intellectual progeny.

Some called it frivolous when Charning halted his cancer research career
peers felt would eventually lead to a Nobel prize to instead perfect his
legendary pipetting skills. His gold medal performance in the 3 liter medley
in Oslo in 2005, 3 medals in the Helsinki Invitational in 2006, and,
finally, the world record in dispensing over 3000 separate samples in a time
of 5:02:03954 last year, shattering Professor Jan Gulbricks of the
Netherlands time by a massive 5 hundeths of a second, made his appearance on
this years UK team a slam-dunk.

Wen asked what drives him onward, Alan adjusted his thick glasses, fumbled a
bit with the glass tube in his hand, and cleared his throat. Tears welled in
his eyes. "My personal hero was Jesse Owens. In my own way, I'm doing my
part to let the world know that Lab Science can be as rewarding as any other
Olympic sport. We can create life on a competitive playing field and send it
crawling off when we're done. The spoils don't go to the victors but to the
storm drains that surround the venues we compete in. We're changing the
world. I'm honored to be a part of it."


On Fri, Mar 21, 2008 at 11:20 AM, John Cumbers <johncumbers at gmail.com>
wrote:

> *What previously underrecognized sport or pastime should be included in
> the Olympic Games?*
>
> The contestants are given a bag of spinach and asked to isolate the DNA,
> purify the ribulose-1,5-bisphosphate carboxylase, and separate the rRNA from
> the mRNA. This would be a timed trial with certain as-yet-undetermined
> constraints, but leaning towards the low-tech.
> from: http://www.nature.com/nature/journal/v422/n6932/full/422567a.html
>
> Are you thinking what I'm thinking?
>
> --
> John Cumbers, Graduate Student
> Molecular Biology, Cell Biology, and Biochemistry
> Biology and Medicine, Brown University, Box G-W
> Providence, Rhode Island, 02912, USA
> Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824
>
> Delivery address: Brown University (EEB) Biomed Stock Room
> 34 OLIVE ST, Providence, RI 02912
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From rvidal at openwetware.org  Fri Mar 21 16:10:26 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Fri, 21 Mar 2008 16:10:26 -0400
Subject: [OWW-Discuss] Evernote (giveaway for the day)
Message-ID: <213fc43b0803211310o2d0b9472k795cc7150773a9b1@mail.gmail.com>

Evernote is having a giveaway of their software for a day. There's about 12
hours left to get it free before it goes back to it's normal 50 USD price.

http://www.giveawayoftheday.com/evernote-beta/

Thought it could be useful for some. There's Mac and Win versions available.

More info on Evernote - www.evernote.com

-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From austin at csail.mit.edu  Sun Mar 23 19:27:22 2008
From: austin at csail.mit.edu (Austin Che)
Date: Sun, 23 Mar 2008 19:27:22 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff Resistance
Message-ID: <87skyhxbqd.fsf@nitsua.mit.edu>


    http://www.sciencemag.org/cgi/content/full/319/5870/1598
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From bcanton at MIT.EDU  Sun Mar 23 22:13:57 2008
From: bcanton at MIT.EDU (Barry Canton)
Date: Sun, 23 Mar 2008 22:13:57 -0400
Subject: [OWW-Discuss] WikiPathways
In-Reply-To: <213fc43b0803182013w7bd8d857sca4e8e3811ef7aef@mail.gmail.com>
References: <213fc43b0803182013w7bd8d857sca4e8e3811ef7aef@mail.gmail.com>
Message-ID: <52c0d2160803231913p2cf35535n15057f80255743e0@mail.gmail.com>

Seems like they also have a custom editor for entering pathways -

http://www.wikipathways.org/index.php/Help:Tutorial:Step_2

On 3/18/08, Ricardo Vidal <rvidal at openwetware.org> wrote:
> Here's a good example of mediawiki put to action for biological pathways
>
> http://www.wikipathways.org/index.php/WikiPathways
>
> Some good ideas to take into consideration from their homepage. Featured
> content, use of Google custom search (?), etc.
>  --
> Ricardo Vidal
> rvidal at gmail.com | http://my.biotechlife.net
> http://www.openwetware.org - Share your Science
> _______________________________________________
>  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) 401-7320 (Grand Central)
Email1: bcanton at mit.edu
Email2: bcanton at gmail.com


From dan.bolser at gmail.com  Mon Mar 24 10:26:00 2008
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 24 Mar 2008 15:26:00 +0100
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <87skyhxbqd.fsf@nitsua.mit.edu>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
Message-ID: <2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>

"That we would wholesale start changing people's records goes against
our idea of an archive," says David Lipman, director of the National
Center for Biotechnology Information (NCBI), GenBank's home in
Bethesda, Maryland. "It would be chaos."

I think that quote highlights the problem (ignorance) that we have to
overcome. People simply don't understand the nature of community
projects. Just take the open source software movement for example;
community + tools for basic collaboration = massively successful
projects.

How many databases in the molecular biology community include even the
most basic of tools - a public bug tracker? If there is one out there,
I don't know it. I find this fact simultaneously infuriating and
dumbfounding, because it is simply unjustifiable. How about a public
database project with a publically archived mailing lists? I had to
start my own because the NCBI refused to do so;

http://www.bioinformatics.org/mailman/listinfo/ssml-general


I am having a similar running battle with the PDB, who staunchly
refuse to alter (some of) their data, even though it contains clear
errors. The recent remediation has been a huge improvement, but it
doesn't go far enough.

We simply need to build the kind of community annotation projects that
will show the way for others. I have given up on the above kind of
stupidity. There are only so many times that you can tell someone they
need to install a public bug tracker before you get too tired to care
that they won't install one any more.


With hope for the future,

Dan.


----

http://BioDatabase.Org
http://PDBWiki.org


From tk at csail.mit.edu  Mon Mar 24 11:07:45 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Mon, 24 Mar 2008 11:07:45 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
Message-ID: <82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>

I think we all share this frustration.  An example of just how bad 
things are might be useful.

About a year ago, I started working with yeast recombination, and 
wanted to use a pair of yeast artificial chromosome  vectors that had 
been developed in the early '90s.  The developer was kind and helpful, 
and provided the vectors, but there was no sequence information 
available (not unusual for early vectors, where sequencing was 
difficult and expensive).  One of the things I did was to fully 
sequence the vectors and to deposit the vector sequences into Genbank.

I listed the original reference to the vectors as publication 
information.  Apparently, this is not allowed.  There was no way in 
which I could link the sequence I had just deposited with the source of 
the vector (or even to give credit for where it came from).  The only 
link is the name of the plasmid, which I suppose is unique enough.

But this madness has to stop.


On Mar 24, 2008, at 10:26 AM, Dan Bolser wrote:

> "That we would wholesale start changing people's records goes against
> our idea of an archive," says David Lipman, director of the National
> Center for Biotechnology Information (NCBI), GenBank's home in
> Bethesda, Maryland. "It would be chaos."
>
> I think that quote highlights the problem (ignorance) that we have to
> overcome. People simply don't understand the nature of community
> projects. Just take the open source software movement for example;
> community + tools for basic collaboration = massively successful
> projects.
>
> How many databases in the molecular biology community include even the
> most basic of tools - a public bug tracker? If there is one out there,
> I don't know it. I find this fact simultaneously infuriating and
> dumbfounding, because it is simply unjustifiable. How about a public
> database project with a publically archived mailing lists? I had to
> start my own because the NCBI refused to do so;
>
> http://www.bioinformatics.org/mailman/listinfo/ssml-general
>
>
> I am having a similar running battle with the PDB, who staunchly
> refuse to alter (some of) their data, even though it contains clear
> errors. The recent remediation has been a huge improvement, but it
> doesn't go far enough.
>
> We simply need to build the kind of community annotation projects that
> will show the way for others. I have given up on the above kind of
> stupidity. There are only so many times that you can tell someone they
> need to install a public bug tracker before you get too tired to care
> that they won't install one any more.
>
>
> With hope for the future,
>
> Dan.
>
>
> ----
>
> http://BioDatabase.Org
> http://PDBWiki.org
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss



From rvidal at openwetware.org  Mon Mar 24 11:38:56 2008
From: rvidal at openwetware.org (Ricardo Vidal)
Date: Mon, 24 Mar 2008 11:38:56 -0400
Subject: [OWW-Discuss] Top 5 reasons it sucks to be an engineering student
Message-ID: <213fc43b0803240838v6634282ayd3b6eaa89bb13a11@mail.gmail.com>

http://blog.wired.com/wiredscience/2008/03/top-5-reasons-i.html

This is intended to be a humorous blog post but looking at all the comments
from visitors, it doesn't look like much laughter came about.

-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From macowell at gmail.com  Mon Mar 24 12:47:08 2008
From: macowell at gmail.com (Mackenzie Cowell)
Date: Mon, 24 Mar 2008 12:47:08 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
Message-ID: <54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>

Why doesn't someone start mirroring ncbi and layering a lightweight
revisioning layer on top of the content?  It could live at ncbi2.org.  Or it
could be mirrored directly into freebase.com, which already provides those
tools.

Mac

On Mon, Mar 24, 2008 at 11:07 AM, Tom Knight <tk at csail.mit.edu> wrote:

> I think we all share this frustration.  An example of just how bad
> things are might be useful.
>
> About a year ago, I started working with yeast recombination, and
> wanted to use a pair of yeast artificial chromosome  vectors that had
> been developed in the early '90s.  The developer was kind and helpful,
> and provided the vectors, but there was no sequence information
> available (not unusual for early vectors, where sequencing was
> difficult and expensive).  One of the things I did was to fully
> sequence the vectors and to deposit the vector sequences into Genbank.
>
> I listed the original reference to the vectors as publication
> information.  Apparently, this is not allowed.  There was no way in
> which I could link the sequence I had just deposited with the source of
> the vector (or even to give credit for where it came from).  The only
> link is the name of the plasmid, which I suppose is unique enough.
>
> But this madness has to stop.
>
>
> On Mar 24, 2008, at 10:26 AM, Dan Bolser wrote:
>
> > "That we would wholesale start changing people's records goes against
> > our idea of an archive," says David Lipman, director of the National
> > Center for Biotechnology Information (NCBI), GenBank's home in
> > Bethesda, Maryland. "It would be chaos."
> >
> > I think that quote highlights the problem (ignorance) that we have to
> > overcome. People simply don't understand the nature of community
> > projects. Just take the open source software movement for example;
> > community + tools for basic collaboration = massively successful
> > projects.
> >
> > How many databases in the molecular biology community include even the
> > most basic of tools - a public bug tracker? If there is one out there,
> > I don't know it. I find this fact simultaneously infuriating and
> > dumbfounding, because it is simply unjustifiable. How about a public
> > database project with a publically archived mailing lists? I had to
> > start my own because the NCBI refused to do so;
> >
> > http://www.bioinformatics.org/mailman/listinfo/ssml-general
> >
> >
> > I am having a similar running battle with the PDB, who staunchly
> > refuse to alter (some of) their data, even though it contains clear
> > errors. The recent remediation has been a huge improvement, but it
> > doesn't go far enough.
> >
> > We simply need to build the kind of community annotation projects that
> > will show the way for others. I have given up on the above kind of
> > stupidity. There are only so many times that you can tell someone they
> > need to install a public bug tracker before you get too tired to care
> > that they won't install one any more.
> >
> >
> > With hope for the future,
> >
> > Dan.
> >
> >
> > ----
> >
> > http://BioDatabase.Org
> > http://PDBWiki.org
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>



-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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From await at genetics.med.harvard.edu  Mon Mar 24 14:29:45 2008
From: await at genetics.med.harvard.edu (Alexander Wait Zaranek)
Date: Mon, 24 Mar 2008 14:29:45 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
Message-ID: <8b89c0c0803241129x25e5ca49v2b06f38000eaa5c1@mail.gmail.com>

On Mon, Mar 24, 2008 at 12:47 PM, Mackenzie Cowell <macowell at gmail.com> wrote:
> Why doesn't someone start mirroring ncbi and layering a lightweight
> revisioning layer on top of the content?  It could live at ncbi2.org.  Or it
> could be mirrored directly into freebase.com, which already provides those
> tools.
>
Concretely, what do people want to see mirrored?  Are we talking about
a periodic grab of  ftp://ftp.ncbi.nih.gov/blast/db/  something else?
We are interested in the human assemblies (mostly hg18) and the Watson
and Venter reads.

