From johncumbers at gmail.com  Thu May  1 10:13:20 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Thu, 1 May 2008 07:13:20 -0700
Subject: [OWW-Discuss] Fwd: Next OWW Steering Committee meeting on May 14 at
	12noon
In-Reply-To: <6ac0a26a0804260631w55d3b7dn874f3f83b6e88410@mail.gmail.com>
References: <6ac0a26a0804260631w55d3b7dn874f3f83b6e88410@mail.gmail.com>
Message-ID: <cfd758050805010713m692cef78m67d41e108380ae94@mail.gmail.com>

Just a reminder that there is no meeting today, instead May 14th at noon.
Best,
John

---------- Forwarded message ----------
From: Lorrie LeJeune <lorrielejeune at gmail.com>
Date: Sat, Apr 26, 2008 at 6:31 AM
Subject: [OWW-Discuss] Next OWW Steering Committee meeting on May 14 at
12noon
To: "discuss at openwetware.org" <discuss at openwetware.org>
Cc: team at openwetware.org


Hi Folks,

The next steering committee meeting will take place on Wednesday, May
14 at 12noon. I'll send a reminder a few days before the meeting with
a teleconference number and chat info.

Every OWW user is welcome to attend.

Best,
--Lorrie
_______________________________________________
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 suckale at mpi-cbg.de  Mon May  5 13:33:04 2008
From: suckale at mpi-cbg.de (Jakob Suckale)
Date: Mon, 5 May 2008 19:33:04 +0200
Subject: [OWW-Discuss] protocol icons
Message-ID: <918eed010805051033k796089dcpe96b60788c2c2f07@mail.gmail.com>

What do you guys thing about decorating our protocols a little with
icons highlighting important parts of the instructions like: critical
and/or difficult steps, time info, and possible points to interrupt
the experiment.
http://openwetware.org/wiki/User:Jakob_Suckale/Ideas#icons_for_protocols

Ciao, Jakob


From bill.altmail at gmail.com  Mon May  5 15:14:17 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 5 May 2008 15:14:17 -0400
Subject: [OWW-Discuss] protocol icons
In-Reply-To: <918eed010805051033k796089dcpe96b60788c2c2f07@mail.gmail.com>
References: <918eed010805051033k796089dcpe96b60788c2c2f07@mail.gmail.com>
Message-ID: <26428aaa0805051214x6aeb273do1598647d64e59741@mail.gmail.com>

I'm a total sucker for great looking graphics created to meet specific
purposes. I like the idea a lot. Your icons are fantastic.

Let's assume we were to use them. Would you think other people (i.e., not
the original authors of the protocols) go through and add the icons? There
are a lot of existing protocols already on OWW; it would be nice to think
about how this could be applied to them.

If anyone were to do that, there may be a few other things we could to
simply annotate protocols.

Making them small fits in with the way our current sidebar icons work. What
do you think of using the icons without the words until someone either
hovered on them or asked what they meant? Maybe a key to their meaning would
also work.


Thanks for the great work.

Bill


On Mon, May 5, 2008 at 1:33 PM, Jakob Suckale <suckale at mpi-cbg.de> wrote:

> What do you guys thing about decorating our protocols a little with
> icons highlighting important parts of the instructions like: critical
> and/or difficult steps, time info, and possible points to interrupt
> the experiment.
> http://openwetware.org/wiki/User:Jakob_Suckale/Ideas#icons_for_protocols
>
> Ciao, Jakob
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
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From Torsten.Waldminghaus at rr-research.no  Mon May  5 15:46:52 2008
From: Torsten.Waldminghaus at rr-research.no (Torsten Waldminghaus)
Date: Mon, 5 May 2008 21:46:52 +0200
Subject: [OWW-Discuss] protocol icons
References: <918eed010805051033k796089dcpe96b60788c2c2f07@mail.gmail.com>
	<26428aaa0805051214x6aeb273do1598647d64e59741@mail.gmail.com>
Message-ID: <AFE5B2464F1EB547BBACE62CCE8E402001054538@mr3k6001.ad.medicalresearch.no>

I would keep the words with the icons, but that is my personal preference. There are also icons in Nature Protocols (for example http://www.nature.com/nprot/journal/v3/n1/full/nprot.2007.473.html) as inspiration. However, I like Jakobs icons much better.

Torsten


-----Urspr?ngliche Nachricht-----
Von: oww-discuss-bounces at mit.edu im Auftrag von Bill F
Gesendet: Mo 05.05.2008 21:14
An: Jakob Suckale
Cc: oww-discuss at mit.edu
Betreff: Re: [OWW-Discuss] protocol icons
 
I'm a total sucker for great looking graphics created to meet specific
purposes. I like the idea a lot. Your icons are fantastic.

Let's assume we were to use them. Would you think other people (i.e., not
the original authors of the protocols) go through and add the icons? There
are a lot of existing protocols already on OWW; it would be nice to think
about how this could be applied to them.

If anyone were to do that, there may be a few other things we could to
simply annotate protocols.

Making them small fits in with the way our current sidebar icons work. What
do you think of using the icons without the words until someone either
hovered on them or asked what they meant? Maybe a key to their meaning would
also work.


Thanks for the great work.

Bill


On Mon, May 5, 2008 at 1:33 PM, Jakob Suckale <suckale at mpi-cbg.de> wrote:

> What do you guys thing about decorating our protocols a little with
> icons highlighting important parts of the instructions like: critical
> and/or difficult steps, time info, and possible points to interrupt
> the experiment.
> http://openwetware.org/wiki/User:Jakob_Suckale/Ideas#icons_for_protocols
>
> Ciao, Jakob
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>

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From wjf42 at MIT.EDU  Wed May  7 16:31:36 2008
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Wed, 7 May 2008 16:31:36 -0400
Subject: [OWW-Discuss] Google Sitemap and Search
Message-ID: <26428aaa0805071331v6fd3b302u5bfed81e0471544@mail.gmail.com>

Thanks to Reshma's suggestion and Ricardo providing the firm hand on the
tiller to navigate through the treacherous waters of enabling MediaWiki's
support for Google SiteMaps, they now are enabled.

This should move content locations to Google much faster and efficiently
than it was done in the past. We initially have the period for update set
for 1 day but will move it up to a higher number when the process is stable.


The next step is to make it easier to use Google to  search. We're adding  a
"Google Search" icon directly to the search box. We're working on this now.

We are not planning on disabling either the "Go" or "Search" buttons.

If anyone has any comments, questions, or suggestions, let me know.

Thanks.

Bill Flanagan
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From wjf42 at MIT.EDU  Sun May 11 11:34:18 2008
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Sun, 11 May 2008 11:34:18 -0400
Subject: [OWW-Discuss] Try out the search box on mw11. It has been googlized.
Message-ID: <26428aaa0805110834y2deb87b4g4a4e4e5cec135824@mail.gmail.com>

It's a bit weird since the pages point to openwetware pages rather than to
the mw11 pages. You need to use the back button to return to mw11. This
won't be the case when it gets installed in OWW. Try to search from here:


*http://openwetware.org/mw11/index.php/Main_Page
*

I'm trying to allow this search to continue to coexist with the current MW
search. Once you use this a bit, you have to ask, 'why bother!' when you see
the results. Keeping search working in the private wikis is my biggest
concern.

Personally, I like it. I'd like to hear what you folks think of it before
moving it into OWW.

Questions:

1. Are you seeing ads displayed with the results? I've registered a custom
search that will block ads since we're a nonprofit educational institution.

2. What about the way the results are displayed? Any comments?

3. We can add other sites to the search. I don't know how we would do this
yet but blogs and mailing list archives are on the table.

4. Has anyone seen other sites using Google's search that have any details
worth looking into?

5. I think we may be able to come up with a special protocol search as well
as other site-subset searches or even searches that span OWW and a set of
other sites.

6. I need to make sure this search is done in a way that does not interfere
with searches of private wikis. Since Google can't see them, they will have
to continue to rely upon the built-in search.

7. We could restrict the search to specific namespaces or title prefixes
within OWW.  This is a good way to exclude some of the extraneous content
that might be picked up along the way. This is similar to the sub-searches
we use for Lab Notebooks or other page ranges.


Signed,

The Googlizer
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From bill.altmail at gmail.com  Sun May 11 11:57:17 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 11 May 2008 11:57:17 -0400
Subject: [OWW-Discuss] Image searching.
Message-ID: <26428aaa0805110857t3c88de20x34bec4935b39d81b@mail.gmail.com>

The Google search api and the recent indexing of all of our content via
google including images means that we can come up with an image search with
OWW that displays the relevant images rather than a text pointer in the
not-too-distant future.

The Google Ajax Search API can be used with Javascript or any high-level
language. We could return the image results as a gallery of thumbnails. This
is a lot more useful than the current 'special page' search we are stuck
with.

One concern I have is that there's very little annotation of the uploaded
images we have within OWW. In that sense, we can get a lot more interesting
interaction but it can't come without making the way we capture images a lot
more expressive than it currently is.

If anyone has used Google Search APi in the past and would like to volunteer
to help us look into this, please let me know. This doesn't  just involve
programming: if you know this area and have an interest in helping out, let
me know.

If there are other non-Google alternatives you have experience with, we're
not wedded to Google!
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From bill.altmail at gmail.com  Sun May 11 12:49:20 2008
From: bill.altmail at gmail.com (Bill F)
Date: Sun, 11 May 2008 12:49:20 -0400
Subject: [OWW-Discuss] Working Google Image Search example on OWW
Message-ID: <26428aaa0805110949x72ee0d0fsa754d90e5e76e401@mail.gmail.com>

This is a very preliminary demo of Google's Image search.

http://openwetware.org/wiki/User:Bill_Flanagan/Google_Image_Search

The first time it places OpenWetWare in the search box. From then on the
script does it for you.

There are actually a few searches being done:

1. Image
2. Video
3. Abbreviated image search.

We may be able to get different results by using the 'Image' tag within the
wiki pages. I'm still looking at how to pull the context information from
the wiki page in which the image is located as a way of providing a better
way to select the ordering of images.

This is implied in the regular Image search: Google uses the html page
context to identify the most appropriate image. When Google spiders the
site, it pulls HTML and not the wiki text. That means the bitmap name is
connected to the html context. Since MediaWiki has a separate name for both
the "image page entity" and the bitmap file itself, there may be room to
find a way to better relate the image page  to the image and to the page
it's called from. We don't generally associate category tags with images: I
don't even know if you can. If this was done, we may end up with an even
more meaningful way of providing for contextual linking of images to
keywords.

Beware: the current page where the Google Image Searchis based looks like a
google demo page and not a regular OWW page. For this reason, be careful of
using my current code: it will result in a similar look in another page if
you try it there.

The other thing missing from the image data is the name of the person who
created it. This means that for now, there's no way to relate images to
users. I have a solution for this based on the namespace/user name info in
MediaWiki but not by using Google.

As I said before, please let me know if this is useful and whether you have
something further to contribute. I'm going to move these messages into OWW
so that they get searched and accessed by other people outside of the
Discuss list.

B.
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From bill.altmail at gmail.com  Mon May 12 09:01:38 2008
From: bill.altmail at gmail.com (Bill F)
Date: Mon, 12 May 2008 09:01:38 -0400
Subject: [OWW-Discuss] Weekend diversion: twitter in mediawiki/OWW
Message-ID: <26428aaa0805120601g28b8336epd13d1e209ca638c8@mail.gmail.com>

I wrote an extension to display a user's twitter stream inside of an OWW
page via a parser tag, "<ShowTwitter>".