Sasha


From johncumbers at gmail.com  Mon Mar 24 22:04:25 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 24 Mar 2008 22:04:25 -0400
Subject: [OWW-Discuss] any objections to delaying the next steering
	committee meeting 1 week until noon Thu April 10th?
Message-ID: <cfd758050803241904r52cee0duf579fb4b8dd43677@mail.gmail.com>

Hi all,
Any objections to delaying the next steering committee meeting 1 week until
noon Thu April 10th?  The planned time of Thu next week will be difficult
for me to make it.  I'd also like to delay the proposed publishing meeting
until we've found a new publishing chair to take over this role. I'd prefer
not to do both, are there any volunteers?
Cheers,
John

-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From johncumbers at gmail.com  Mon Mar 24 22:19:28 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 24 Mar 2008 22:19:28 -0400
Subject: [OWW-Discuss] Hot off the SC blog..
Message-ID: <cfd758050803241919v7872b437qa4e7ecc9218dc302@mail.gmail.com>

Hot off the SC blog..
John writes: Hi all just a quick note to say hello, I'll be taking over from
Jason Kelly as steering committee coordinator for the next 6 months. This
could possibly be the busiest 6 months of my life as I'll be moving to
California for the summer too. The first meeting that I'll chair will be on
Thu April 10th at noon EST where I'll be chairing a discussion focused on
where OWW has been, where it is going and how to make sure that you feel
able to contribute to its continued success. Please keep an eye out on the
discuss at openwetware.org mailing list for details of how to call in and take
part. We're particularly reaching out to new members wanting to get involved
in how the site is run and the direction that it is taking.

Cheers, John


-- 
John Cumbers, Graduate Student
Molecular Biology, Cell Biology, and Biochemistry
Biology and Medicine, Brown University, Box G-W
Providence, Rhode Island, 02912, USA
Tel USA: +1 401 523 8190, Fax: +1 401 863-2166, UK to USA: 0207 617 7824

Delivery address: Brown University (EEB) Biomed Stock Room
34 OLIVE ST, Providence, RI 02912
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From dan.bolser at gmail.com  Tue Mar 25 06:54:29 2008
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 25 Mar 2008 11:54:29 +0100
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
Message-ID: <2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>

On 24/03/2008, Mackenzie Cowell <macowell at gmail.com> wrote:
>
> Why doesn't someone start mirroring ncbi and layering a lightweight
> revisioning layer on top of the content?  It could live at ncbi2.org.  Or
> it could be mirrored directly into freebase.com, which already provides
> those tools.


The difficulty comes in 'merging' back with the original data. This requires
some thinking about, but is generally do-able (I believe).

The conceptually cleanest way to think about the problem is in terms of a
versioning (revisioning) system such as SVN. (Sorry, that is what you just
said - I should read more carefully!)

Lets say we do the following,

a) grab all the data from the PDB (for example)
b) stick all the data into a revisioning system
c) allow users to freely edit the data, including automatic clean up 'bots',
algorithms, etc., etc.
d) have all changes automatically emailed to a mailing list for community
review, approval etc.

Now, once we get to step d, in the time since step a, the PDB data has been
updated by the PDB. We now need to merge the updated PDB data with our
independently modified data. (This is where we need to go beyond a simple
revisioning system).

Merges should be automatic where possible (i.e. new entries give us no
problem), modified entries that do not conflict can be merged. Conflicts,
however, need to be flagged and resolved - the community needs to manually
merge alternative 'fixes' or updates. We need flexible rules for how to
merge conflicts.

In this way each data entry will have a certain status (as well as a certain
version); oringinal, comunity updated, conflicting, ... Its actually not
that complex when it comes down to it - The PDB record has a release
version, we have our 'community version' and the text of the two may differ
or not. The differences may come from several sources, and where possible
they should be resolved.

Here things start to resemble a bug-tracker more than a revisioning
system...

Finally, all outstanding community 'fixes' need to be regularly emailed to
the PDB for review.

In summary, I think it is 'doable', but it isn't a case of simply mirroring
into a revisioning system. We need to work on some protocols for
synchronization.




Mac
>
> On Mon, Mar 24, 2008 at 11:07 AM, Tom Knight <tk at csail.mit.edu> wrote:
>
> > I think we all share this frustration.  An example of just how bad
> > things are might be useful.
> >
> > About a year ago, I started working with yeast recombination, and
> > wanted to use a pair of yeast artificial chromosome  vectors that had
> > been developed in the early '90s.  The developer was kind and helpful,
> > and provided the vectors, but there was no sequence information
> > available (not unusual for early vectors, where sequencing was
> > difficult and expensive).  One of the things I did was to fully
> > sequence the vectors and to deposit the vector sequences into Genbank.
> >
> > I listed the original reference to the vectors as publication
> > information.  Apparently, this is not allowed.  There was no way in
> > which I could link the sequence I had just deposited with the source of
> > the vector (or even to give credit for where it came from).  The only
> > link is the name of the plasmid, which I suppose is unique enough.
> >
> > But this madness has to stop.
> >
> >
> > On Mar 24, 2008, at 10:26 AM, Dan Bolser wrote:
> >
> > > "That we would wholesale start changing people's records goes against
> > > our idea of an archive," says David Lipman, director of the National
> > > Center for Biotechnology Information (NCBI), GenBank's home in
> > > Bethesda, Maryland. "It would be chaos."
> > >
> > > I think that quote highlights the problem (ignorance) that we have to
> > > overcome. People simply don't understand the nature of community
> > > projects. Just take the open source software movement for example;
> > > community + tools for basic collaboration = massively successful
> > > projects.
> > >
> > > How many databases in the molecular biology community include even the
> > > most basic of tools - a public bug tracker? If there is one out there,
> > > I don't know it. I find this fact simultaneously infuriating and
> > > dumbfounding, because it is simply unjustifiable. How about a public
> > > database project with a publically archived mailing lists? I had to
> > > start my own because the NCBI refused to do so;
> > >
> > > http://www.bioinformatics.org/mailman/listinfo/ssml-general
> > >
> > >
> > > I am having a similar running battle with the PDB, who staunchly
> > > refuse to alter (some of) their data, even though it contains clear
> > > errors. The recent remediation has been a huge improvement, but it
> > > doesn't go far enough.
> > >
> > > We simply need to build the kind of community annotation projects that
> > > will show the way for others. I have given up on the above kind of
> > > stupidity. There are only so many times that you can tell someone they
> > > need to install a public bug tracker before you get too tired to care
> > > that they won't install one any more.
> > >
> > >
> > > With hope for the future,
> > >
> > > Dan.
> > >
> > >
> > > ----
> > >
> > > http://BioDatabase.Org
> > > http://PDBWiki.org
> > > _______________________________________________
> > > OpenWetWare Discussion Mailing List
> > > discuss at openwetware.org
> > > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
>
>
>
> --
> Mac Cowell
> iGEM Coordinator
> igem.org
> 231.313.9062




-- 
hello
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From await at genetics.med.harvard.edu  Tue Mar 25 07:57:41 2008
From: await at genetics.med.harvard.edu (Alexander Wait Zaranek)
Date: Tue, 25 Mar 2008 07:57:41 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
	<2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
Message-ID: <8b89c0c0803250457h73a84fefx40de6f120449022b@mail.gmail.com>

On Tue, Mar 25, 2008 at 6:54 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
> In summary, I think it is 'doable', but it isn't a case of simply mirroring
> into a revisioning system. We need to work on some protocols for
> synchronization.
>
Efficient merging (not just forking) is an active area of version
control systems research.  Eg.:

* http://git.or.cz/
* http://bazaar-vcs.org/
* http://darcs.net/

If you'd enjoy seeing Linus Torvalds talk to Google about why he hates
subversion--Google employs a few of the key subversion authors--I
found his talk amusing, if not entirely illuminating:
http://www.youtube.com/watch?v=4XpnKHJAok8

Just as a test, I'm making a mirror of ftp://ftp.wwpdb.org/pub/pdb/
and I'll put the results in our content addressable storage system
where the data is striped across our cluster and available for batch
processing.

"c) allow users to freely edit the data, including automatic clean up
'bots', algorithms, etc., etc.
d) have all changes automatically emailed to a mailing list for
community review, approval etc."

Can you elaborate on this?

Sasha

PS. Speaking of the subversion authors, I also really enjoyed the
subversion authors talk on making a "successful free software
project":  http://www.youtube.com/watch?v=ZSFDm3UYkeE   They give a
pretty firm warning that a successful project should have a very
narrow focus or risk being unsuccessful in everything.


From austin at csail.mit.edu  Tue Mar 25 08:09:46 2008
From: austin at csail.mit.edu (Austin Che)
Date: Tue, 25 Mar 2008 08:09:46 -0400
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
	(Dan Bolser's message of "Tue, 25 Mar 2008 11:54:29 +0100")
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
	<2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
Message-ID: <87fxufvwc5.fsf@nitsua.mit.edu>


> a) grab all the data from the PDB (for example)
> b) stick all the data into a revisioning system
> c) allow users to freely edit the data, including automatic clean up 'bots',
> algorithms, etc., etc.
> d) have all changes automatically emailed to a mailing list for community
> review, approval etc.
>
> Now, once we get to step d, in the time since step a, the PDB data has been
> updated by the PDB. We now need to merge the updated PDB data with our
> independently modified data. (This is where we need to go beyond a simple
> revisioning system).

    That was supposed to be the goal of wikiproteins
    http://www.wikiproteins.org/Meta:Wikiproteins
    Roughly speaking, it does exactly the above. It works with
    databases like swiss-prot and downloads all the data into a
    semantic wiki form allowing edits. The changes made by the
    community can be kept separate from the "authoritative" version
    and periodically it's sent back to the original source for
    updating. At least that's the idea. They collaborate with those
    databases so not all of the databases are resisting this idea.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From dan.bolser at gmail.com  Tue Mar 25 09:53:36 2008
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 25 Mar 2008 14:53:36 +0100
Subject: [OWW-Discuss] Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <8b89c0c0803250457h73a84fefx40de6f120449022b@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
	<2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
	<8b89c0c0803250457h73a84fefx40de6f120449022b@mail.gmail.com>
Message-ID: <2c8757af0803250653r7961eb9ep66cb3fd4431f3f60@mail.gmail.com>

On 25/03/2008, Alexander Wait Zaranek <await at genetics.med.harvard.edu>
wrote:
>
> On Tue, Mar 25, 2008 at 6:54 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
> > In summary, I think it is 'doable', but it isn't a case of simply
> mirroring
> > into a revisioning system. We need to work on some protocols for
> > synchronization.
> >
>
> Efficient merging (not just forking) is an active area of version
> control systems research.  Eg.:
>
> * http://git.or.cz/
> * http://bazaar-vcs.org/
> * http://darcs.net/
>
> If you'd enjoy seeing Linus Torvalds talk to Google about why he hates
> subversion--Google employs a few of the key subversion authors--I
> found his talk amusing, if not entirely illuminating:
> http://www.youtube.com/watch?v=4XpnKHJAok8
>
> Just as a test, I'm making a mirror of ftp://ftp.wwpdb.org/pub/pdb/
> and I'll put the results in our content addressable storage system
> where the data is striped across our cluster and available for batch
> processing.
>
>
> "c) allow users to freely edit the data, including automatic clean up
> 'bots', algorithms, etc., etc.
> d) have all changes automatically emailed to a mailing list for
> community review, approval etc."
>
>
> Can you elaborate on this?


d) I have seen software projects with 'svn-mailing-lists', which email
everyone on the list with any / all changes that are committed into the SVN.
In this way the developers can see all relevant changes to the software as
they happen, and can then go remove / improve (/ comment on?) those changes.
The automatic email prompts discussion of the given 'commit'. I think when
it comes to a project the size of genbank, we would need to think about how
to define sub-communities, such as fungal vs. primate people.

c) Sometimes people don't want to fix just one little problem with one
specific entry - they want to change the data on all entries. For example, I
may want to update all the UniProt codes for all the PDB entries, and I may
write a script to do that every week. To do that I would write a script to
apply my newly collected data to the whole archive. Subsequently people
would need to be given the opportunity to accept / reject my algorithm
'en-masse'. Here I start to get bogged down with general 'hetrogeneous data
integration' issues... Perhaps sites like freebase.com can help us here.




Sasha
>
> PS. Speaking of the subversion authors, I also really enjoyed the
> subversion authors talk on making a "successful free software
> project":  http://www.youtube.com/watch?v=ZSFDm3UYkeE   They give a
> pretty firm warning that a successful project should have a very
> narrow focus or risk being unsuccessful in everything.
>



-- 
hello
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From dan.bolser at gmail.com  Tue Mar 25 09:57:07 2008
From: dan.bolser at gmail.com (Dan Bolser)
Date: Tue, 25 Mar 2008 14:57:07 +0100
Subject: [OWW-Discuss] Fwd: Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <2c8757af0803250646t51ece9d0sb4a6118294c28357@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
	<2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
	<87fxufvwc5.fsf@nitsua.mit.edu>
	<2c8757af0803250646t51ece9d0sb4a6118294c28357@mail.gmail.com>
Message-ID: <2c8757af0803250657w79091dafv59107ddbf3ad7be8@mail.gmail.com>

On 25/03/2008, Austin Che <austin at csail.mit.edu> wrote:
>
>
> > a) grab all the data from the PDB (for example)
> > b) stick all the data into a revisioning system
> > c) allow users to freely edit the data, including automatic clean up
> 'bots',
> > algorithms, etc., etc.
> > d) have all changes automatically emailed to a mailing list for
> community
> > review, approval etc.
> >
> > Now, once we get to step d, in the time since step a, the PDB data has
> been
> > updated by the PDB. We now need to merge the updated PDB data with our
> > independently modified data. (This is where we need to go beyond a
> simple
> > revisioning system).
>
>
>     That was supposed to be the goal of wikiproteins
>     http://www.wikiproteins.org/Meta:Wikiproteins
>     Roughly speaking, it does exactly the above. It works with
>     databases like swiss-prot and downloads all the data into a
>     semantic wiki form allowing edits. The changes made by the
>     community can be kept separate from the "authoritative" version
>     and periodically it's sent back to the original source for
>     updating. At least that's the idea. They collaborate with those
>     databases so not all of the databases are resisting this idea.



Yeah, I like the idea, and its good to see database developers on board with
that project. I spent some time hanging out near some wikiproteins
developers (as close as I could get) in irc://irc.freenode.net/#omegawiki -
I was disappointed at their lack of communication. For example, I have
worked on a Swiss-Prot parser, so I was curious as to how they had decided
to relationally model the data (if at all),  but I couldn't get any feed
back from them. Perhaps I was in the wrong place / asking the wrong
questions / etc.

Also some of the concepts that they expound at wikiproteins are really
confusing, and so far they have not decided to answer my questions about
them.  For example,

http://www.wikiproteins.org/Partner_talk:Knewco
http://www.wikiproteins.org/Meta_talk:Wikiproteins

http://www.wikiproteins.org/Meta_talk:Personal_Desktop
http://www.wikiproteins.org/Meta_talk:Alerts


I am sure wikiproteins will deliver, I am just not sure when (or what
really)... Did anyone try the new beta release?



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



-- 
hello

-- 
hello
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From wjf42 at MIT.EDU  Tue Mar 25 11:16:43 2008
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Tue, 25 Mar 2008 11:16:43 -0400
Subject: [OWW-Discuss] Fwd: Proposal to 'Wikify' GenBank Meets Stiff
	Resistance
In-Reply-To: <2c8757af0803250657w79091dafv59107ddbf3ad7be8@mail.gmail.com>
References: <87skyhxbqd.fsf@nitsua.mit.edu>
	<2c8757af0803240726u34f9d0a5oc65595d5710e8317@mail.gmail.com>
	<82ea197fda4aa0b6c73cee89ad57551e@csail.mit.edu>
	<54746a3f0803240947j1c46967ci393bcf800454ca4a@mail.gmail.com>
	<2c8757af0803250354i1e81a027r4b792ef13327ac30@mail.gmail.com>
	<87fxufvwc5.fsf@nitsua.mit.edu>
	<2c8757af0803250646t51ece9d0sb4a6118294c28357@mail.gmail.com>
	<2c8757af0803250657w79091dafv59107ddbf3ad7be8@mail.gmail.com>
Message-ID: <26428aaa0803250816t58beb7d9y1a590e5d07696099@mail.gmail.com>

I'm excited by the discussion. Let me share a few observations.

One of the real problems we're dealing with at the moment is that
'wikifying' is, in theory, a great thing to do to stimulate discussion and
collaboration. To date, we've found that finding specific information within
MediaWiki can be daunting for many users.  One suggestion for documents
generated by a wiki has been,

*"Expose 'em all, an' let Google sort 'em out".
*
Brute force searching of this data may not be the best, or at least the
only, way to make navigation through wiki data useful. If this data set is
to have "legs" and grow, consider the existing wiki paradigm and how it
applies to this effort.

If a dataset this large is to be put into a format that can be manipulated
via many contributors, I'd strongly suggest a few things:

1. Before deciding to come up with a new storage structure such as SVN for
creating such a massive dataset, see if MW can be used. In theory, it's more
than capable of handling 2 million discrete entries, the current size of the
Wikipedia dataset. I have no idea how many revisions there are but the
number must be in excess of 10 million. Add to this a talk page per document
and you have a LOT of data.

I know you folks can point to millions of lines of source code under
management. But repurposing SVN to have a key role in a new system will
require changes. For instance, there's no way to use SVN to directly enforce
submission standards in entries in the system. Sure: we can specify filters
or other gatekeepers to do it. But this is what MediaWiki is, at its core.
The travesty that templates in the system have become notwithstanding, the
core is reliably handling a lot of documents. Don't underestimate the kind
of problems the WikiMedia team has overcome to get where they are now.

2. Have a clear delineation between pages created within the system that
directly reflect a specific entry in one of the biological databases and
those created on a more 'ad-hoc' basis by users of such a system. Our
experience has shown that docs defining a specific protocol are hard to sort
out from those referencing such protocols. We're concretely dealing with
this right now. Full-text indexing doesn't currently help with this.
Categories are too loosely defined. We don't really have a good taxonomy,
never mind an ontology! We're moving toward a relevance-ranked search
(Lucene) but even this won't pull apart all of the information we think our
users come to us looking for.

3. Explore using the Lucene Search engine rather than the default MediaWiki
engine. The number of documents in this system would greatly exceed the
capacity of MySQL's noble but potentially useless search engine that is the
MW default. Estimates are that Lucence can provide an order of magnitude
performance increase over the MySQL search. It can be located on a separate
server. One instance can support multiple clustered servers.

4. Programatically enforce the way the taxonomy of the information as well
as other metadata is managed. My current experience with OWW indicates that
the value of the content will be greatly enhanced if the community founded
around the enhancement of the core information will use tools that, over
time, drive the general creation of computer process-friendly and
user-friendly data (knowledge, dare I say?). Otherwise, this effort may find
limits to the utility of the data collection.

5. This may be an appropriate use for something like the Semantic MediaWiki
extensions. If the 'shape' of a certain class of data can be maintained and
enhanced, the ability to connect these entities into other higher level
abstractions will be dramatically improved. Please don't quote me on this.
The jury is still WAY out on the scalability of Semantic MediaWiki. But some
kind of focused editor for managing data entry requirements is imperative.

6. There currently is no other open source solution, in PHP, Python, Java,
Ruby, Perl, or who knows what, that is driving the search and update volume
that Wikipedia sustains. GenBank and other bioinformatic databases may see a
greater volume under much more real-time driven constraints. But none are
allowing hundreds of millions of people to view and at least tens of
thousands of people to create and edit document simultaneously. In this
sense, I wouldn't encourage adopting Semantic Mediawiki until the developer
community has similar sized datasets that are actively being used by their
communities.