You can see it here:

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

This is the tag that allows it to work:

<ShowTwitter>wjf42</ShowTwitter>

The extension uses a script written by Remy Sharp (
http://remysharp.com/2007/05/18/add-twitter-to-your-blog-step-by-step/).
It's outrageous.

I've not enabled setting all of the variables yet. I added this just so I
can keep OWW members abreast of what I'm doing, most specifically if it
relates to OWW. I may extend this to update a Wiki page as a log file to
keep a long-term history within OWW. I can always retrieve this from Twitter
via their API. Making it searchable within OWW may be useful.

If there are server problems, it's yet another trivial way to keep on top of
what we're doing to fix it. I already reserved OpenWetWare as another
twitter name to make it more official if we ever choose to go there.

If anyone has suggestions how to make this more useful, let me know.

To set twitter status, there are a lot of different tools. Since I use the
Linux shell as much as I do, I have a pretty simple script to send out my
current status from the command prompt. We can update this status via php
calls as part of using OWW as well. I'm not doing this now but I may some
night when I have some time.

Twitter is free. We can create as many names as needed. If you have buddies
(friends, tweets, whatever), their status displays along with yours. This
has some interesting possibilities for loosely coordinating teams using OWW.
Like labs or IGEM teams? Writing projects? Lab exercises?

Thanks.
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From johncumbers at gmail.com  Mon May 12 12:06:18 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 12 May 2008 09:06:18 -0700
Subject: [OWW-Discuss] Weekend diversion: twitter in mediawiki/OWW
In-Reply-To: <26428aaa0805120601g28b8336epd13d1e209ca638c8@mail.gmail.com>
References: <26428aaa0805120601g28b8336epd13d1e209ca638c8@mail.gmail.com>
Message-ID: <cfd758050805120906v10e2c151y69b5cc070c95e897@mail.gmail.com>

very cool Bill..

On Mon, May 12, 2008 at 6:01 AM, Bill F <bill.altmail at gmail.com> wrote:

> I wrote an extension to display a user's twitter stream inside of an OWW
> page via a parser tag, "<ShowTwitter>".
>
> You can see it here:
>
> http://openwetware.org/wiki/User:Bill_Flanagan
>
> This is the tag that allows it to work:
>
> <ShowTwitter>wjf42</ShowTwitter>
>
> The extension uses a script written by Remy Sharp (
> http://remysharp.com/2007/05/18/add-twitter-to-your-blog-step-by-step/).
> It's outrageous.
>
> I've not enabled setting all of the variables yet. I added this just so I
> can keep OWW members abreast of what I'm doing, most specifically if it
> relates to OWW. I may extend this to update a Wiki page as a log file to
> keep a long-term history within OWW. I can always retrieve this from Twitter
> via their API. Making it searchable within OWW may be useful.
>
> If there are server problems, it's yet another trivial way to keep on top
> of what we're doing to fix it. I already reserved OpenWetWare as another
> twitter name to make it more official if we ever choose to go there.
>
> If anyone has suggestions how to make this more useful, let me know.
>
> To set twitter status, there are a lot of different tools. Since I use the
> Linux shell as much as I do, I have a pretty simple script to send out my
> current status from the command prompt. We can update this status via php
> calls as part of using OWW as well. I'm not doing this now but I may some
> night when I have some time.
>
> Twitter is free. We can create as many names as needed. If you have
> buddies (friends, tweets, whatever), their status displays along with yours.
> This has some interesting possibilities for loosely coordinating teams using
> OWW. Like labs or IGEM teams? Writing projects? Lab exercises?
>
> Thanks.
>
>
>
> _______________________________________________
> 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 rvidal at gmail.com  Mon May 12 12:10:13 2008
From: rvidal at gmail.com (Ricardo Vidal)
Date: Mon, 12 May 2008 12:10:13 -0400
Subject: [OWW-Discuss] Weekend diversion: twitter in mediawiki/OWW
In-Reply-To: <cfd758050805120906v10e2c151y69b5cc070c95e897@mail.gmail.com>
References: <26428aaa0805120601g28b8336epd13d1e209ca638c8@mail.gmail.com>
	<cfd758050805120906v10e2c151y69b5cc070c95e897@mail.gmail.com>
Message-ID: <213fc43b0805120910i65de688m6c86a3ed8fba237d@mail.gmail.com>

I think first step would be to use the OWW twitter account to show
improvements and work being done on OWW. Not by placing the twits on the
wiki but simply by following other users and keeping the twitter bio
community (which is rather large already) informed.

I'll give this a go.

R

On Mon, May 12, 2008 at 12:06 PM, John Cumbers <johncumbers at gmail.com>
wrote:

> very cool Bill..
>
> On Mon, May 12, 2008 at 6:01 AM, Bill F <bill.altmail at gmail.com> wrote:
>
> > I wrote an extension to display a user's twitter stream inside of an OWW
> > page via a parser tag, "<ShowTwitter>".
> >
> > You can see it here:
> >
> > http://openwetware.org/wiki/User:Bill_Flanagan
> >
> > This is the tag that allows it to work:
> >
> > <ShowTwitter>wjf42</ShowTwitter>
> >
> > The extension uses a script written by Remy Sharp (
> > http://remysharp.com/2007/05/18/add-twitter-to-your-blog-step-by-step/).
> > It's outrageous.
> >
> > I've not enabled setting all of the variables yet. I added this just so
> > I can keep OWW members abreast of what I'm doing, most specifically if it
> > relates to OWW. I may extend this to update a Wiki page as a log file to
> > keep a long-term history within OWW. I can always retrieve this from Twitter
> > via their API. Making it searchable within OWW may be useful.
> >
> > If there are server problems, it's yet another trivial way to keep on
> > top of what we're doing to fix it. I already reserved OpenWetWare as another
> > twitter name to make it more official if we ever choose to go there.
> >
> > If anyone has suggestions how to make this more useful, let me know.
> >
> > To set twitter status, there are a lot of different tools. Since I use
> > the Linux shell as much as I do, I have a pretty simple script to send out
> > my current status from the command prompt. We can update this status via php
> > calls as part of using OWW as well. I'm not doing this now but I may some
> > night when I have some time.
> >
> > Twitter is free. We can create as many names as needed. If you have
> > buddies (friends, tweets, whatever), their status displays along with yours.
> > This has some interesting possibilities for loosely coordinating teams using
> > OWW. Like labs or IGEM teams? Writing projects? Lab exercises?
> >
> > Thanks.
> >
> >
> >
> > _______________________________________________
> > 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
>
>


-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From lorrielejeune at gmail.com  Tue May 13 10:16:39 2008
From: lorrielejeune at gmail.com (Lorrie LeJeune)
Date: Tue, 13 May 2008 10:16:39 -0400
Subject: [OWW-Discuss] OWW Steering Committee meeting tomorrow, May 14,
	at 12 noon
Message-ID: <6ac0a26a0805130716x254efea0w9ca6041612851f44@mail.gmail.com>

Hi Folks,
Just a reminder that we're having a steering committee meeting this
Wednesday, May 14, at 12 noon EDT. The conference number is
617-324-7520. We'll also have a simultaneous chat session at
http://openwetware.org/chat/.

See http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting
for topics and details.

Lorrie & John


From johncumbers at gmail.com  Wed May 14 09:52:45 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 14 May 2008 06:52:45 -0700
Subject: [OWW-Discuss] Reminder: OWW teleconference today at 12 noon EST...
	617-324-7520.
Message-ID: <cfd758050805140652u3265236fk218aa1f9bd7fc364@mail.gmail.com>

Hi all
Just a reminder that we're having a steering committee meeting today
at 12 noon EST, the conference number is 617-324-7520. We'll also have
a simultaneous chat session at
http://openwetware.org/chat/.  Lorrie will be presenting some ideas
for a framing strategy for OWW that is pretty exciting and I hope can
present that to the OWW SC for review and feedback.

See you there,
cheers,
John

See http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting
for topics and details.

_______________________________________________
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


From lorrielejeune at gmail.com  Wed May 14 11:46:49 2008
From: lorrielejeune at gmail.com (Lorrie LeJeune)
Date: Wed, 14 May 2008 11:46:49 -0400
Subject: [OWW-Discuss] Reminder: OWW Steering Committee meeting at 12 noon
	today
Message-ID: <6ac0a26a0805140846h713515bfo1cec449fa9050166@mail.gmail.com>

Hi Folks,
Just a reminder that we're having a steering committee meeting at 12
noon EDT today. The conference number is 1-617-324-7520. We'll also
have a simultaneous chat session at http://openwetware.org/chat/.

See http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting
for topics and details.

--Lorrie


From lorrielejeune at gmail.com  Wed May 14 11:59:01 2008
From: lorrielejeune at gmail.com (Lorrie LeJeune)
Date: Wed, 14 May 2008 11:59:01 -0400
Subject: [OWW-Discuss] Steering committee meeting: logging into OWW chat
Message-ID: <6ac0a26a0805140859q137fc1e5n5b138fe9d950d074@mail.gmail.com>

1) Go to http://openwetware.org/chat/

2) login using your OWW login and pw

3) Click 'conferences' at the bottom.

4) Double click on 'lounge'


From kanzure at gmail.com  Wed May 14 19:07:44 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Wed, 14 May 2008 18:07:44 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more
Message-ID: <200805141807.44247.kanzure@gmail.com>

Hey all,

I am not able to attend the week-day conference calls because of high 
school scheduling issues, but otherwise I've been meaning to suggest 
something to the group. I'll just send it here instead. :-)

I wrote an email about this in the context of space-based manufacturing:
http://heybryan.org/2008-05-09.html

But let me try to put things into context. I know that OWW has a good 
representation of programmers around these parts, so when I reference 
debian, I'm hoping it's not entirely lost. Take a look here:

http://debian.org/ and its Wikipedia article,
http://ubuntu.org/ And more concisely:
 "Debian is known for strict adherence to the Unix and free software 
philosophies. Debian is also known for its abundance of options ? the 
current release includes over twenty-six thousand software packages for 
eleven computer architectures. These architectures range from the 
Intel/AMD 32-bit/64-bit architectures commonly found in personal 
computers to the ARM architecture commonly found in embedded systems 
and the IBM eServer zSeries mainframes. Throughout Debian's lifetime, 
other distributions have taken it as a basis to develop their own, 
including: Ubuntu, MEPIS, Dreamlinux, Damn Small Linux, Xandros, 
Knoppix, Linspire, sidux, Kanotix, and LinEx among others. A 
university's study concluded that Debian's 283 million source code 
lines would cost 10 billion USA Dollars to develop by proprietary 
means."

"Ubuntu's popularity has climbed steadily since its 2004 release. It has 
been the most viewed Linux distribution on Distrowatch.com in 2005,[4] 
2006,[5] In an August 2007 survey of 38,500 visitors on 
DesktopLinux.com, Ubuntu was the most popular distribution with 30.3 
percent of respondents using it.[7] Third party sites have arisen to 
provide Ubuntu packages outside of the Ubuntu organization. Ubuntu was 
awarded the Reader Award for best Linux distribution at the 2005 
LinuxWorld Conference and Expo in London.[107] It has been favorably 
reviewed in online and print publications.[108][109][110] Ubuntu won 
InfoWorld's 2007 Bossie Award for Best Open Source Client OS.[111] Mark 
Shuttleworth indicates that there were at least 8 million Ubuntu users 
at the end of 2006.[112] The large user-base has resulted in a large 
stable of non-Canonical websites. These include general help sites like 
Easy Ubuntu Linux,[113] dedicated weblogs (Ubuntu Gazette),[114] and 
niche sites within the Ubuntu Linux niche itself (Ubuntu Women).[115] 
The year 2007 saw the online publication of the first magazine 
dedicated to Ubuntu, Full Circle.[116]"

So, just what made these so successful? To the point where debian 
represents $10 billion USD of effort, all done by volunteer work? 
There's a bit more to mention:

http://advogato.org/article/972.html

"What are the issues? Why is it so important to go "distributed"? 