7. Don't assume the MW concept of a Wiki is appropriate for all aspects of
the management of this dataset. MW can provide the fabric and storage model
of the system. But, a more structured set of tools may be the best way to
manage aspects of this data. Currently, the model is to add extensions to
the core MW application to do this. I can't agree this is the best way to
proceed. The MW framework is a terrible platform for designing programs.
It's more like writing assembler language for a computer designed by kids
stuck in a junior high school detention room than doing contemporary
development work. This disinvites innovation by making access and extension
of the dataset the province of the Initiate rather than the many people who
can program but lack experience with MediaWiki.

Conclusion

Putting data onto a server is one thing. Making it useful and sustainable is
quite another thing. I'm 100% behind doing something to open up control of
the annotation and commentary around this kind of data. I'm just not
convinced that this exercise will lead to a useful utility for doing great
science unless it's viewed as such and not as a data management exercise. I
hope this doesn't come off as sour grapes. If you want to do something right
that makes a difference to a lot of researchers, please look at the scope of
the end-to-end problem you're trying to solve.


On Tue, Mar 25, 2008 at 9:57 AM, Dan Bolser <dan.bolser at gmail.com> wrote:

>
> On 25/03/2008, Austin Che <austin at csail.mit.edu> wrote:
>
> >
> > > a) grab all the data from the PDB (for example)
> > > b) stick all the data into a revisioning system
> > > c) allow users to freely edit the data, including automatic clean up
> > 'bots',
> > > algorithms, etc., etc.
> > > d) have all changes automatically emailed to a mailing list for
> > community
> > > review, approval etc.
> > >
> > > Now, once we get to step d, in the time since step a, the PDB data has
> > been
> > > updated by the PDB. We now need to merge the updated PDB data with our
> > > independently modified data. (This is where we need to go beyond a
> > simple
> > > revisioning system).
> >
> >
> >     That was supposed to be the goal of wikiproteins
> >     http://www.wikiproteins.org/Meta:Wikiproteins
> >     Roughly speaking, it does exactly the above. It works with
> >     databases like swiss-prot and downloads all the data into a
> >     semantic wiki form allowing edits. The changes made by the
> >     community can be kept separate from the "authoritative" version
> >     and periodically it's sent back to the original source for
> >     updating. At least that's the idea. They collaborate with those
> >     databases so not all of the databases are resisting this idea.
>
>
>
> Yeah, I like the idea, and its good to see database developers on board
> with that project. I spent some time hanging out near some wikiproteins
> developers (as close as I could get) in irc://irc.freenode.net/#omegawiki -
> I was disappointed at their lack of communication. For example, I have
> worked on a Swiss-Prot parser, so I was curious as to how they had decided
> to relationally model the data (if at all),  but I couldn't get any feed
> back from them. Perhaps I was in the wrong place / asking the wrong
> questions / etc.
>
> Also some of the concepts that they expound at wikiproteins are really
> confusing, and so far they have not decided to answer my questions about
> them.  For example,
>
> http://www.wikiproteins.org/Partner_talk:Knewco
> http://www.wikiproteins.org/Meta_talk:Wikiproteins
>
> http://www.wikiproteins.org/Meta_talk:Personal_Desktop
> http://www.wikiproteins.org/Meta_talk:Alerts
>
>
> I am sure wikiproteins will deliver, I am just not sure when (or what
> really)... Did anyone try the new beta release?
>
>
>
> --
> > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> >
>
>
>
> --
> hello
>
> --
> hello
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From bill.altmail at gmail.com  Thu Mar 27 15:22:18 2008
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 27 Mar 2008 15:22:18 -0400
Subject: [OWW-Discuss] OWW and yacy.net: yacybot is killing performance
Message-ID: <26428aaa0803271222w40ac0086o1575b6b0c647968f@mail.gmail.com>

Does Anyone know anything about a spider bot called "yacybot":

http://www.yacy.net

It's a German host where you download the code from.

They claim to be affiliated with the Karlsrueh Institute of Technology.
They're really killing our database performace.

The IP address used in the request is invalid. Since this is the case, this
may be a denial-of-service attack. I was unable to access the system for
over a minute a few hours ago. The database has been timing out because of
the level of activity.

One indicator of how intrusive they are is that when I search for them, I'm
coming up with logfile entries for hosts all over the net that this bot is
also hitting.

This caims to be a peer-to-peer search engine.

They're now in the 'deny 'list in robots.txt. They do appear to read the
file when they start. If I see them continuing to hit us, we'll take the
next step and treat any system running this bot as a spammer.

Before we take further measure to throttle them, I just want to know if
anyone has experience with them.

Thanks.

Bill
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From sjkoch at unm.edu  Thu Mar 27 22:59:19 2008
From: sjkoch at unm.edu (Steven J. Koch)
Date: Thu, 27 Mar 2008 20:59:19 -0600
Subject: [OWW-Discuss] Problems with OWW?
Message-ID: <003c01c8907f$b7b13730$2713a590$@edu>

Over the last 24 hours or so, I've encountered a lot of errors on OWW, many
of them causing me to lose data.  For example, this one:

Parse error: syntax error, unexpected ')' in
/data/web/extensions/active/LNCalendar1.php on line 93

Upon hitting "back" or refresh, I can't recover the form data.

Also, I was receiving messages about something like "too many connections"
cannot connect to OWW.

I'm guessing this is related to upgrades or something, but thought I would
post, in case nobody knows of the problems.

--Steve Koch

www.openwetware.org/wiki/Koch_Lab



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From bill.altmail at gmail.com  Fri Mar 28 02:28:56 2008
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 28 Mar 2008 02:28:56 -0400
Subject: [OWW-Discuss] Problems with OWW?
In-Reply-To: <003c01c8907f$b7b13730$2713a590$@edu>
References: <003c01c8907f$b7b13730$2713a590$@edu>
Message-ID: <26428aaa0803272328s2657d810ldb28a5b1744fe0c@mail.gmail.com>

Steve,

We were hammered today by a system spidering the OWW server out of control.
We worked with Rackspace into the evening to make sure that the server got
out from under the barrage. We ran well over twice our daily bandwidth and
database activity. This started last evening. The system was periodically
throwing database error as it started. The php errors were caused when we
added a new extension.

I'm very sorry you lost data. After this weekend, OWW will finally be
running or an up-to-date version of linux (Red Hat Enterprise Linux 5).
We'll also have a fairly big local server (shmoo) running on a system we can
test with that has the same version of Linux as the production server. Our
current local development server (beta) has been severely challenged to keep
up with the burden we put on it.


Sincerely,

Bill Flanagan




On Thu, Mar 27, 2008 at 10:59 PM, Steven J. Koch <sjkoch at unm.edu> wrote:

>  Over the last 24 hours or so, I've encountered a lot of errors on OWW,
> many of them causing me to lose data.  For example, this one:
>
> *Parse error*: syntax error, unexpected ')' in*
> /data/web/extensions/active/LNCalendar1.php* on line* 93***
>
> Upon hitting "back" or refresh, I can't recover the form data.
>
> Also, I was receiving messages about something like "too many connections"cannot connect to OWW.
>
> I'm guessing this is related to upgrades or something, but thought I would
> post, in case nobody knows of the problems.
>
> --Steve Koch
>
> *****www.openwetware.org/wiki/Koch_Lab*<http://www.openwetware.org/wiki/Koch_Lab>
>
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From goderisa at cs.man.ac.uk  Fri Mar 28 17:03:34 2008
From: goderisa at cs.man.ac.uk (Antoon Goderis)
Date: Fri, 28 Mar 2008 21:03:34 +0000 (GMT)
Subject: [OWW-Discuss] Joint paper on sharing and finding protocols?
Message-ID: <Pine.GSO.4.42.0803282012540.9338-100000@phoebus>


Dear OWW'ers,

I'm currently writing a paper on the sharing and retrieval of
computational workflows in bioinformatics ("in silico protocols"), based
on our experiences with a Web 2.0 social networking site called
myExperiment.org. I think it would be interesting to extend the paper
with a case study on the sharing and retrieval of protocols on OWW.

We have run a survey with 24 users and are analysing our Web logs for how
our users do retrieval. I noticed your recent user survey as well as
your musings on incentive models for sharing. It would be nice to
contrast this with the behaviour we encounter. Similarly, an analysis of
your logs could be revealing.

If anyone is interested in exploring this, please get in touch.

Cheers,

Antoon
--
Antoon Goderis
School of Computer Science
University of Manchester
United Kingdom
http://www.openwetware.org/wiki/User:AntoonGoderis
http://www.myexperiment.org







From bill.altmail at gmail.com  Mon Mar 31 16:40:12 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 31 Mar 2008 16:40:12 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity feature?
Message-ID: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>

A large part of all of OWW's traffic comes from referrals from either Google
or Yahoo. That means a user sees a small tag on the search result line prior
to clicking on it that identifies the page as part of OWW.

Once they click on the link to go to OWW, Barry pointed out that when they
land on one of our pages other than Main_Page or one of a dozen or fewer
other pages, there's nothing on the top of the page or in the sidebar to
identify the site. We become anonymous. The viewer has to scroll to the
bottom of the page to find a small link for "about openwetware.org".

Our first attempt to address the problem will go online soon. We're adding a
one-time display of the text from the OWW main page telling users who we are
and inviting them to join. Once they have a cookie from our site, they will
never see it again. If they visit once and see a link that's not relevant to
them, the nxt time they visit and get wowed by our info, they may not
connect the fact they found value at OWW and thus fail to look around on the
site.

Does anyone have any thoughts about other ways to address this? Even in UMS,
every page has a banner identifying the site as OWW.

We can add a banner to the skin over the white area of the page. This banner
would not ever be displayed on hosted lab's sites since the dewikify app
doesn't export the skins. I'm no artists. If anyone has a simple and clear
way to express who we are to visitors in an unobtrusive but clear way, I'd
love to hear about it.

Thanks!

B.
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From austin at csail.mit.edu  Mon Mar 31 16:54:57 2008
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 31 Mar 2008 16:54:57 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	(Bill F.'s message of "Mon, 31 Mar 2008 16:40:12 -0400")
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
Message-ID: <87bq4u397i.fsf@nitsua.mit.edu>


> Once they click on the link to go to OWW, Barry pointed out that when they
> land on one of our pages other than Main_Page or one of a dozen or fewer
> other pages, there's nothing on the top of the page or in the sidebar to
> identify the site. We become anonymous. The viewer has to scroll to the
> bottom of the page to find a small link for "about openwetware.org".

    I think people are familiar enough with looking at the url in
    their browser to know what site they're on. Also, the title of
    every page clearly includes OpenWetWare. Every browser I know
    includes this as part of the browser window title.
    
> Our first attempt to address the problem will go online soon. We're adding a
> one-time display of the text from the OWW main page telling users who we are
> and inviting them to join. Once they have a cookie from our site, they will
> never see it again. If they visit once and see a link that's not relevant to
> them, the nxt time they visit and get wowed by our info, they may not
> connect the fact they found value at OWW and thus fail to look around on the
> site.

    This seems like a nice idea to try.
    
> Does anyone have any thoughts about other ways to address this? Even in UMS,
> every page has a banner identifying the site as OWW.

    I don't think this is a problem. 
    
> We can add a banner to the skin over the white area of the page. This banner
> would not ever be displayed on hosted lab's sites since the dewikify app
> doesn't export the skins. I'm no artists. If anyone has a simple and clear
> way to express who we are to visitors in an unobtrusive but clear way, I'd
> love to hear about it.

    I don't think we should waste screen space for banners advertising
    who we are. Anyone who cares (i.e. if there's useful content and
    they're looking for more) will have no problem finding the main
    page.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From julius.lucks at gmail.com  Mon Mar 31 17:04:20 2008
From: julius.lucks at gmail.com (julius.lucks)
Date: Mon, 31 Mar 2008 14:04:20 -0700
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <87bq4u397i.fsf@nitsua.mit.edu>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
Message-ID: <352A7BA7-6C8A-4478-8F67-D5CBEF7B2136@gmail.com>

I do think it's a good idea to put a 'Join OWW' button somewhere  
prominent on every page.  Even when I have told collaborators to  
join, I searched for 'join' to find the join page - i.e., it wasn't  
obvious where the join page was from some button or link.  A  
prominent join button/image/link that says 'Join OWW' other than the  
'create an account/log in' link would both advertise who we are, and  
give people an easy way to join (esp. those not familiar with the  
mediawiki links in the top right).

Cheers,

Julius

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



On Mar 31, 2008, at 1:54 PM, Austin Che wrote:

>
>> Once they click on the link to go to OWW, Barry pointed out that  
>> when they
>> land on one of our pages other than Main_Page or one of a dozen or  
>> fewer
>> other pages, there's nothing on the top of the page or in the  
>> sidebar to
>> identify the site. We become anonymous. The viewer has to scroll  
>> to the
>> bottom of the page to find a small link for "about openwetware.org".
>
>     I think people are familiar enough with looking at the url in
>     their browser to know what site they're on. Also, the title of
>     every page clearly includes OpenWetWare. Every browser I know
>     includes this as part of the browser window title.
>
>> Our first attempt to address the problem will go online soon.  
>> We're adding a
>> one-time display of the text from the OWW main page telling users  
>> who we are
>> and inviting them to join. Once they have a cookie from our site,  
>> they will
>> never see it again. If they visit once and see a link that's not  
>> relevant to
>> them, the nxt time they visit and get wowed by our info, they may not
>> connect the fact they found value at OWW and thus fail to look  
>> around on the
>> site.
>
>     This seems like a nice idea to try.
>
>> Does anyone have any thoughts about other ways to address this?  
>> Even in UMS,
>> every page has a banner identifying the site as OWW.
>
>     I don't think this is a problem.
>
>> We can add a banner to the skin over the white area of the page.  
>> This banner
>> would not ever be displayed on hosted lab's sites since the  
>> dewikify app
>> doesn't export the skins. I'm no artists. If anyone has a simple  
>> and clear
>> way to express who we are to visitors in an unobtrusive but clear  
>> way, I'd
>> love to hear about it.
>
>     I don't think we should waste screen space for banners advertising
>     who we are. Anyone who cares (i.e. if there's useful content and
>     they're looking for more) will have no problem finding the main
>     page.
>
> -- 
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss

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From tk at csail.mit.edu  Mon Mar 31 17:04:21 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Mon, 31 Mar 2008 17:04:21 -0400
Subject: [OWW-Discuss] NIH Open Access comment period
Message-ID: <dbc13935e650ada21c1b5caf9a8d2edf@csail.mit.edu>

Today is the first day of the public comment period, running through 
May 31, on the NIH Open Access publication policy.
You may wish to make your comments on the web site here, or to view 
other comments:
http://publicaccess.nih.gov/comments.htm



From tk at csail.mit.edu  Mon Mar 31 17:08:30 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Mon, 31 Mar 2008 17:08:30 -0400
Subject: [OWW-Discuss] Recently visited pages
Message-ID: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu>

Other highly linked sites maintain a list of the last half-dozen or so 
pages visited on the site by you as a click menu on the page.  This 
seems like it would be a very welcome navigation feature in OWW.  I 
often find myself wanting to switch quickly between several pages.




From jason.p.morrison at gmail.com  Mon Mar 31 17:09:07 2008
From: jason.p.morrison at gmail.com (Jason Morrison)
Date: Mon, 31 Mar 2008 17:09:07 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <87bq4u397i.fsf@nitsua.mit.edu>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
Message-ID: <8ba0586d0803311409l786ded76y950d4d9cf5aef43a@mail.gmail.com>

I definitely agree with the concern - i.e. looking at some random page (say
http://openwetware.org/wiki/Bone_Marrow_Macrophages), it is difficult to
determine who is responsible for the content, and I get no branding
association to OWW.

The one-time pop sounds like a good way to address this.  Does it occlude
the content the user is looking for, or is it in-line text (say, above the
article/talk/edit/history tabs, or between these and the H1)?  Occluding or
blocking or significantly pushing down the desired content could be quite
irritating for a user, but a subtle approach would likely address the issue
while not keeping users from their desired content.  Also, be careful that
spiders do not receive this pop, as that might hurt indexing.

It might also help to put "OpenWetWare" and a tagline on the upper-left wiki
badge image, much like http://en.wikipedia.org/images/wiki-en.png (and
Julius' suggested "Join OWW" button right next to or under this?)

Jason

On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:

>
> > Once they click on the link to go to OWW, Barry pointed out that when
> they
> > land on one of our pages other than Main_Page or one of a dozen or fewer
> > other pages, there's nothing on the top of the page or in the sidebar to
> > identify the site. We become anonymous. The viewer has to scroll to the
> > bottom of the page to find a small link for "about openwetware.org".
>
>     I think people are familiar enough with looking at the url in
>    their browser to know what site they're on. Also, the title of
>    every page clearly includes OpenWetWare. Every browser I know
>    includes this as part of the browser window title.
>
> > Our first attempt to address the problem will go online soon. We're
> adding a
> > one-time display of the text from the OWW main page telling users who we
> are
> > and inviting them to join. Once they have a cookie from our site, they
> will
> > never see it again. If they visit once and see a link that's not
> relevant to
> > them, the nxt time they visit and get wowed by our info, they may not
> > connect the fact they found value at OWW and thus fail to look around on
> the
> > site.
>
>     This seems like a nice idea to try.
>
> > Does anyone have any thoughts about other ways to address this? Even in
> UMS,
> > every page has a banner identifying the site as OWW.
>
>     I don't think this is a problem.
>
> > We can add a banner to the skin over the white area of the page. This
> banner
> > would not ever be displayed on hosted lab's sites since the dewikify app
> > doesn't export the skins. I'm no artists. If anyone has a simple and
> clear
> > way to express who we are to visitors in an unobtrusive but clear way,
> I'd
> > love to hear about it.
>
>     I don't think we should waste screen space for banners advertising
>    who we are. Anyone who cares (i.e. if there's useful content and
>    they're looking for more) will have no problem finding the main
>    page.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>



-- 
Jason Morrison
jason.p.morrison at gmail.com
http://jayunit.net
(585) 216-5657
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From bill.altmail at gmail.com  Mon Mar 31 17:13:29 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 31 Mar 2008 17:13:29 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <87bq4u397i.fsf@nitsua.mit.edu>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
Message-ID: <26428aaa0803311413l89eb4a5g5ca79f6f05b0ccad@mail.gmail.com>

On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:

>
> > Once they click on the link to go to OWW, Barry pointed out that when
> they
> > land on one of our pages other than Main_Page or one of a dozen or fewer
> > other pages, there's nothing on the top of the page or in the sidebar to
> > identify the site. We become anonymous. The viewer has to scroll to the
> > bottom of the page to find a small link for "about openwetware.org".
>
>     I think people are familiar enough with looking at the url in
>    their browser to know what site they're on. Also, the title of
>    every page clearly includes OpenWetWare. Every browser I know
>    includes this as part of the browser window title.
>

I'm not pointing this out from a correctness perspective. I have no evidence
to dispute or corroborate your point regarding most people. I'm only me and
even that's hard for me to track on occasion. We can look into this but I'm
wary of making a generalization based upon what I experience.


>
> > Our first attempt to address the problem will go online soon. We're
> adding a
> > one-time display of the text from the OWW main page telling users who we
> are
> > and inviting them to join. Once they have a cookie from our site, they
> will
> > never see it again. If they visit once and see a link that's not
> relevant to
> > them, the nxt time they visit and get wowed by our info, they may not
> > connect the fact they found value at OWW and thus fail to look around on
> the
> > site.
>
>     This seems like a nice idea to try.
>
> > Does anyone have any thoughts about other ways to address this? Even in
> UMS,
> > every page has a banner identifying the site as OWW.
>
>     I don't think this is a problem.
>

I'm not worried about this as a problem as much as I'm pointing this out as
an opportunity missed to acquaint the many visitors to our site with who we
are. One goal I'd think we all share is to get more people to become members
of OWW or to get more people to, based on what we offer, link to us and,
thereby, increase the exposure of the system in the eyes of relevance-ranked
search engines.


>
> > We can add a banner to the skin over the white area of the page. This
> banner
> > would not ever be displayed on hosted lab's sites since the dewikify app
> > doesn't export the skins. I'm no artist. If anyone has a simple and
> clear
> > way to express who we are to visitors in an unobtrusive but clear way,
> I'd
> > love to hear about it.
>
>     I don't think we should waste screen space for banners advertising
>    who we are. Anyone who cares (i.e. if there's useful content and
>    they're looking for more) will have no problem finding the main
>    page.
>

I appreciate your opinion. Maybe you're right. I hope we're not saying that
if we don't connect to a visitor on the specific search term that brought
the user to us, we don't want to encourage them to come back. We sort of
appear to be a bunch of pages to people coming in from Google and not a
specific site.

Take a look at how other online bio communities and web sites handle this.
Compare to information points we can all corroborate. if most other places
don't tell who they are to people coming in from Google, I agree: we don't
need to be concerned. But if we're not currently using good search metrics
to get more people involved in OWW, maybe we can.