Debian is the largest independent of the longest-running of the Free 
Software Distributions in existence. There are over 1000 maintainers; 
nearly 20,000 packages. There are over 40 "Primary" Mirrors, and 
something like one hundred secondary mirrors (listed here - I'm stunned 
and shocked at the numbers!). 14 architectures are supported - 13 Linux 
ports and one GNU/Hurd port but only for i386 (aww bless iiit). A 
complete copy of the mirrors and their architectures, including source 
code, is over 160 gigabytes. 

At the last major upgrade of Debian/Stable, all the routers at the major 
International fibreoptic backbone sites across the world redlined for a 
week. 

To say that Debian is "big" is an understatement of the first order. 

Many mirror sites simply cannot cope with the requirements. Statistics 
on the Debian UK Mirror for July 2004 to June 2005 show 1.4 Terabytes 
of data served. As you can see from the list of mirror sites, many of 
the Secondary Mirrors and even a couple of the Primary ones have 
dropped certain architectures. 

security.debian.org - perhaps the most important of all the Debian 
sites - is definitely overloaded and undermirrored. 

This isn't all: there are mailing lists (the statistics show almost 
30,000 people on each of the announce and security lists, alone), and 
IRC channels - and both of those are over-spammed. The load on the 
mailing list server is so high that an idea (discussed informally at 
Debconf7 and outlined here later in this article, for completeness) to 
create an opt-in spam/voting system for people to "vet" postings and 
comments, was met with genuine concern and trepidation by the mailing 
list's maintainers. 

It's incredible that Debian Distribution and Development hasn't fallen 
into a big steaming heap of broken pieces, with administrators, users 
and ISPs all screaming at each other and wanting to scratch each 
others' eyes out on the mailing lists and IRC channels, only to find 
that those aren't there either. 

So it's basically coming through loud and clear: "server-based" 
infrastructure is simply not scalable, and the situation is only going 
to get worse as time progresses. That leaves "distributed 
architecture" - aka peer-to-peer architecture - as the viable 
alternative."

In other words, it's the social structure and community around debian, 
the 26,000 software packages, and that incredibly easy command where 
you can grab *any* software package and have it immediately installed. 
It's from a software repository. Kind of like biobricks, except 
functional. By that I don't mean biobricks is dysfunctional, but that 
biobricks is about data, debian's apt is about software and 
functionality. 

This is what one of my projects focuses on - that sort of easy gradient 
by which not only programs and software can be downloaded, but open 
access information, and open source projects of any sort, whether from 
the Maker Communities, the diybio groups, debian, gentoo, etc. 

For a dense explanation:
http://heybryan.org/exp.html

The 'architecture' is really ridiculously simple, it's just putting 
together some components that have been out on the web for a while. For 
example, all wikis have a revision control system, even the mediawiki 
installation for OWW. These revision systems, though, existed long 
before wikis popped up, I am particularly interested in 'git'. And for 
this reason I am also interested in ikiwiki, which can be made to look 
exactly like mediawiki, except with the important difference that it's 
based on 'git' for the revision control / history. This means that 
pages can be branched and so on, by anybody interested. 

It also means that you're not just providing open access data, but also 
the entire project [if the researcher is interested in going that far, 
of course]. All of the files - source code, CAD, diagrams via dia or 
graphviz, SVG, documentation, latex-source of the papers, notes, etc. 

It's really easy to implement. 

It's an extension of "open access" and "open source" in that it makes 
the whole "semantic web" thing really truly functional, making it 
actually *do* something.

And it's a useful way of doing research. What's the quote? The one from 
Gregory Wilson on bottlenecks in scientific computing? 
http://www.americanscientist.org/template/AssetDetail/assetid/48548
http://www.cs.toronto.edu/~gvwilson/
'figuring out how to make scientific programmers more productive'

"Those Who Will Not Learn From History..." 
Beautiful Code 
"Requirements in the Wild" 
"DrProject: A Software Project Management Portal to Meet Educational 
Needs" 
"Software Carpentry" 
Data Crunching 
"Learning By Doing: Introducing Version Control as a Way to Manage 
Student Assignments" 
"Where's the Real Bottleneck in Scientific Computing?" 
"Extensible Programming for the 21st Century" 
"Open Source, Cold Shoulder"

Anyway, the only thing left for implementation is changing up mediawiki 
a bit, writing some introductory tutorials [which I am doing anyway on 
another front], and then figuring out the file structure format (using 
YAML, so it's just writing classes in python), which frankly I think is 
something that individual researchers would be more suited to doing. 
For example, that's why we have the excellent Systems Biology Markup 
Language (sbml.org), and I don't exactly have a broad enough overview 
of the field to make it happen.

You get all of the benefits of software reuse, but with project reuse, 
with all of the sharing and acceleration of progress that the internet 
can allow for. So what are the general thoughts on this?

- Bryan
________________________________________
http://heybryan.org/



From johncumbers at gmail.com  Wed May 14 19:31:11 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Wed, 14 May 2008 16:31:11 -0700
Subject: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more
In-Reply-To: <200805141807.44247.kanzure@gmail.com>
References: <200805141807.44247.kanzure@gmail.com>
Message-ID: <cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com>

BRyan,
 I don't really understand what you are proposing and if you posted an
executive summary then it might prompt more of a discussion.  I think you're
saying is that you are going to implement something and then let us see the
results, which sounds like a great way to better understand what it is you
are proposing,
cheers,
JOhn



On Wed, May 14, 2008 at 4:07 PM, Bryan Bishop <kanzure at gmail.com> wrote:

> Hey all,
>
> I am not able to attend the week-day conference calls because of high
> school scheduling issues, but otherwise I've been meaning to suggest
> something to the group. I'll just send it here instead. :-)
>
> I wrote an email about this in the context of space-based manufacturing:
> http://heybryan.org/2008-05-09.html
>
> But let me try to put things into context. I know that OWW has a good
> representation of programmers around these parts, so when I reference
> debian, I'm hoping it's not entirely lost. Take a look here:
>
> http://debian.org/ and its Wikipedia article,
> http://ubuntu.org/ And more concisely:
>  "Debian is known for strict adherence to the Unix and free software
> philosophies. Debian is also known for its abundance of options ? the
> current release includes over twenty-six thousand software packages for
> eleven computer architectures. These architectures range from the
> Intel/AMD 32-bit/64-bit architectures commonly found in personal
> computers to the ARM architecture commonly found in embedded systems
> and the IBM eServer zSeries mainframes. Throughout Debian's lifetime,
> other distributions have taken it as a basis to develop their own,
> including: Ubuntu, MEPIS, Dreamlinux, Damn Small Linux, Xandros,
> Knoppix, Linspire, sidux, Kanotix, and LinEx among others. A
> university's study concluded that Debian's 283 million source code
> lines would cost 10 billion USA Dollars to develop by proprietary
> means."
>
> "Ubuntu's popularity has climbed steadily since its 2004 release. It has
> been the most viewed Linux distribution on Distrowatch.com in 2005,[4]
> 2006,[5] In an August 2007 survey of 38,500 visitors on
> DesktopLinux.com, Ubuntu was the most popular distribution with 30.3
> percent of respondents using it.[7] Third party sites have arisen to
> provide Ubuntu packages outside of the Ubuntu organization. Ubuntu was
> awarded the Reader Award for best Linux distribution at the 2005
> LinuxWorld Conference and Expo in London.[107] It has been favorably
> reviewed in online and print publications.[108][109][110] Ubuntu won
> InfoWorld's 2007 Bossie Award for Best Open Source Client OS.[111] Mark
> Shuttleworth indicates that there were at least 8 million Ubuntu users
> at the end of 2006.[112] The large user-base has resulted in a large
> stable of non-Canonical websites. These include general help sites like
> Easy Ubuntu Linux,[113] dedicated weblogs (Ubuntu Gazette),[114] and
> niche sites within the Ubuntu Linux niche itself (Ubuntu Women).[115]
> The year 2007 saw the online publication of the first magazine
> dedicated to Ubuntu, Full Circle.[116]"
>
> So, just what made these so successful? To the point where debian
> represents $10 billion USD of effort, all done by volunteer work?
> There's a bit more to mention:
>
> http://advogato.org/article/972.html
>
> "What are the issues? Why is it so important to go "distributed"?
>
> Debian is the largest independent of the longest-running of the Free
> Software Distributions in existence. There are over 1000 maintainers;
> nearly 20,000 packages. There are over 40 "Primary" Mirrors, and
> something like one hundred secondary mirrors (listed here - I'm stunned
> and shocked at the numbers!). 14 architectures are supported - 13 Linux
> ports and one GNU/Hurd port but only for i386 (aww bless iiit). A
> complete copy of the mirrors and their architectures, including source
> code, is over 160 gigabytes.
>
> At the last major upgrade of Debian/Stable, all the routers at the major
> International fibreoptic backbone sites across the world redlined for a
> week.
>
> To say that Debian is "big" is an understatement of the first order.
>
> Many mirror sites simply cannot cope with the requirements. Statistics
> on the Debian UK Mirror for July 2004 to June 2005 show 1.4 Terabytes
> of data served. As you can see from the list of mirror sites, many of
> the Secondary Mirrors and even a couple of the Primary ones have
> dropped certain architectures.
>
> security.debian.org - perhaps the most important of all the Debian
> sites - is definitely overloaded and undermirrored.
>
> This isn't all: there are mailing lists (the statistics show almost
> 30,000 people on each of the announce and security lists, alone), and
> IRC channels - and both of those are over-spammed. The load on the
> mailing list server is so high that an idea (discussed informally at
> Debconf7 and outlined here later in this article, for completeness) to
> create an opt-in spam/voting system for people to "vet" postings and
> comments, was met with genuine concern and trepidation by the mailing
> list's maintainers.
>
> It's incredible that Debian Distribution and Development hasn't fallen
> into a big steaming heap of broken pieces, with administrators, users
> and ISPs all screaming at each other and wanting to scratch each
> others' eyes out on the mailing lists and IRC channels, only to find
> that those aren't there either.
>
> So it's basically coming through loud and clear: "server-based"
> infrastructure is simply not scalable, and the situation is only going
> to get worse as time progresses. That leaves "distributed
> architecture" - aka peer-to-peer architecture - as the viable
> alternative."
>
> In other words, it's the social structure and community around debian,
> the 26,000 software packages, and that incredibly easy command where
> you can grab *any* software package and have it immediately installed.
> It's from a software repository. Kind of like biobricks, except
> functional. By that I don't mean biobricks is dysfunctional, but that
> biobricks is about data, debian's apt is about software and
> functionality.
>
> This is what one of my projects focuses on - that sort of easy gradient
> by which not only programs and software can be downloaded, but open
> access information, and open source projects of any sort, whether from
> the Maker Communities, the diybio groups, debian, gentoo, etc.
>
> For a dense explanation:
> http://heybryan.org/exp.html
>
> The 'architecture' is really ridiculously simple, it's just putting
> together some components that have been out on the web for a while. For
> example, all wikis have a revision control system, even the mediawiki
> installation for OWW. These revision systems, though, existed long
> before wikis popped up, I am particularly interested in 'git'. And for
> this reason I am also interested in ikiwiki, which can be made to look
> exactly like mediawiki, except with the important difference that it's
> based on 'git' for the revision control / history. This means that
> pages can be branched and so on, by anybody interested.
>
> It also means that you're not just providing open access data, but also
> the entire project [if the researcher is interested in going that far,
> of course]. All of the files - source code, CAD, diagrams via dia or
> graphviz, SVG, documentation, latex-source of the papers, notes, etc.
>
> It's really easy to implement.
>
> It's an extension of "open access" and "open source" in that it makes
> the whole "semantic web" thing really truly functional, making it
> actually *do* something.
>
> And it's a useful way of doing research. What's the quote? The one from
> Gregory Wilson on bottlenecks in scientific computing?
> http://www.americanscientist.org/template/AssetDetail/assetid/48548
> http://www.cs.toronto.edu/~gvwilson/<http://www.cs.toronto.edu/%7Egvwilson/>
> 'figuring out how to make scientific programmers more productive'
>
> "Those Who Will Not Learn From History..."
> Beautiful Code
> "Requirements in the Wild"
> "DrProject: A Software Project Management Portal to Meet Educational
> Needs"
> "Software Carpentry"
> Data Crunching
> "Learning By Doing: Introducing Version Control as a Way to Manage
> Student Assignments"
> "Where's the Real Bottleneck in Scientific Computing?"
> "Extensible Programming for the 21st Century"
> "Open Source, Cold Shoulder"
>
> Anyway, the only thing left for implementation is changing up mediawiki
> a bit, writing some introductory tutorials [which I am doing anyway on
> another front], and then figuring out the file structure format (using
> YAML, so it's just writing classes in python), which frankly I think is
> something that individual researchers would be more suited to doing.
> For example, that's why we have the excellent Systems Biology Markup
> Language (sbml.org), and I don't exactly have a broad enough overview
> of the field to make it happen.
>
> You get all of the benefits of software reuse, but with project reuse,
> with all of the sharing and acceleration of progress that the internet
> can allow for. So what are the general thoughts on this?
>
> - Bryan
> ________________________________________
> http://heybryan.org/
>
> _______________________________________________
> 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

NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371
Moffett Field, CA 94035
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From kanzure at gmail.com  Wed May 14 22:22:58 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Wed, 14 May 2008 21:22:58 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more
In-Reply-To: <cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com>
References: <200805141807.44247.kanzure@gmail.com>
	<cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com>
Message-ID: <200805142122.59791.kanzure@gmail.com>

On Wednesday 14 May 2008, "John Cumbers" <johncumbers at gmail.com> wrote:
> ?I don't really understand what you are proposing and if you posted
> an executive summary then it might prompt more of a discussion.

It's a software architecture that lets us do what debian did for 
software -- aggregating tens of thousands of programmers -- but with 
other projects, on OWW it's science. Instead of a dry wiki, you have a 
wiki that is built on a file repository, with data files provided by 
whoever submits content, which can be immediately used in other 
projects. And then you get easy "apt-get install <centrifuge>" 
commands, or "apt-get install <uncoli>" etc. I am actually not too good 
at predicting what projects will show up on the map, but those are 
valid guesses.

- Bryan
________________________________________
http://heybryan.org/



From russell2 at qiezi.net  Wed May 14 23:01:02 2008
From: russell2 at qiezi.net (=?utf-8?B?UnVzc2VsbCBIYW5zb24=?=)
Date: Thu, 15 May 2008 03:01:02 +0000
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <200805142122.59791.kanzure@gmail.com>
References: <200805141807.44247.kanzure@gmail.com><cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com><200805142122.59791.kanzure@gmail.com>
Message-ID: <1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>

Yo Bryan, 

I don't know of any situation where this config/build scenario would apply to any domain of molecular biology or molecular engineering.  One of my conclusions after trying to teach molecular biophysics, etc. to people well versed in Linux, etc.  was that both the level of education needed and the money to buy the chemicals and equipment used in the lab have an "appropriately" high barrier.  Obviously people have had high-powered PCs in their homes since they were kids and you can pick up another for a few hundred bucks: not the case for molecular biology/chemical engineering.  The people who are in the position to contribute the most in terms of research projects are precisely the people who already have so much going on they don't contribute to open-source software type projects.  There are not tens of thousands of people out there looking for new "open and wet" projects, and there isn't the money available from the 'funding agencies' to support or supply those "open and wet" projects.  I think the money and educational barriers trump the sociological engineering reasons for this.  However, this is different from the self-fab and reprap-type stuff....  

peace, 
Russell 

-----Original Message-----
From: Bryan Bishop <kanzure at gmail.com>

Date: Wed, 14 May 2008 21:22:58 
To:discuss at openwetware.org
Subject: Re: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more


On Wednesday 14 May 2008, "John Cumbers" <johncumbers at gmail.com> wrote:
> ?I don't really understand what you are proposing and if you posted
> an executive summary then it might prompt more of a discussion.

It's a software architecture that lets us do what debian did for 
software -- aggregating tens of thousands of programmers -- but with 
other projects, on OWW it's science. Instead of a dry wiki, you have a 
wiki that is built on a file repository, with data files provided by 
whoever submits content, which can be immediately used in other 
projects. And then you get easy "apt-get install <centrifuge>" 
commands, or "apt-get install <uncoli>" etc. I am actually not too good 
at predicting what projects will show up on the map, but those are 
valid guesses.

- Bryan
________________________________________
http://heybryan.org/

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



From fenn at sdf.lonestar.org  Wed May 14 23:25:44 2008
From: fenn at sdf.lonestar.org (ben lipkowitz)
Date: Thu, 15 May 2008 03:25:44 +0000 (UTC)
Subject: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more
Message-ID: <Pine.NEB.4.64.0805150253250.20099@sdf.lonestar.org>

Hello list,

It seems Bryan can't write an email in plain english, so I feel obligated 
to explain for him:

The idea behind what we're working on is to end up with a Matter Compiler 
- a set of programs hooked up to manufacturing equipment that can take any 
arbitrary design data and either build it with tools that you have, or 
make the tools to make the tools ... to make what you wanted in the first 
place.

Biology lends itself to this concept readily because it is already a 
digital manufacturing system; a unique DNA/RNA/peptide sequence is the 
same molecule no matter what enzyme put it together, unlike a car engine 
which may be different depending on which factory it came from or the 
phase of the moon. (Yeah yeah I know about isotopes.) Additionally, tools 
already exist to make short sequences of DNA, to replicate them into vast 
numbers in vitro or vivo, and we can do cool things with those pieces such 
as making DNA origami or aptamers.

At this point you may be thinking "I dont need some silly program to tell 
me how to send a sequence off to sequences-r-us!" but that isn't the 
point. The reason this makes sense for OWW is that in order to direct a 
computer to make the tools to make the tools, we must already have a 
formalized description of processes, properties, and functionality. So, 
provided that our system is general/abstract enough, it should be able to 
model complex biological systems as well. I intend to include that 
capability anyway because some biological systems are useful in a 
manufacturing context. I dont know what OWW needs, but maybe it doesn't 
even matter: since the design is open and decentralized, you can clone a 
local copy for yourself and put your super-secret academic research 
projects in it, or maybe even contribute it back to the rest of the world.
On the other hand, I'd hate to make a poor design decision in the early 
stages simply because I didnt know what you guys need.

> The people who are in the position to contribute the most in terms of 
> research projects are precisely the people who already have so much 
> going on they don't contribute to open-source software type projects.

This is a damn shame. What are they doing with all those research results 
anyway?

   -fenn


From kanzure at gmail.com  Wed May 14 23:31:21 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Wed, 14 May 2008 22:31:21 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
References: <200805141807.44247.kanzure@gmail.com>
	<200805142122.59791.kanzure@gmail.com>
	<1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
Message-ID: <200805142231.21536.kanzure@gmail.com>

Hey Russell, long time no chat.

On Wednesday 14 May 2008, Russell Hanson wrote:
> I don't know of any situation where this config/build scenario would
> apply to any domain of molecular biology or molecular engineering.

Model repositories can easily fit within this umbrella. I've been 
playing with some molecular physics and molecular dynamics before. 
Technically, programs in debian or gentoo repositories are already 
doing this, so duplicating the effort would be silly. What if instead 
of publishing latex we'd publish in SBML and other notations to 
illustrate models and so on? Lots of fun possibilities, and it requires 
some initial "bootup" work to be done to organize a community of that 
sort before it skyrockets and become easier on all of us.

Another possible way that this could be used in mol-bio would be in 
terms of the tools that are available, on top of the scientific models 
anyway. You could easily argue for proprietary systems, but I don't 
know how far that would fly around here. Straw man, I know, I know.

> ?One of my conclusions after trying to teach molecular biophysics,
> etc. to people well versed in Linux, etc. ?was that both the level of
> education needed and the money to buy the chemicals and equipment
> used in the lab have an "appropriately" high barrier. ?Obviously

Why would you want a barrier to entry?

> people have had high-powered PCs in their homes since they were kids
> and you can pick up another for a few hundred bucks: not the case for
> molecular biology/chemical engineering. ?The people who are in the

That's the current status quo for mol-bio/ChE, so I don't see why we 
wouldn't want to change that. It's not about profit margins.

> position to contribute the most in terms of research projects are
> precisely the people who already have so much going on they don't
> contribute to open-source software type projects. ?There are not tens

I don't think that we want to bother those super-workers anyway. It's 
mostly students and amateurs that would probably contribute at first. 
People from Make, that crowd too.

> of thousands of people out there looking for new "open and wet"

Are you sure about that? I've been noticing explosive growth in wikihow, 
instructables (hi Saul :-), youtube, Wikipedia, howstuffworks, 
howtoons, wikihow, Make Magazine, howtodothings, etc. etc. 

> projects, and there isn't the money available from the 'funding
> agencies' to support or supply those "open and wet" projects. ?I

Who says it has to cost much? I don't understand. When you do research, 
don't you work with computational models? When you make a new piece of 
equipment for your lab, don't you use schematics? Would it hurt to 
spend a few minutes uploading that data into a formalized data package 
for others to use?

> think the money and educational barriers trump the sociological
> engineering reasons for this. ?However, this is different from the
> self-fab and reprap-type stuff.... ?

>From what I've seen about lablife, once you get in to it you start to 
realize that it's all 'diy' anyway, except now you have some support in 
realtime from people actually standing around [though on their own 
projects]. As for the educational barriers, tell me how those exist. I 
went from zero, zip-nadda, to what I know now, through the net and 
maybe to some extent high school, but the extent to which that is true 
can be determined by http://heybryan.org/school/ - everything else is 
because of the web. 