>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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From bill.altmail at gmail.com  Mon Mar 31 17:17:54 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 31 Mar 2008 17:17:54 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <8ba0586d0803311409l786ded76y950d4d9cf5aef43a@mail.gmail.com>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
	<8ba0586d0803311409l786ded76y950d4d9cf5aef43a@mail.gmail.com>
Message-ID: <26428aaa0803311417t49881ad5u3782b1fb86fbc635@mail.gmail.com>

On Mon, Mar 31, 2008 at 5:09 PM, Jason Morrison <jason.p.morrison at gmail.com>
wrote:

> I definitely agree with the concern - i.e. looking at some random page
> (say http://openwetware.org/wiki/Bone_Marrow_Macrophages), it is difficult
> to determine who is responsible for the content, and I get no branding
> association to OWW.
>
> The one-time pop sounds like a good way to address this.  Does it occlude
> the content the user is looking for, or is it in-line text (say, above the
> article/talk/edit/history tabs, or between these and the H1)?


Nothing is occcluded. It's invisible to lab websites as well since the tag
is bracketed by "<wikionly>" tags.


> Occluding or blocking or significantly pushing down the desired content
> could be quite irritating for a user, but a subtle approach would likely
> address the issue while not keeping users from their desired content.  Also,
> be careful that spiders do not receive this pop, as that might hurt
> indexing.
>

This isn't a popup. It's a section of the page that's invisible to returning
visitors. In other words, the "visiblility" attribute is by default set to
'invisible'.


>
> It might also help to put "OpenWetWare" and a tagline on the upper-left
> wiki badge image, much like http://en.wikipedia.org/images/wiki-en.png(and Julius' suggested "Join OWW" button right next to or under this?)
>
> Jason
>
>
> On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:
>
> >
> > > Once they click on the link to go to OWW, Barry pointed out that when
> > they
> > > land on one of our pages other than Main_Page or one of a dozen or
> > fewer
> > > other pages, there's nothing on the top of the page or in the sidebar
> > to
> > > identify the site. We become anonymous. The viewer has to scroll to
> > the
> > > bottom of the page to find a small link for "about openwetware.org".
> >
> >     I think people are familiar enough with looking at the url in
> >    their browser to know what site they're on. Also, the title of
> >    every page clearly includes OpenWetWare. Every browser I know
> >    includes this as part of the browser window title.
> >
> > > Our first attempt to address the problem will go online soon. We're
> > adding a
> > > one-time display of the text from the OWW main page telling users who
> > we are
> > > and inviting them to join. Once they have a cookie from our site, they
> > will
> > > never see it again. If they visit once and see a link that's not
> > relevant to
> > > them, the nxt time they visit and get wowed by our info, they may not
> > > connect the fact they found value at OWW and thus fail to look around
> > on the
> > > site.
> >
> >     This seems like a nice idea to try.
> >
> > > Does anyone have any thoughts about other ways to address this? Even
> > in UMS,
> > > every page has a banner identifying the site as OWW.
> >
> >     I don't think this is a problem.
> >
> > > We can add a banner to the skin over the white area of the page. This
> > banner
> > > would not ever be displayed on hosted lab's sites since the dewikify
> > app
> > > doesn't export the skins. I'm no artists. If anyone has a simple and
> > clear
> > > way to express who we are to visitors in an unobtrusive but clear way,
> > I'd
> > > love to hear about it.
> >
> >     I don't think we should waste screen space for banners advertising
> >    who we are. Anyone who cares (i.e. if there's useful content and
> >    they're looking for more) will have no problem finding the main
> >    page.
> >
> > --
> > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
>
>
>
> --
> Jason Morrison
> jason.p.morrison at gmail.com
> http://jayunit.net
> (585) 216-5657
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From austin at csail.mit.edu  Mon Mar 31 17:22:07 2008
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 31 Mar 2008 17:22:07 -0400
Subject: [OWW-Discuss] Recently visited pages
In-Reply-To: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu> (Tom Knight's
	message of "Mon, 31 Mar 2008 17:08:30 -0400")
References: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu>
Message-ID: <8763v237y8.fsf@nitsua.mit.edu>

Tom Knight <tk at csail.mit.edu> wrote:

> Other highly linked sites maintain a list of the last half-dozen or so 
> pages visited on the site by you as a click menu on the page.  This 
> seems like it would be a very welcome navigation feature in OWW.  I 
> often find myself wanting to switch quickly between several pages.

    Add the following to monobook.js under your userpage or go to
    http://openwetware.org/wiki/Special:Mypage/monobook.js
    document.write('<script type="text/javascript" src="http://openwetware.org/index.php?title=User:Austin_J._Che/Extensions/history.js&action=raw&ctype=text/javascript"></script>');

    This should add a drop down list of your most recently visited
    pages.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From sjkoch at unm.edu  Mon Mar 31 17:27:18 2008
From: sjkoch at unm.edu (Steven J. Koch)
Date: Mon, 31 Mar 2008 15:27:18 -0600
Subject: [OWW-Discuss] I vote for putting text under OWW logo & join
	buttonRE: Oww-discuss Digest, Vol 18, Issue 27
In-Reply-To: <mailman.253074.1206998312.13433.oww-discuss@mit.edu>
References: <mailman.253074.1206998312.13433.oww-discuss@mit.edu>
Message-ID: <009401c89376$00525980$00f70c80$@edu>

Sorry, I got a little lost in the discussion, so I may have missed some
ideas.  I want to second a couple motions:

1.  Text under the wonderful OWW DNA handshake logo, similar to Wikipedia
(title plus motto) is a great idea for branding.
2.  A Prominent / Permanent "Join OWW" would be nice.  I too have to search
when referring people.
3.  I am hesitant to endorse the one-time "new visitor" addition.  It does
sound fine as described, but I'd vote for erring on the side of caution when
automatically modifying the page content.  A different idea would be to add
an OWW "motto" to the title bar (again similar to Wikipedia), instead of
just "OpenWetWare" as it is now.

-----Original Message-----
From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu] On
Behalf Of oww-discuss-request at mit.edu
Sent: Monday, March 31, 2008 3:19 PM
To: oww-discuss at mit.edu
Subject: Oww-discuss Digest, Vol 18, Issue 27

Send Oww-discuss mailing list submissions to
	oww-discuss at mit.edu

To subscribe or unsubscribe via the World Wide Web, visit
	http://mailman.mit.edu/mailman/listinfo/oww-discuss
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Oww-discuss digest..."


Today's Topics:

   1. Recently visited pages (Tom Knight)
   2. Re: OpenWetWare.org: identity problem/identity	feature?
      (Jason Morrison)
   3. Re: OpenWetWare.org: identity problem/identity	feature? (Bill F)
   4. Re: OpenWetWare.org: identity problem/identity	feature? (Bill F)


----------------------------------------------------------------------

Message: 1
Date: Mon, 31 Mar 2008 17:08:30 -0400
From: Tom Knight <tk at csail.mit.edu>
Subject: [OWW-Discuss] Recently visited pages
To: discuss at openwetware.org
Message-ID: <86c53ac85998da3b9417dab1030d0442 at csail.mit.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Other highly linked sites maintain a list of the last half-dozen or so 
pages visited on the site by you as a click menu on the page.  This 
seems like it would be a very welcome navigation feature in OWW.  I 
often find myself wanting to switch quickly between several pages.




------------------------------

Message: 2
Date: Mon, 31 Mar 2008 17:09:07 -0400
From: "Jason Morrison" <jason.p.morrison at gmail.com>
Subject: Re: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
To: "discuss at openwetware.org" <discuss at openwetware.org>
Message-ID:
	<8ba0586d0803311409l786ded76y950d4d9cf5aef43a at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

I definitely agree with the concern - i.e. looking at some random page (say
http://openwetware.org/wiki/Bone_Marrow_Macrophages), it is difficult to
determine who is responsible for the content, and I get no branding
association to OWW.

The one-time pop sounds like a good way to address this.  Does it occlude
the content the user is looking for, or is it in-line text (say, above the
article/talk/edit/history tabs, or between these and the H1)?  Occluding or
blocking or significantly pushing down the desired content could be quite
irritating for a user, but a subtle approach would likely address the issue
while not keeping users from their desired content.  Also, be careful that
spiders do not receive this pop, as that might hurt indexing.

It might also help to put "OpenWetWare" and a tagline on the upper-left wiki
badge image, much like http://en.wikipedia.org/images/wiki-en.png (and
Julius' suggested "Join OWW" button right next to or under this?)

Jason

On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:

>
> > Once they click on the link to go to OWW, Barry pointed out that when
> they
> > land on one of our pages other than Main_Page or one of a dozen or fewer
> > other pages, there's nothing on the top of the page or in the sidebar to
> > identify the site. We become anonymous. The viewer has to scroll to the
> > bottom of the page to find a small link for "about openwetware.org".
>
>     I think people are familiar enough with looking at the url in
>    their browser to know what site they're on. Also, the title of
>    every page clearly includes OpenWetWare. Every browser I know
>    includes this as part of the browser window title.
>
> > Our first attempt to address the problem will go online soon. We're
> adding a
> > one-time display of the text from the OWW main page telling users who we
> are
> > and inviting them to join. Once they have a cookie from our site, they
> will
> > never see it again. If they visit once and see a link that's not
> relevant to
> > them, the nxt time they visit and get wowed by our info, they may not
> > connect the fact they found value at OWW and thus fail to look around on
> the
> > site.
>
>     This seems like a nice idea to try.
>
> > Does anyone have any thoughts about other ways to address this? Even in
> UMS,
> > every page has a banner identifying the site as OWW.
>
>     I don't think this is a problem.
>
> > We can add a banner to the skin over the white area of the page. This
> banner
> > would not ever be displayed on hosted lab's sites since the dewikify app
> > doesn't export the skins. I'm no artists. If anyone has a simple and
> clear
> > way to express who we are to visitors in an unobtrusive but clear way,
> I'd
> > love to hear about it.
>
>     I don't think we should waste screen space for banners advertising
>    who we are. Anyone who cares (i.e. if there's useful content and
>    they're looking for more) will have no problem finding the main
>    page.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>



-- 
Jason Morrison
jason.p.morrison at gmail.com
http://jayunit.net
(585) 216-5657
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Message: 3
Date: Mon, 31 Mar 2008 17:13:29 -0400
From: "Bill F" <bill.altmail at gmail.com>
Subject: Re: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
To: "Austin Che" <austin at csail.mit.edu>
Cc: "discuss at openwetware.org" <discuss at openwetware.org>
Message-ID:
	<26428aaa0803311413l89eb4a5g5ca79f6f05b0ccad at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:

>
> > Once they click on the link to go to OWW, Barry pointed out that when
> they
> > land on one of our pages other than Main_Page or one of a dozen or fewer
> > other pages, there's nothing on the top of the page or in the sidebar to
> > identify the site. We become anonymous. The viewer has to scroll to the
> > bottom of the page to find a small link for "about openwetware.org".
>
>     I think people are familiar enough with looking at the url in
>    their browser to know what site they're on. Also, the title of
>    every page clearly includes OpenWetWare. Every browser I know
>    includes this as part of the browser window title.
>

I'm not pointing this out from a correctness perspective. I have no evidence
to dispute or corroborate your point regarding most people. I'm only me and
even that's hard for me to track on occasion. We can look into this but I'm
wary of making a generalization based upon what I experience.


>
> > Our first attempt to address the problem will go online soon. We're
> adding a
> > one-time display of the text from the OWW main page telling users who we
> are
> > and inviting them to join. Once they have a cookie from our site, they
> will
> > never see it again. If they visit once and see a link that's not
> relevant to
> > them, the nxt time they visit and get wowed by our info, they may not
> > connect the fact they found value at OWW and thus fail to look around on
> the
> > site.
>
>     This seems like a nice idea to try.
>
> > Does anyone have any thoughts about other ways to address this? Even in
> UMS,
> > every page has a banner identifying the site as OWW.
>
>     I don't think this is a problem.
>

I'm not worried about this as a problem as much as I'm pointing this out as
an opportunity missed to acquaint the many visitors to our site with who we
are. One goal I'd think we all share is to get more people to become members
of OWW or to get more people to, based on what we offer, link to us and,
thereby, increase the exposure of the system in the eyes of relevance-ranked
search engines.


>
> > We can add a banner to the skin over the white area of the page. This
> banner
> > would not ever be displayed on hosted lab's sites since the dewikify app
> > doesn't export the skins. I'm no artist. If anyone has a simple and
> clear
> > way to express who we are to visitors in an unobtrusive but clear way,
> I'd
> > love to hear about it.
>
>     I don't think we should waste screen space for banners advertising
>    who we are. Anyone who cares (i.e. if there's useful content and
>    they're looking for more) will have no problem finding the main
>    page.
>

I appreciate your opinion. Maybe you're right. I hope we're not saying that
if we don't connect to a visitor on the specific search term that brought
the user to us, we don't want to encourage them to come back. We sort of
appear to be a bunch of pages to people coming in from Google and not a
specific site.

Take a look at how other online bio communities and web sites handle this.
Compare to information points we can all corroborate. if most other places
don't tell who they are to people coming in from Google, I agree: we don't
need to be concerned. But if we're not currently using good search metrics
to get more people involved in OWW, maybe we can.



>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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Message: 4
Date: Mon, 31 Mar 2008 17:17:54 -0400
From: "Bill F" <bill.altmail at gmail.com>
Subject: Re: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
To: "Jason Morrison" <jason.p.morrison at gmail.com>
Cc: "discuss at openwetware.org" <discuss at openwetware.org>
Message-ID:
	<26428aaa0803311417t49881ad5u3782b1fb86fbc635 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

On Mon, Mar 31, 2008 at 5:09 PM, Jason Morrison <jason.p.morrison at gmail.com>
wrote:

> I definitely agree with the concern - i.e. looking at some random page
> (say http://openwetware.org/wiki/Bone_Marrow_Macrophages), it is difficult
> to determine who is responsible for the content, and I get no branding
> association to OWW.
>
> The one-time pop sounds like a good way to address this.  Does it occlude
> the content the user is looking for, or is it in-line text (say, above the
> article/talk/edit/history tabs, or between these and the H1)?


Nothing is occcluded. It's invisible to lab websites as well since the tag
is bracketed by "<wikionly>" tags.


> Occluding or blocking or significantly pushing down the desired content
> could be quite irritating for a user, but a subtle approach would likely
> address the issue while not keeping users from their desired content.
Also,
> be careful that spiders do not receive this pop, as that might hurt
> indexing.
>

This isn't a popup. It's a section of the page that's invisible to returning
visitors. In other words, the "visiblility" attribute is by default set to
'invisible'.


>
> It might also help to put "OpenWetWare" and a tagline on the upper-left
> wiki badge image, much like http://en.wikipedia.org/images/wiki-en.png(and
Julius' suggested "Join OWW" button right next to or under this?)
>
> Jason
>
>
> On Mon, Mar 31, 2008 at 4:54 PM, Austin Che <austin at csail.mit.edu> wrote:
>
> >
> > > Once they click on the link to go to OWW, Barry pointed out that when
> > they
> > > land on one of our pages other than Main_Page or one of a dozen or
> > fewer
> > > other pages, there's nothing on the top of the page or in the sidebar
> > to
> > > identify the site. We become anonymous. The viewer has to scroll to
> > the
> > > bottom of the page to find a small link for "about openwetware.org".
> >
> >     I think people are familiar enough with looking at the url in
> >    their browser to know what site they're on. Also, the title of
> >    every page clearly includes OpenWetWare. Every browser I know
> >    includes this as part of the browser window title.
> >
> > > Our first attempt to address the problem will go online soon. We're
> > adding a
> > > one-time display of the text from the OWW main page telling users who
> > we are
> > > and inviting them to join. Once they have a cookie from our site, they
> > will
> > > never see it again. If they visit once and see a link that's not
> > relevant to
> > > them, the nxt time they visit and get wowed by our info, they may not
> > > connect the fact they found value at OWW and thus fail to look around
> > on the
> > > site.
> >
> >     This seems like a nice idea to try.
> >
> > > Does anyone have any thoughts about other ways to address this? Even
> > in UMS,
> > > every page has a banner identifying the site as OWW.
> >
> >     I don't think this is a problem.
> >
> > > We can add a banner to the skin over the white area of the page. This
> > banner
> > > would not ever be displayed on hosted lab's sites since the dewikify
> > app
> > > doesn't export the skins. I'm no artists. If anyone has a simple and
> > clear
> > > way to express who we are to visitors in an unobtrusive but clear way,
> > I'd
> > > love to hear about it.
> >
> >     I don't think we should waste screen space for banners advertising
> >    who we are. Anyone who cares (i.e. if there's useful content and
> >    they're looking for more) will have no problem finding the main
> >    page.
> >
> > --
> > Austin Che           <austin at csail.mit.edu>          (617)253-5899
> > _______________________________________________
> > OpenWetWare Discussion Mailing List
> > discuss at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-discuss
> >
>
>
>
> --
> Jason Morrison
> jason.p.morrison at gmail.com
> http://jayunit.net
> (585) 216-5657
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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------------------------------

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


End of Oww-discuss Digest, Vol 18, Issue 27
*******************************************



From jason.p.morrison at gmail.com  Mon Mar 31 17:38:39 2008
From: jason.p.morrison at gmail.com (Jason Morrison)
Date: Mon, 31 Mar 2008 17:38:39 -0400
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <26428aaa0803311417t49881ad5u3782b1fb86fbc635@mail.gmail.com>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
	<8ba0586d0803311409l786ded76y950d4d9cf5aef43a@mail.gmail.com>
	<26428aaa0803311417t49881ad5u3782b1fb86fbc635@mail.gmail.com>
Message-ID: <8ba0586d0803311438l3be18b00s4aada56f2245caa3@mail.gmail.com>

> Nothing is occcluded. It's invisible to lab websites as well since the tag
> is bracketed by "<wikionly>" tags.
> (...)
> This isn't a popup. It's a section of the page that's invisible to
> returning visitors. In other words, the "visiblility" attribute is by
> default set to 'invisible'.
>

Bill, this sounds great, then!  :)  I think the overall idea is worth
pursuing, and will be valuable to OWW.

I'll take a minute to explain my SEO pedantry:

Unfortunately, we can't count on spiders to appropriately deal with a
"visibility: none" attribute.  So, if the markup is something like:

<p style="visibility: none;">OpenWetWare is an effort to promote the sharing
of information, know-how, and wisdom among researchers and groups who are
working in biology & biological engineering</p>
<p>Plaque assay for gHV-68 using 3T12 fibroblasts.</p>

then it's possible that the Google search result looks like:

*GHV-68 Plaque Assay *- OpenWetWare
OpenWetWare is an effort to promote the sharing of information, know-how,
and wisdom among researchers and groups who are working...
openwetware.org/wiki/GHV-68_Plaque_Assay*

*rather than the current result (
http://www.google.com/search?q=GHV-68%20Plaque%20Assay) with a more targeted
description line.

Also, we probably can't rely on the search engines to establish a session,
so they are fed a visible branding section anyhow.

I'd suggest that OWW.org suppress the branding information for search
engines, say by identifying the User-Agent field in the HTTP request (see
something like http://www.pgts.com.au/download/data/robots_list.txt, or just
look for bot/spider/crawler in the UA field.)  I imagine that this is
convenient to do at the same time as when you check for a session.

Again, I think this is a great idea to support the OWW branding, and just
don't want to see the organic search value drop as a result.

Cheers,
Jason

-- 
Jason Morrison
jason.p.morrison at gmail.com
http://jayunit.net
(585) 216-5657
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From julius.lucks at gmail.com  Mon Mar 31 18:22:06 2008
From: julius.lucks at gmail.com (julius.lucks)
Date: Mon, 31 Mar 2008 15:22:06 -0700
Subject: [OWW-Discuss] OpenWetWare.org: identity problem/identity
	feature?
In-Reply-To: <8ba0586d0803311438l3be18b00s4aada56f2245caa3@mail.gmail.com>
References: <26428aaa0803311340p1dedd5d5sb48f8948bdfe1168@mail.gmail.com>
	<87bq4u397i.fsf@nitsua.mit.edu>
	<8ba0586d0803311409l786ded76y950d4d9cf5aef43a@mail.gmail.com>
	<26428aaa0803311417t49881ad5u3782b1fb86fbc635@mail.gmail.com>
	<8ba0586d0803311438l3be18b00s4aada56f2245caa3@mail.gmail.com>
Message-ID: <0C812A04-4572-4688-A801-8CBEC440CE02@gmail.com>

I'd like to point out that we could also chat about this in real  
time.  See http://openwetware.org/wiki/Help:Chat for instructions on  
how to set up a client to use the openwetware chat server.

Brian Bishop and I are sitting in on the chat room at  
lounge at openwetware.org .