- Bryan
________________________________________
http://heybryan.org/



From jason.p.morrison at gmail.com  Wed May 14 23:29:38 2008
From: jason.p.morrison at gmail.com (Jason Morrison)
Date: Wed, 14 May 2008 23:29:38 -0400
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
References: <200805141807.44247.kanzure@gmail.com>
	<cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com>
	<200805142122.59791.kanzure@gmail.com>
	<1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
Message-ID: <8ba0586d0805142029t2049c0bdic8649011f96976b@mail.gmail.com>

Bryan, the projects you propose a collection of - are they
descriptions/data, like a lab protocol description?  If this is the case, I
think there's a huge space for the systemization and distributed
production/annotation of these.  I'd love to have well-tagged protocols that
other software can say "hey, where's a protocol for performing abc on
substrate uvw in conditions xyz?"
I'm curious what specific types of files you see going into the <centrifuge>
or <uncoli> projects.

Russell, you bring up a good point about the difference in initial capital
investment between software and wetware development.  Might a
http://techshop.ws/ for biology be a game changer here?  Specifically: would
there be enough interested individuals if the capital investment were the
same?  Let's say $3/day instead of $150/day to do mol bio.  (That's assuming
a $100/mo membership to TechLab, perhaps a high number.  $150/day from est.
$75k to bootstrap a mol bio lab plus a year of consumables.  Compare to a
$1000 development box, which brings us back to $3/day for the first year in
the software realm)

Cheers,
Jason

On Wed, May 14, 2008 at 11:01 PM, Russell Hanson <russell2 at qiezi.net> wrote:

> Yo Bryan,
>
> I don't know of any situation where this config/build scenario would apply
> to any domain of molecular biology or molecular engineering.  One of my
> conclusions after trying to teach molecular biophysics, etc. to people well
> versed in Linux, etc.  was that both the level of education needed and the
> money to buy the chemicals and equipment used in the lab have an
> "appropriately" high barrier.  Obviously people have had high-powered PCs in
> their homes since they were kids and you can pick up another for a few
> hundred bucks: not the case for molecular biology/chemical engineering.  The
> people who are in the position to contribute the most in terms of research
> projects are precisely the people who already have so much going on they
> don't contribute to open-source software type projects.  There are not tens
> of thousands of people out there looking for new "open and wet" projects,
> and there isn't the money available from the 'funding agencies' to support
> or supply those "open and wet" projects.  I think the money and educational
> barriers trump the sociological engineering reasons for this.  However, this
> is different from the self-fab and reprap-type stuff....
>
> peace,
> Russell
>
> -----Original Message-----
> From: Bryan Bishop <kanzure at gmail.com>
>
> Date: Wed, 14 May 2008 21:22:58
> To:discuss at openwetware.org <To%3Adiscuss at openwetware.org>
> Subject: Re: [OWW-Discuss] Tapping into open source / open access and doing
>        slightly more
>
>
> On Wednesday 14 May 2008, "John Cumbers" <johncumbers at gmail.com> wrote:
> >  I don't really understand what you are proposing and if you posted
> > an executive summary then it might prompt more of a discussion.
>
> It's a software architecture that lets us do what debian did for
> software -- aggregating tens of thousands of programmers -- but with
> other projects, on OWW it's science. Instead of a dry wiki, you have a
> wiki that is built on a file repository, with data files provided by
> whoever submits content, which can be immediately used in other
> projects. And then you get easy "apt-get install <centrifuge>"
> commands, or "apt-get install <uncoli>" etc. I am actually not too good
> at predicting what projects will show up on the map, but those are
> valid guesses.
>
> - Bryan
> ________________________________________
> http://heybryan.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
>



-- 
Jason Morrison
jason.p.morrison at gmail.com
http://jayunit.net
(585) 216-5657
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From kanzure at gmail.com  Wed May 14 23:48:49 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Wed, 14 May 2008 22:48:49 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <8ba0586d0805142029t2049c0bdic8649011f96976b@mail.gmail.com>
References: <200805141807.44247.kanzure@gmail.com>
	<1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
	<8ba0586d0805142029t2049c0bdic8649011f96976b@mail.gmail.com>
Message-ID: <200805142248.49858.kanzure@gmail.com>

On Wednesday 14 May 2008, Jason Morrison wrote:
> Bryan, the projects you propose a collection of - are they
> descriptions/data, like a lab protocol description? ?If this is the

Yes, they could include lab protocol descriptions [that hopefully one 
day could be followed by machine and human alike, if properly written 
in some machine-parseable format]. But it would also include other 
constructable items, not just constructable life / life-states via 
protocols and chemical concoctions.

> case, I think there's a huge space for the systemization and
> distributed production/annotation of these. ?I'd love to have
> well-tagged protocols that other software can say "hey, where's a
> protocol for performing abc on substrate uvw in conditions xyz?"

Yes, this system is completely 'tagged'. You search for data types if 
you want, or you can search the natural language description, and 
really -- how it works now -- you'd want to search for people that 
might be able to point you in the right direction with the least amount 
of pain involved on their end. That's also part of the project, social 
facilitation, in that the project -- SKDB -- can have some files for 
each project that specify data like FOAF (friend of a friend; it's some 
new stuff going around the social-networking scene apparently), or a 
list of contributors to contact. I fully expect these projects to be 
off-site in many cases, although Sourceforge is an example of onsite 
versioning systems. Either way works. Still tagged. 

http://heybryan.org/mediawiki/index.php/SDKB

> I'm curious what specific types of files you see going into the
> <centrifuge> or <uncoli> projects.

Centrifuge might have a CAD file or two. This would describe the 
physical structure, or at the very least physical parameters for the 
structure, and then the procedures to make it (it's a manufacturing 
database to some extent). The beauty of it is that you don't have to 
specify it down to every last detail, since you can just blackbox it 
sort of [as long as you provide references to literature that isn't yet 
integrated -- or at least a few names to people to track down in case 
somebody wants to start formalizing it]. But it's important that you 
try to use the same tags, else we get into huge bushes and vineyards 
that criss-cross in weird ways. Maybe an automated program can fix 
these hairy issues, but I suspect if the information is organized 
cleanly enough, and the quality assessment teams that verify packages 
before throwing them into the 'main branch' of SKDB do their job well, 
then it should stay pretty clean. [New ontologies/taggings can be 
ghosted on top if it easily enough, but it takes effort (refactoring)].

> Russell, you bring up a good point about the difference in initial
> capital investment between software and wetware development. ?Might a
> http://techshop.ws/ for biology be a game changer here?

I tried signing up for the Austin techshop but nobody has gotten back to 
me on that. So that's peculiar. What I'm thinking of is that if things 
go well enough and the manufacturing systems / SKDB takeoff, I'll do my 
own techshop of sorts so that I can work on bootstrapping the system 
back down to the basics, help make standardized parts, etc. [plus it's 
always neat to have your own shop/lab-space to work in].

> ?Specifically: would there be enough interested individuals if the
> capital investment were the same? ?Let's say $3/day instead of
> $150/day to do mol bio. ?(That's assuming a $100/mo membership to
> TechLab, perhaps a high number. ?$150/day from est. $75k to bootstrap
> a mol bio lab plus a year of consumables. ?Compare to a $1000
> development box, which brings us back to $3/day for the first year in
> the software realm)

Yikes, $75k to bootstrap a mol bio lab? What if all of these parts were 
manufactured for free, by energy and materials obtained for free? At 
the root of all of this there's the concept of "philanthropic 
bootstrapping", but it needs to be at a very central point; I haven't 
developed this argument fully yet, but I'll probably be trying to hack 
out a few lines on it later this week. I might also call it "a 
philanthropic gateway".
http://heybryan.org/exp.html

- Bryan
________________________________________
http://heybryan.org/



From heathmatlock at gmail.com  Thu May 15 01:01:26 2008
From: heathmatlock at gmail.com (Heath Matlock)
Date: Thu, 15 May 2008 00:01:26 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <884665765-1210825949-cardhu_decombobulator_blackberry.rim.net-192322845-@bxe011.bisx.prod.on.blackberry>
References: <200805141807.44247.kanzure@gmail.com>
	<cfd758050805141631taca0529meae07b5369e30348@mail.gmail.com>
	<200805142122.59791.kanzure@gmail.com>
	<1654041719-1210820613-cardhu_decombobulator_blackberry.rim.net-1056795843-@bxe011.bisx.prod.on.blackberry>
	<9a5d05440805142108h7fa9d4dbxa9f3baa01f561575@mail.gmail.com>
	<884665765-1210825949-cardhu_decombobulator_blackberry.rim.net-192322845-@bxe011.bisx.prod.on.blackberry>
Message-ID: <9a5d05440805142201j7fd646f8xbb533a6870d70a8@mail.gmail.com>

Resent, thanks for the heads up Russell.
Hi everyone else on the mailing list since I've yet to introduce myself :)

Russell, the price to synthesize is decreasing rapidly as Drew Endy and
others have pointed out before, and so the field is becoming a lot more
accessible than it has been in the past. I don't see what you mean by people
not having time to contribute open and wet projects when openwetware is tied
so closely to the Biobricks Foundation, with its public licensed parts.
Perhaps, you meant something completely different though, will you clarify
your statements?

On Wed, May 14, 2008 at 11:29 PM, Russell Hanson <russell2 at qiezi.net> wrote:

> Hey Heath,
>
> Not sure how your headers are set up but it looks to me like you just
> replied to me personally instead of the list as well.  If that is/is not
> what you intended...
>
> Russell
>
> -----Original Message-----
> From: "Heath Matlock" <heathmatlock at gmail.com>
>
> Date: Wed, 14 May 2008 23:08:28
> To:russell2 at qiezi.net <To%3Arussell2 at qiezi.net>
> Subject: Re: [OWW-Discuss] Tapping into open source / open access and
> doingslightly more
>
>
> Hey Russell and everyone else on the mailing list since I've yet to
> introduce myself :)
>
> The price to synthesize is decreasing rapidly as Drew Endy and others have
> pointed out before, and so the field is becoming a lot more accessible than
> it has been in the past. I don't see what you mean by people not having time
> to contribute open and wet projects when openwetware is tied so closely to
> the Biobricks Foundation, with its public licensed parts. Perhaps, you meant
> something completely different though, could you clarify?
>
>
> On Wed, May 14, 2008 at 10:01 PM, Russell Hanson <russell2 at qiezi.net<mailto:
> russell2 at qiezi.net> > wrote:
>  Yo Bryan,
>
>  I don't know of any situation where this config/build scenario would apply
> to any domain of molecular biology or molecular engineering.  One of my
> conclusions after trying to teach molecular biophysics, etc. to people well
> versed in Linux, etc.  was that both the level of education needed and the
> money to buy the chemicals and equipment used in the lab have an
> "appropriately" high barrier.  Obviously people have had high-powered PCs in
> their homes since they were kids and you can pick up another for a few
> hundred bucks: not the case for molecular biology/chemical engineering.  The
> people who are in the position to contribute the most in terms of research
> projects are precisely the people who already have so much going on they
> don't contribute to open-source software type projects.  There are not tens
> of thousands of people out there looking for new "open and wet" projects,
> and there isn't the money available from the 'funding agencies' to support
> or supply those "open and wet" projects.  I think the money and educational
> barriers trump the sociological engineering reasons for this.  However, this
> is different from the self-fab and reprap-type stuff....
>
>  peace,
>  Russell
>
>  -----Original Message-----
>  From: Bryan Bishop <kanzure at gmail.com <mailto:kanzure at gmail.com> >
>
>  Date: Wed, 14 May 2008 21:22:58
>  To:discuss at openwetware.org <To%3Adiscuss at openwetware.org> <mailto:
> To%3Adiscuss at openwetware.org <To%253Adiscuss at openwetware.org>>
>  Subject: Re: [OWW-Discuss] Tapping into open source / open access and
> doing
>         slightly more
>
>
>  On Wednesday 14 May 2008, "John Cumbers" <johncumbers at gmail.com <mailto:
> johncumbers at gmail.com> > wrote:
>  >  I don't really understand what you are proposing and if you posted
>  > an executive summary then it might prompt more of a discussion.
>
>  It's a software architecture that lets us do what debian did for
>  software -- aggregating tens of thousands of programmers -- but with
>  other projects, on OWW it's science. Instead of a dry wiki, you have a
>  wiki that is built on a file repository, with data files provided by
>  whoever submits content, which can be immediately used in other
>  projects. And then you get easy "apt-get install <centrifuge>"
>  commands, or "apt-get install <uncoli>" etc. I am actually not too good
>  at predicting what projects will show up on the map, but those are
>  valid guesses.
>
>  - Bryan
>  ________________________________________
>  http://heybryan.org/ <http://heybryan.org/>
>
>  _______________________________________________
>  OpenWetWare Discussion Mailing List
>  discuss at openwetware.org <mailto:discuss at openwetware.org>
>  http://mailman.mit.edu/mailman/listinfo/oww-discuss <
> http://mailman.mit.edu/mailman/listinfo/oww-discuss>
>
>  _______________________________________________
>  OpenWetWare Discussion Mailing List
>  discuss at openwetware.org <mailto:discuss at openwetware.org>
>  http://mailman.mit.edu/mailman/listinfo/oww-discuss <
> http://mailman.mit.edu/mailman/listinfo/oww-discuss>
>
>
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From russell2 at qiezi.net  Thu May 15 01:00:28 2008
From: russell2 at qiezi.net (=?utf-8?B?UnVzc2VsbCBIYW5zb24=?=)
Date: Thu, 15 May 2008 05:00:28 +0000
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <Pine.NEB.4.64.0805150253250.20099@sdf.lonestar.org>
References: <Pine.NEB.4.64.0805150253250.20099@sdf.lonestar.org>
Message-ID: <304655022-1210827794-cardhu_decombobulator_blackberry.rim.net-1827005967-@bxe011.bisx.prod.on.blackberry>