Cheers,

Julius

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



On Mar 31, 2008, at 2:38 PM, Jason Morrison wrote:

>
> Nothing is occcluded. It's invisible to lab websites as well since  
> the tag is bracketed by "<wikionly>" tags.
> (...)
> This isn't a popup. It's a section of the page that's invisible to  
> returning visitors. In other words, the "visiblility" attribute is  
> by default set to 'invisible'.
>
> Bill, this sounds great, then!  :)  I think the overall idea is  
> worth pursuing, and will be valuable to OWW.
>
> I'll take a minute to explain my SEO pedantry:
>
> Unfortunately, we can't count on spiders to appropriately deal with  
> a "visibility: none" attribute.  So, if the markup is something like:
>
> <p style="visibility: none;">OpenWetWare is an effort to promote  
> the sharing of information, know-how, and wisdom among researchers  
> and groups who are working in biology & biological engineering</p>
> <p>Plaque assay for gHV-68 using 3T12 fibroblasts.</p>
>
> then it's possible that the Google search result looks like:
>
> GHV-68 Plaque Assay - OpenWetWare
> OpenWetWare is an effort to promote the sharing of information,  
> know-how, and wisdom among researchers and groups who are working...
> openwetware.org/wiki/GHV-68_Plaque_Assay
>
> rather than the current result (http://www.google.com/search? 
> q=GHV-68%20Plaque%20Assay) with a more targeted description line.
>
> Also, we probably can't rely on the search engines to establish a  
> session, so they are fed a visible branding section anyhow.
>
> I'd suggest that OWW.org suppress the branding information for  
> search engines, say by identifying the User-Agent field in the HTTP  
> request (see something like http://www.pgts.com.au/download/data/ 
> robots_list.txt, or just look for bot/spider/crawler in the UA  
> field.)  I imagine that this is convenient to do at the same time  
> as when you check for a session.
>
> Again, I think this is a great idea to support the OWW branding,  
> and just don't want to see the organic search value drop as a result.
>
> Cheers,
> Jason
>
> -- 
> Jason Morrison
> jason.p.morrison at gmail.com
> http://jayunit.net
> (585) 216-5657
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss

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From austin at csail.mit.edu  Mon Mar 31 18:24:45 2008
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 31 Mar 2008 18:24:45 -0400
Subject: [OWW-Discuss] I vote for putting text under OWW logo & join
	buttonRE: Oww-discuss Digest, Vol 18, Issue 27
In-Reply-To: <009401c89376$00525980$00f70c80$@edu> (Steven J. Koch's message
	of "Mon, 31 Mar 2008 15:27:18 -0600")
References: <mailman.253074.1206998312.13433.oww-discuss@mit.edu>
	<009401c89376$00525980$00f70c80$@edu>
Message-ID: <87y77y1qhe.fsf@nitsua.mit.edu>

"Steven J. Koch" <sjkoch at unm.edu> wrote:

> 1.  Text under the wonderful OWW DNA handshake logo, similar to Wikipedia
> (title plus motto) is a great idea for branding.

    Agree.
    
> 2.  A Prominent / Permanent "Join OWW" would be nice.  I too have to search
> when referring people.

    Agree.
    
> 3.  I am hesitant to endorse the one-time "new visitor" addition.  It does
> sound fine as described, but I'd vote for erring on the side of caution when
> automatically modifying the page content.  A different idea would be to add
> an OWW "motto" to the title bar (again similar to Wikipedia), instead of
> just "OpenWetWare" as it is now.

    I think adding a motto to the title is a great idea and less
    intrusive than adding a banner to all pages.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From tk at csail.mit.edu  Mon Mar 31 18:29:43 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Mon, 31 Mar 2008 18:29:43 -0400
Subject: [OWW-Discuss] Recently visited pages
In-Reply-To: <8763v237y8.fsf@nitsua.mit.edu>
References: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu>
	<8763v237y8.fsf@nitsua.mit.edu>
Message-ID: <c91ed2e88ff23b209cfdcea43f882228@csail.mit.edu>

While I welcome this advice, it is quite different from making it a  
standard feature of the site.

On Mar 31, 2008, at 5:22 PM, Austin Che wrote:

> Tom Knight <tk at csail.mit.edu> wrote:
>
>> Other highly linked sites maintain a list of the last half-dozen or so
>> pages visited on the site by you as a click menu on the page.  This
>> seems like it would be a very welcome navigation feature in OWW.  I
>> often find myself wanting to switch quickly between several pages.
>
>     Add the following to monobook.js under your userpage or go to
>     http://openwetware.org/wiki/Special:Mypage/monobook.js
>     document.write('<script type="text/javascript"  
> src="http://openwetware.org/index.php?title=User:Austin_J._Che/ 
> Extensions/history.js&action=raw&ctype=text/javascript"></script>');
>
>     This should add a drop down list of your most recently visited
>     pages.
>
> -- 
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss



From austin at csail.mit.edu  Mon Mar 31 18:44:48 2008
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 31 Mar 2008 18:44:48 -0400
Subject: [OWW-Discuss] Recently visited pages
In-Reply-To: <c91ed2e88ff23b209cfdcea43f882228@csail.mit.edu> (Tom Knight's
	message of "Mon, 31 Mar 2008 18:29:43 -0400")
References: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu>
	<8763v237y8.fsf@nitsua.mit.edu>
	<c91ed2e88ff23b209cfdcea43f882228@csail.mit.edu>
Message-ID: <87prta1pjz.fsf@nitsua.mit.edu>


    If we wanted to make it sitewide, someone would just have to add
    that line to: http://openwetware.org/wiki/MediaWiki:Monobook.js
    
    But as no one appears to have even tried it out or uses it other
    than me (as far as I know), it clearly hasn't been a highly
    desired feature. As it changes the UI on every single page, it
    would require some consensus that people wanted it.
    
> While I welcome this advice, it is quite different from making it a
> standard feature of the site.
>
> On Mar 31, 2008, at 5:22 PM, Austin Che wrote:
>
>> Tom Knight <tk at csail.mit.edu> wrote:
>>
>>> Other highly linked sites maintain a list of the last half-dozen or so
>>> pages visited on the site by you as a click menu on the page.  This
>>> seems like it would be a very welcome navigation feature in OWW.  I
>>> often find myself wanting to switch quickly between several pages.
>>
>>     Add the following to monobook.js under your userpage or go to
>>     http://openwetware.org/wiki/Special:Mypage/monobook.js
>>     document.write('<script type="text/javascript"
>> src="http://openwetware.org/index.php?title=User:Austin_J._Che/
>> Extensions/history.js&action=raw&ctype=text/javascript"></script>');
>>
>>     This should add a drop down list of your most recently visited
>>     pages.

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


From bcanton at MIT.EDU  Mon Mar 31 19:12:27 2008
From: bcanton at MIT.EDU (Barry Canton)
Date: Mon, 31 Mar 2008 19:12:27 -0400
Subject: [OWW-Discuss] Recently visited pages
In-Reply-To: <87prta1pjz.fsf@nitsua.mit.edu>
References: <86c53ac85998da3b9417dab1030d0442@csail.mit.edu>
	<8763v237y8.fsf@nitsua.mit.edu>
	<c91ed2e88ff23b209cfdcea43f882228@csail.mit.edu>
	<87prta1pjz.fsf@nitsua.mit.edu>
Message-ID: <52c0d2160803311612n942f91aw8272625e039ed084@mail.gmail.com>

I think such a feature would be very useful (I frequently view recent
changes to find the pages I've been editing recently which is a bit
more awkward).

But given that we are talking about a sitewide change, I'd be
interested to get Bill's take on it and also have some users test it
prior to implementing sitewide.

Barry

On Mon, Mar 31, 2008 at 6:44 PM, Austin Che <austin at csail.mit.edu> wrote:
>
>     If we wanted to make it sitewide, someone would just have to add
>     that line to: http://openwetware.org/wiki/MediaWiki:Monobook.js
>
>     But as no one appears to have even tried it out or uses it other
>     than me (as far as I know), it clearly hasn't been a highly
>     desired feature. As it changes the UI on every single page, it
>     would require some consensus that people wanted it.
>
>
>
>  > While I welcome this advice, it is quite different from making it a
>  > standard feature of the site.
>  >
>  > On Mar 31, 2008, at 5:22 PM, Austin Che wrote:
>  >
>  >> Tom Knight <tk at csail.mit.edu> wrote:
>  >>
>  >>> Other highly linked sites maintain a list of the last half-dozen or so
>  >>> pages visited on the site by you as a click menu on the page.  This
>  >>> seems like it would be a very welcome navigation feature in OWW.  I
>  >>> often find myself wanting to switch quickly between several pages.
>  >>
>  >>     Add the following to monobook.js under your userpage or go to
>  >>     http://openwetware.org/wiki/Special:Mypage/monobook.js
>  >>     document.write('<script type="text/javascript"
>  >> src="http://openwetware.org/index.php?title=User:Austin_J._Che/
>  >> Extensions/history.js&action=raw&ctype=text/javascript"></script>');
>  >>
>  >>     This should add a drop down list of your most recently visited
>  >>     pages.
>
>  --
>  Austin Che           <austin at csail.mit.edu>          (617)253-5899
>  _______________________________________________
>  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) 401-7320 (Grand Central)
Email1: bcanton at mit.edu
Email2: bcanton at gmail.com


From jasonk at MIT.EDU  Mon Mar 31 20:39:42 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 31 Mar 2008 20:39:42 -0400
Subject: [OWW-Discuss] I vote for putting text under OWW logo & join
	buttonRE: Oww-discuss Digest, Vol 18, Issue 27
In-Reply-To: <87y77y1qhe.fsf@nitsua.mit.edu>
References: <mailman.253074.1206998312.13433.oww-discuss@mit.edu>
	<009401c89376$00525980$00f70c80$@edu> <87y77y1qhe.fsf@nitsua.mit.edu>
Message-ID: <7c085c480803311739g5bcd8767o70052daf6ccb37ec@mail.gmail.com>

I really like the idea of the "new visitor banner", as I understand it
there wouldn't be any changes to the wiki-code underlying any page -
it would just pop-up a small bar at the top explaining what the site
is (and would only do this the 1st time you visit the site).

I think having the 'join oww' link and the name 'openwetware' under
the logo are good ideas, but they don't tell the visitor what
openwetware is at all.  And without being told, unless they are very
curious, I doubt many will click a "join OWW" link.

It seems like this is a very easy thing to try out for a week or two,
and we can see if there is an uptick in new accounts.

I'm thinking something like this:
http://openwetware.org/wiki/OpenWetWare:New_visitor_blurb
(I inserted the DNA ligation page below it as an example)

keeping in mind jason's comments about treating the spiders properly,
what other downside is there?  I wasn't clear on exactly what your
concern was, steve.

thanks,
jason


On Mon, Mar 31, 2008 at 6:24 PM, Austin Che <austin at csail.mit.edu> wrote:
> "Steven J. Koch" <sjkoch at unm.edu> wrote:
>
>  > 1.  Text under the wonderful OWW DNA handshake logo, similar to Wikipedia
>  > (title plus motto) is a great idea for branding.
>
>     Agree.
>
>
>  > 2.  A Prominent / Permanent "Join OWW" would be nice.  I too have to search
>  > when referring people.
>
>     Agree.
>
>
>  > 3.  I am hesitant to endorse the one-time "new visitor" addition.  It does
>  > sound fine as described, but I'd vote for erring on the side of caution when
>  > automatically modifying the page content.  A different idea would be to add
>  > an OWW "motto" to the title bar (again similar to Wikipedia), instead of
>  > just "OpenWetWare" as it is now.
>
>     I think adding a motto to the title is a great idea and less
>     intrusive than adding a banner to all pages.
>
>  --
>
>
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
>  _______________________________________________
>  OpenWetWare Discussion Mailing List
>  discuss at openwetware.org
>  http://mailman.mit.edu/mailman/listinfo/oww-discuss
>