Hey Ben,

Well, I'd make sure your blueprints fit into the format supported by manufacturing outsourcing companies like MFG.com and Alibaba.com.  My hunch is that if you're trying to get an industry-accepted standard (how is a matter compiler different than a schematic, CAD, bill of materials, etc.? As this is typically how things get made.), you can talk to industry all you want, and they'll go off and do it themselves so it fits their needs, anyway.  

R- 

-----Original Message-----
From: ben lipkowitz <fenn at sdf.lonestar.org>

Date: Thu, 15 May 2008 03:25:44 
To:oww-discuss at mit.edu
Subject: [OWW-Discuss] Tapping into open source / open access and doing
	slightly more


Hello list,

It seems Bryan can't write an email in plain english, so I feel obligated 
to explain for him:

The idea behind what we're working on is to end up with a Matter Compiler 
- a set of programs hooked up to manufacturing equipment that can take any 
arbitrary design data and either build it with tools that you have, or 
make the tools to make the tools ... to make what you wanted in the first 
place.

Biology lends itself to this concept readily because it is already a 
digital manufacturing system; a unique DNA/RNA/peptide sequence is the 
same molecule no matter what enzyme put it together, unlike a car engine 
which may be different depending on which factory it came from or the 
phase of the moon. (Yeah yeah I know about isotopes.) Additionally, tools 
already exist to make short sequences of DNA, to replicate them into vast 
numbers in vitro or vivo, and we can do cool things with those pieces such 
as making DNA origami or aptamers.

At this point you may be thinking "I dont need some silly program to tell 
me how to send a sequence off to sequences-r-us!" but that isn't the 
point. The reason this makes sense for OWW is that in order to direct a 
computer to make the tools to make the tools, we must already have a 
formalized description of processes, properties, and functionality. So, 
provided that our system is general/abstract enough, it should be able to 
model complex biological systems as well. I intend to include that 
capability anyway because some biological systems are useful in a 
manufacturing context. I dont know what OWW needs, but maybe it doesn't 
even matter: since the design is open and decentralized, you can clone a 
local copy for yourself and put your super-secret academic research 
projects in it, or maybe even contribute it back to the rest of the world.
On the other hand, I'd hate to make a poor design decision in the early 
stages simply because I didnt know what you guys need.

> The people who are in the position to contribute the most in terms of 
> research projects are precisely the people who already have so much 
> going on they don't contribute to open-source software type projects.

This is a damn shame. What are they doing with all those research results 
anyway?

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



From kanzure at gmail.com  Thu May 15 01:13:30 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Thu, 15 May 2008 00:13:30 -0500
Subject: [OWW-Discuss] Tapping into open source / open access and
	doingslightly more
In-Reply-To: <304655022-1210827794-cardhu_decombobulator_blackberry.rim.net-1827005967-@bxe011.bisx.prod.on.blackberry>
References: <Pine.NEB.4.64.0805150253250.20099@sdf.lonestar.org>
	<304655022-1210827794-cardhu_decombobulator_blackberry.rim.net-1827005967-@bxe011.bisx.prod.on.blackberry>
Message-ID: <200805150013.30525.kanzure@gmail.com>

On Thursday 15 May 2008, Russell Hanson wrote:
> Well, I'd make sure your blueprints fit into the format supported by
> manufacturing outsourcing companies like MFG.com and Alibaba.com. ?My
> hunch is that if you're trying to get an industry-accepted standard
> (how is a matter compiler different than a schematic, CAD, bill of
> materials, etc.? As this is typically how things get made.), you can
> talk to industry all you want, and they'll go off and do it
> themselves so it fits their needs, anyway. ?

Why the focus on industry acceptance? Although I agree that talking with 
industry is important, and perhaps even insightful [who knows, perhaps 
NIST, IEEE, etc., has something to offer], I don't think that's a high 
priority at all. That's like telling linux that they need to go talk to 
Microsoft.

- Bryan
________________________________________
http://heybryan.org/



From bill.altmail at gmail.com  Thu May 15 15:10:49 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Thu, 15 May 2008 15:10:49 -0400
Subject: [OWW-Discuss] Google sitemap of OWW is working.
Message-ID: <26428aaa0805151210g4576958fva71fa2264d0581c4@mail.gmail.com>

I didn't check the Google site: page count before, but at this point, we're
indexing 35,023 OWW pages via Google. That should mean that any content on
any OWW page is accessible via Google.

I'm going to put the other Google-derived metrics up on a page for people to
look at within OWW. This includes the most popular search terms we're being
shown as part of the search results and which of those people are choosing
to follow through to OWW from.

I can't say what this means re: how we internally categorize or order
content but it's worth spending time to follow up.

Thanks.

Bill Flanagan
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From bill.altmail at gmail.com  Sat May 17 13:54:29 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 13:54:29 -0400
Subject: [OWW-Discuss] Google HuddleChat vs 37 Signals Campfire: When Open
	Source gets... trumped?
Message-ID: <26428aaa0805171054o2595598bg499efe87bc11d8df@mail.gmail.com>

When is Open Source turned into the minion of the "Not-DoEvi"l Empire?

It's hard to not want to mention this one. Consider this as it relates to
OWW, Open Source, Open Science, Intellectual Propert, Innovation, and
Sales/Marketing Tactics and Strategy.


We're having a lot of internal discussion here at OWW re: our chat app. The
old one was a great concept but didn't scale well. I really mean this.
Austin wrote it and I really like the concept of it. The scaling issues came
from the use of a free chat program that is a bit flaky and sucks the heck
out of our server's capacity when in use. We've been working to use a
Jabber-based chat as a replacement. We're having scattered connectivity
issues with it, but it's the way we're headed. We'll get there sooner or
later. Again, Austin is moving this one along. I think we started this
effort based upon comments from Mr. Bishop some months back.

I'm really not asking for solutions in this message. Please use OWW to
discuss chat here:

http://openwetware.org/wiki/OpenWetWare:Software/Projects/Chat/Discuss

There are a number of dimensions that have recently popped up that
cumulatively put Huddle/Campfire chat  in the middle of a more general
discussion related to Open Source and everything else. Oddly, the tone is
very similar to the way Microsoft used to get called out for adding
functionality from other company's apps into the base Windows OS. I've lived
through a lot of this well before open source was a specific focus of the
discussion. The names have changed. I'm also pretty sure the story has
changed in this case.

37 Signals, everyone's favorite Web 2.0 developer (Ruby on Rails and
BaseCamp for instance), was very critical of a decision by Google to release
the source to a Python/Django app called 'Huddle Chat'. The app was a very
close approximation of 37 Signal's Campfire, a really nice chat program that
works flawlessly. It's close to what we at OWW would like our free HTML chat
to be.

37 Signals does their work in Ruby on Rails : they pretty much wrote Ruby on
Rails. They're funded by Amazon. You can't even buy Campfire: you have to
rent it per-month from them. It runs on Amazon's S3/EC2 backend.

Google released this as part of their free Google Web App initiative. For
now, you don't pay for the design tools, the apps, the source code, or even
the cycles and bandwidth the app uses. It's all free. The source was Open.

Google soon (within a few weeks) dropped the Huddle Chat source code
example. If it were there, I would have lobbied to try it out at least for
OWW. Instead, we can use another chat app or an ad-supported version of
someone else's chat app. We know there are a few other services offering
free chat: we may still go with the best of the lot if we need to.

This is al that now remains (http://www.huddlechat.com/):

Hi, a couple of our colleagues wrote Huddle Chat in their spare time as a
sample application for other developers to demonstrate the power and
flexibility of Google App Engine. We've heard some complaints from the
developer community about it and because of that we've decided to take it
down. If you'd like to see more sample applications written on Google App
Engine please check out our documentation and our App Gallery.

Thanks,
The Google App Engine Team


This is a discusion question re: OWW: what was right and wrong here?

Did Google try to kick the little guy (37 Signals) to signal the big
competitor (Amazon)?

As far as I know, you can't 'steal' the look and feel of an application. I
worked for Lotus Developement when the company tried to sue Microsoft over
Excel. The judge said copyright didn't cover the expression of an
application or the set of features. He said the only way to do that might be
the patent process. Thus came the deluge. In this case, 37 Signals had no
patent protection to trumpet their rights. Instead, they pretty much pointed
a finger at Google and called them thiefs.

As we get more involved with making features from other sites also part of
OWW, what would people here feel?

I'm very interested in this incident as a way to look at some of the ways
Open Source can best be used to do more for biologts and biology.

By the way, I use an Open Source version clone of 37 Signals BaseCamp for my
own internal use. I can't afford their price for the app. If we were to
deploy something like this in OWW, how would it be received? Please package
all tomato and vegetable throwables into styrofoam and send to me.

We can use the pasta sauce more than you can use the monitor cleaning
issues!

Here are a few references:

*37 Signals
*http://www.37signals.com/
*
BaseCamp:
*http://www.basecamphq.com/?source=37s+home

*Campfire: *
http://www.campfirenow.com/?source=37s+home

*Huddle Chat:
*http://www.huddlechat.com/

*Google App Engine:
*http://code.google.com/appengine/

*Amazon Simple Storage Services (S3):
*http://www.amazon.com/gp/browse.html?node=16427261

*Amazon Elastic Compute Cloud (Amazon EC2) - Beta*
http://www.amazon.com/b/ref=amb_link_5164072_1?ie=UTF8&node=201590011&pf_rd_m=ATVPDKIKX0DER&pf_rd_s=auto-sparkle&pf_rd_r=09EMV56PKHPQG1SARREE&pf_rd_t=301&pf_rd_p=299027501&pf_rd_i=EC2
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From bill.altmail at gmail.com  Sat May 17 14:45:15 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 14:45:15 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place to
	enter bugs...
Message-ID: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>

We have a page for it here:

http://openwetware.org/wiki/OpenWetWare:Software/Bugs

Austin started it and I watch it.

But there's no easy way for a user to now it's there.

Any suggestions on how we should publicize it?

Thanks.


Bill
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From rshetty at MIT.EDU  Sat May 17 15:03:25 2008
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Sat, 17 May 2008 15:03:25 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
Message-ID: <6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>

I wonder if we should revamp our toolbox on the bottom lefthand side.
My guess is that "Related changes" and "What links here" are rarely
used.  We could replace those links with something more useful like
"Report a bug".

-Reshma

On Sat, May 17, 2008 at 2:45 PM, Bill Flanagan <bill.altmail at gmail.com> wrote:
> We have a page for it here:
>
> http://openwetware.org/wiki/OpenWetWare:Software/Bugs
>
> Austin started it and I watch it.
>
> But there's no easy way for a user to now it's there.
>
> Any suggestions on how we should publicize it?
>
> Thanks.
>
>
> Bill
>
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>


From julius.lucks at gmail.com  Sat May 17 15:23:49 2008
From: julius.lucks at gmail.com (julius.lucks)
Date: Sat, 17 May 2008 12:23:49 -0700
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
Message-ID: <5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>

That sounds like a good idea to me.  Maybe another mailing list like  
contact at openwetware.

J

---------------------------------------------------------------------------------------
http://www.openwetware.org/wiki/User:Julius_B._Lucks
----------------------------------------------------------------------------------------



On May 17, 2008, at 12:03 PM, Reshma Shetty wrote:

> I wonder if we should revamp our toolbox on the bottom lefthand side.
> My guess is that "Related changes" and "What links here" are rarely
> used.  We could replace those links with something more useful like
> "Report a bug".
>
> -Reshma
>
> On Sat, May 17, 2008 at 2:45 PM, Bill Flanagan  
> <bill.altmail at gmail.com> wrote:
>> We have a page for it here:
>>
>> http://openwetware.org/wiki/OpenWetWare:Software/Bugs
>>
>> Austin started it and I watch it.
>>
>> But there's no easy way for a user to now it's there.
>>
>> Any suggestions on how we should publicize it?
>>
>> Thanks.
>>
>>
>> Bill
>>
>>
>> _______________________________________________
>> 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



From bill.altmail at gmail.com  Sat May 17 15:34:31 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 15:34:31 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
Message-ID: <26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>

Julius,

Good idea. But for now, we already have a page; I get email when it's
updated using the page watch function. For now, I have no problem with this.
Since I'm typically the bug fixer, I don't mind continuing to monitor it.
Anyone else can watch the page and comment.

If we get to the point where we put in a more sophisticated bug tracker,
I'll hope we can just add a package rather than building it ourself; there
are scores of them out there.

My question for the community is how best do we let people know that they
can use the OpenWetWare:Software/Bugs page to report errors?






On Sat, May 17, 2008 at 3:23 PM, julius.lucks <julius.lucks at gmail.com>
wrote:

> That sounds like a good idea to me.  Maybe another mailing list like
> contact at openwetware.
>
> J
>
>
> ---------------------------------------------------------------------------------------
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>
> ----------------------------------------------------------------------------------------
>
>
>
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From kanzure at gmail.com  Sat May 17 15:46:08 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Sat, 17 May 2008 14:46:08 -0500
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
Message-ID: <200805171446.08989.kanzure@gmail.com>

On Saturday 17 May 2008, Bill Flanagan wrote:
> If we get to the point where we put in a more sophisticated bug
> tracker, I'll hope we can just add a package rather than building it
> ourself; there are scores of them out there.

Bugzilla is a favorite of software developers:
http://bugzilla.org/
http://bugzilla.org/download/

- Bryan
________________________________________
http://heybryan.org/


From julius.lucks at gmail.com  Sat May 17 15:49:44 2008
From: julius.lucks at gmail.com (julius.lucks)
Date: Sat, 17 May 2008 12:49:44 -0700
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
Message-ID: <6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>

Hey Bill,

If you want to continue using that page, then put a link to it on the  
toolbar on the front page called 'Report a Bug'.  However this limits  
bug reports to OWW users (probably the majority of people who will  
find bugs), but I bet other non-members will find bugs too.  In that  
case a mailing list would allow everyone to submit bugs, and we've had  
great success with the contact list I think.  Is it easy to inject a  
mailing list into a page?

Cheers,

J

---------------------------------------------------------------------------------------
http://www.openwetware.org/wiki/User:Julius_B._Lucks
----------------------------------------------------------------------------------------



On May 17, 2008, at 12:34 PM, Bill Flanagan wrote:

> Julius,
>
> Good idea. But for now, we already have a page; I get email when  
> it's updated using the page watch function. For now, I have no  
> problem with this. Since I'm typically the bug fixer, I don't mind  
> continuing to monitor it. Anyone else can watch the page and comment.
>
> If we get to the point where we put in a more sophisticated bug  
> tracker, I'll hope we can just add a package rather than building it  
> ourself; there are scores of them out there.
>
> My question for the community is how best do we let people know that  
> they can use the OpenWetWare:Software/Bugs page to report errors?
>
>
>
>
>
>
> On Sat, May 17, 2008 at 3:23 PM, julius.lucks  
> <julius.lucks at gmail.com> wrote:
> That sounds like a good idea to me.  Maybe another mailing list like  
> contact at openwetware.
>
> J
>
> ---------------------------------------------------------------------------------------
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------------------------
>
>
>

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From bcanton at MIT.EDU  Sat May 17 15:59:46 2008
From: bcanton at MIT.EDU (Barry Canton)
Date: Sat, 17 May 2008 15:59:46 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
	<6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
Message-ID: <52c0d2160805171259v5aaa8c97nd07c25bbb1c453e2@mail.gmail.com>

I agree that it would be good to make the path to reporting a bug
obvious.  I also think the "contact us" page might be sufficient.  We
could edit the text on that page to say that if you want to send us
email, do so, alternatively post a bug report at
OpenWetWare:Software/Bugs.

Given that we have quite a few links on the sidebar, it might be
better to maximize usage of "Contact us".  We could edit the title to
something like "Feedback? Bugs? Tell us".

Barry

On Sat, May 17, 2008 at 3:49 PM, julius.lucks <julius.lucks at gmail.com> wrote:
> Hey Bill,
>
> If you want to continue using that page, then put a link to it on the
> toolbar on the front page called 'Report a Bug'.  However this limits bug
> reports to OWW users (probably the majority of people who will find bugs),
> but I bet other non-members will find bugs too.  In that case a mailing list
> would allow everyone to submit bugs, and we've had great success with the
> contact list I think.  Is it easy to inject a mailing list into a page?
>
> Cheers,
>
> J
>
>
> ---------------------------------------------------------------------------------------
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------------------------
>
>
>
>
>
> On May 17, 2008, at 12:34 PM, Bill Flanagan wrote:
> Julius,
>
> Good idea. But for now, we already have a page; I get email when it's
> updated using the page watch function. For now, I have no problem with this.
> Since I'm typically the bug fixer, I don't mind continuing to monitor it.
> Anyone else can watch the page and comment.
>
> If we get to the point where we put in a more sophisticated bug tracker,
> I'll hope we can just add a package rather than building it ourself; there
> are scores of them out there.
>
> My question for the community is how best do we let people know that they
> can use the OpenWetWare:Software/Bugs page to report errors?
>
>
>
>
>
>
> On Sat, May 17, 2008 at 3:23 PM, julius.lucks <julius.lucks at gmail.com>
> wrote:
> > That sounds like a good idea to me.  Maybe another mailing list like
> contact at openwetware.
> >
> > J
> >
> >
> ---------------------------------------------------------------------------------------
> > http://www.openwetware.org/wiki/User:Julius_B._Lucks
> >
> ----------------------------------------------------------------------------------------
> >
> >
> >
> >
> >
>
>
>
> _______________________________________________
>  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 bill.altmail at gmail.com  Sat May 17 16:04:17 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 16:04:17 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
	<6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
Message-ID: <26428aaa0805171304h648d744ap68e766397b8f6581@mail.gmail.com>

Excellent point.

Stupid me!

Ilya just finished moving the late great OWW admin list over to a Google
Group with an integral mailing list. We're doing the same for Discuss when
that one is stable. Already, the Google Group we set up for approving new
members is working well; it's fast, free of spam, and easy to maintain. The
content is much easier to search when needed.

I agree; using something like the 'contact us' extension would be a way to
do it.

For now, I'm concerned about current OWW users; writing seems to break
things more than reading!

B.



On Sat, May 17, 2008 at 3:49 PM, julius.lucks <julius.lucks at gmail.com>
wrote:

> Hey Bill,
> If you want to continue using that page, then put a link to it on the
> toolbar on the front page called 'Report a Bug'.  However this limits bug
> reports to OWW users (probably the majority of people who will find bugs),
> but I bet other non-members will find bugs too.  In that case a mailing list
> would allow everyone to submit bugs, and we've had great success with the
> contact list I think.  Is it easy to inject a mailing list into a page?
>
> Cheers,
>
> J
>
>
> ---------------------------------------------------------------------------------------
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>
> ----------------------------------------------------------------------------------------
>
>
>
> On May 17, 2008, at 12:34 PM, Bill Flanagan wrote:
>
> Julius,
>
> Good idea. But for now, we already have a page; I get email when it's
> updated using the page watch function. For now, I have no problem with this.
> Since I'm typically the bug fixer, I don't mind continuing to monitor it.
> Anyone else can watch the page and comment.
>
> If we get to the point where we put in a more sophisticated bug tracker,
> I'll hope we can just add a package rather than building it ourself; there
> are scores of them out there.
>
> My question for the community is how best do we let people know that they
> can use the OpenWetWare:Software/Bugs page to report errors?
>
>
>
>
>
>
> On Sat, May 17, 2008 at 3:23 PM, julius.lucks <julius.lucks at gmail.com>
> wrote:
>
>> That sounds like a good idea to me.  Maybe another mailing list like
>> contact at openwetware.
>>
>> J
>>
>>
>> ---------------------------------------------------------------------------------------
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>>
>> ----------------------------------------------------------------------------------------
>>
>>
>>
>
>
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From bill.altmail at gmail.com  Sat May 17 16:09:06 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 16:09:06 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171258h3130c8eco11e6638246ebd5c7@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
	<200805171446.08989.kanzure@gmail.com>
	<26428aaa0805171258h3130c8eco11e6638246ebd5c7@mail.gmail.com>
Message-ID: <26428aaa0805171309o150f7228h9d666e88331e4e7e@mail.gmail.com>

I like bugzilla. I but it's more than we need at this point. I'll note your
comments for the time we're in need of it.

Unless there are a LOT more bugs than I hope there are, we're fine.

I'm much more interested in finding with, among other things, the following

requirements:

a stable location
one that's visible on all page
one that's agreeable to you folks

One of the sidebar boxes is fine. Just  let me me know where to put it.

Thanks.

>
>
> B.
>
>
>
> On Sat, May 17, 2008 at 3:46 PM, Bryan Bishop <kanzure at gmail.com> wrote:
>
>> On Saturday 17 May 2008, Bill Flanagan wrote:
>> > If we get to the point where we put in a more sophisticated bug
>> > tracker, I'll hope we can just add a package rather than building it
>> > ourself; there are scores of them out there.
>>
>> Bugzilla is a favorite of software developers:
>> http://bugzilla.org/
>> http://bugzilla.org/download/
>>
>> - Bryan
>> ________________________________________
>> http://heybryan.org/
>> _______________________________________________
>> OpenWetWare Discussion Mailing List
>> discuss at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>>
>
>
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From jasonk at MIT.EDU  Sat May 17 16:25:00 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Sat, 17 May 2008 16:25:00 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171309o150f7228h9d666e88331e4e7e@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<5F4A1DC0-1A0D-4D82-9701-290068E9F638@gmail.com>
	<26428aaa0805171234r2d48b65clf1f0ce9167de0caf@mail.gmail.com>
	<200805171446.08989.kanzure@gmail.com>
	<26428aaa0805171258h3130c8eco11e6638246ebd5c7@mail.gmail.com>
	<26428aaa0805171309o150f7228h9d666e88331e4e7e@mail.gmail.com>
Message-ID: <7c085c480805171325p3ffed570y569d638fac41ac46@mail.gmail.com>

I think if the feedback link was more obvious it would solve the bug
reporting problem -- doesn't seem to be a need for two seperate links.

What if we had something like the attached picture (it's from the
logged in area of another website so cant link to it directly) on the
sidebar?  would be more obvious anyway, and you just click in it and
type then hit send.

thanks,
jason

On Sat, May 17, 2008 at 4:09 PM, Bill Flanagan <bill.altmail at gmail.com> wrote:
> I like bugzilla. I but it's more than we need at this point. I'll note your
> comments for the time we're in need of it.
>
> Unless there are a LOT more bugs than I hope there are, we're fine.
>
> I'm much more interested in finding with, among other things, the following
>
> requirements:
>
> a stable location
> one that's visible on all page
> one that's agreeable to you folks
>
> One of the sidebar boxes is fine. Just  let me me know where to put it.
>
> Thanks.
>>
>>
>> B.
>>
>>
>> On Sat, May 17, 2008 at 3:46 PM, Bryan Bishop <kanzure at gmail.com> wrote:
>>>
>>> On Saturday 17 May 2008, Bill Flanagan wrote:
>>> > If we get to the point where we put in a more sophisticated bug
>>> > tracker, I'll hope we can just add a package rather than building it
>>> > ourself; there are scores of them out there.
>>>
>>> Bugzilla is a favorite of software developers:
>>> http://bugzilla.org/
>>> http://bugzilla.org/download/
>>>
>>> - Bryan
>>> ________________________________________
>>> http://heybryan.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
>
>
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From kanzure at gmail.com  Sat May 17 17:05:14 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Sat, 17 May 2008 16:05:14 -0500
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <26428aaa0805171304h648d744ap68e766397b8f6581@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
	<26428aaa0805171304h648d744ap68e766397b8f6581@mail.gmail.com>
Message-ID: <200805171605.15537.kanzure@gmail.com>

On Saturday 17 May 2008, Bill Flanagan wrote:
> Ilya just finished moving the late great OWW admin list over to a
> Google Group with an integral mailing list. We're doing the same for
> Discuss when that one is stable. Already, the Google Group we set up
> for approving new members is working well; it's fast, free of spam,
> and easy to maintain. The content is much easier to search when
> needed.

Hm, is this mailing list migrating over to Google Groups?

- Bryan
________________________________________
http://heybryan.org/


From bill.altmail at gmail.com  Sat May 17 17:10:55 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 17:10:55 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <200805171605.15537.kanzure@gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6A27F228-4DAD-42B4-BF61-648EAE25FC1E@gmail.com>
	<26428aaa0805171304h648d744ap68e766397b8f6581@mail.gmail.com>
	<200805171605.15537.kanzure@gmail.com>
Message-ID: <26428aaa0805171410t6e905e88l3de9d3226e1dd86e@mail.gmail.com>

It is.

That's the last one we're moving. The internal MediaWiki mailing lists
(List:) aren't moving at this point.

Let us know if you have concerns. We've been having issues related mostly to
spam that the mail list server we were running with that have been causing
many folks to miss messages. Google Groups is free and seems to be reliable.
Indexing of the lists was present on the previous server but Google's is
cleaner and easier for all OWW members to access.

B.


On Sat, May 17, 2008 at 5:05 PM, Bryan Bishop <kanzure at gmail.com> wrote:

> On Saturday 17 May 2008, Bill Flanagan wrote:
> > Ilya just finished moving the late great OWW admin list over to a
> > Google Group with an integral mailing list. We're doing the same for
> > Discuss when that one is stable. Already, the Google Group we set up
> > for approving new members is working well; it's fast, free of spam,
> > and easy to maintain. The content is much easier to search when
> > needed.
>
> Hm, is this mailing list migrating over to Google Groups?
>
> - Bryan
> ________________________________________
> http://heybryan.org/
> _______________________________________________
> 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  Sat May 17 17:44:47 2008
From: tk at csail.mit.edu (Tom Knight)
Date: Sat, 17 May 2008 17:44:47 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
Message-ID: <9fe37c09fa1a96ac62381fa00facabe3@csail.mit.edu>

I use the "what links here" all the time.

On May 17, 2008, at 3:03 PM, Reshma Shetty wrote:

> I wonder if we should revamp our toolbox on the bottom lefthand side.
> My guess is that "Related changes" and "What links here" are rarely
> used.  We could replace those links with something more useful like
> "Report a bug".
>
> -Reshma
>
> On Sat, May 17, 2008 at 2:45 PM, Bill Flanagan 
> <bill.altmail at gmail.com> wrote:
>> We have a page for it here:
>>
>> http://openwetware.org/wiki/OpenWetWare:Software/Bugs
>>
>> Austin started it and I watch it.
>>
>> But there's no easy way for a user to now it's there.
>>
>> Any suggestions on how we should publicize it?
>>
>> Thanks.
>>
>>
>> Bill
>>
>>
>> _______________________________________________
>> 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



From bill.altmail at gmail.com  Sat May 17 20:40:48 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Sat, 17 May 2008 20:40:48 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
	to enter bugs...
In-Reply-To: <9fe37c09fa1a96ac62381fa00facabe3@csail.mit.edu>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>
	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>
	<9fe37c09fa1a96ac62381fa00facabe3@csail.mit.edu>
Message-ID: <26428aaa0805171740v7289ec81m1b4cf028f83e4d8b@mail.gmail.com>

Thanks for the comments. This is great.

I agree with Tom; I use the link as well. We're very lean re: sidebar links
right now. We can add a few more without looking too wordy if we need to.

Let me try Jason's idea of a box.

Reporting a problem isn't the same (to me at least) as sending a comment or
feedback. Both may send a message or post a db record but this is more an
issue of addressing an issue users must be having. Multiplexing a single
link with a select page or doing this as a box both make sense: if you want
to send a message, is it asking too much to click thru a page to get to it?

This would mean we can ask more topics over time. To address the issue
Julius brought up, we can even have some options disabled unless the client
is logged in.



On Sat, May 17, 2008 at 5:44 PM, Tom Knight <tk at csail.mit.edu> wrote:

> I use the "what links here" all the time.
>
>
> On May 17, 2008, at 3:03 PM, Reshma Shetty wrote:
>
>  I wonder if we should revamp our toolbox on the bottom lefthand side.
>> My guess is that "Related changes" and "What links here" are rarely
>> used.  We could replace those links with something more useful like
>> "Report a bug".
>>
>> -Reshma
>>
>> On Sat, May 17, 2008 at 2:45 PM, Bill Flanagan <bill.altmail at gmail.com>
>> wrote:
>>
>>> We have a page for it here:
>>>
>>> http://openwetware.org/wiki/OpenWetWare:Software/Bugs
>>>
>>> Austin started it and I watch it.
>>>
>>> But there's no easy way for a user to now it's there.
>>>
>>> Any suggestions on how we should publicize it?
>>>
>>> Thanks.
>>>
>>>
>>> Bill
>>>
>>>
>>> _______________________________________________
>>> 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 bill.altmail at gmail.com  Mon May 19 14:18:54 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Mon, 19 May 2008 14:18:54 -0400
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
Message-ID: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>

WetPaint.com hosts free wikis. They have a good deal of good press and a lot
of users.

WetPaint just announced a new feature. Start a wiki at their site and
WetPaint both allows you and provides to you the hooks needed to embed your
wiki in pages on other sites.

In a way, a wiki becomes a "bolt-on" to other communities where needed.

Technically it's not an amazing feat. But they're effectively snubbing the
time-tested model for measuring their usage: the page view. By embedding in
other people's pages, they piggy back their entry into other sites. I've not
seen how it works yet. But the model is making people take notice. This
model didn't get in the way of raising investment money. They just got a big
increase in funding and are riding high as the next-big thing for the next
15 minutes.
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From russell2 at qiezi.net  Mon May 19 14:45:23 2008
From: russell2 at qiezi.net (=?utf-8?B?UnVzc2VsbCBIYW5zb24=?=)
Date: Mon, 19 May 2008 18:45:23 +0000
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
Message-ID: <70593526-1211222875-cardhu_decombobulator_blackberry.rim.net-2104992104-@bxe011.bisx.prod.on.blackberry>

Bill,

Isn't this the same thing/idea as a mashup? 

Russell 

-----Original Message-----
From: "Bill Flanagan" <bill.altmail at gmail.com>

Date: Mon, 19 May 2008 14:18:54 
To:"discuss at openwetware.org" <discuss at openwetware.org>
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?


WetPaint.com hosts free wikis. They have a good deal of good press and a lot of users. 

WetPaint just announced a new feature. Start a wiki at their site and WetPaint both allows you and provides to you the hooks needed to embed your wiki in pages on other sites. 
 
In a way, a wiki becomes a "bolt-on" to other communities where needed. 

Technically it's not an amazing feat. But they're effectively snubbing the time-tested model for measuring their usage: the page view. By embedding in other people's pages, they piggy back their entry into other sites. I've not seen how it works yet. But the model is making people take notice. This model didn't get in the way of raising investment money. They just got a big increase in funding and are riding high as the next-big thing for the next 15 minutes.
 

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




From ilyas at MIT.EDU  Mon May 19 18:05:25 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Mon, 19 May 2008 18:05:25 -0400
Subject: [OWW-Discuss] We have no way to let folks know there's a place
 to enter bugs...
In-Reply-To: <26428aaa0805171740v7289ec81m1b4cf028f83e4d8b@mail.gmail.com>
References: <26428aaa0805171145s301a1824ncdefb351ccd3a12@mail.gmail.com>	<6e9f40380805171203gab601c7hbc029de3809709cc@mail.gmail.com>	<9fe37c09fa1a96ac62381fa00facabe3@csail.mit.edu>
	<26428aaa0805171740v7289ec81m1b4cf028f83e4d8b@mail.gmail.com>
Message-ID: <4831F9A5.50203@mit.edu>

I think that using a wiki page for reporting the bugs is a bit clumsy 
(and it precludes non-registered users from submitting reports), so it 
would be best to use the current feedback form.
Also, Bill has already set up and started using an internal bug tracking 
system (http://openwetware.org/projects) that seems to work well though 
it's not accessible to the OWW users directly.  So, the way I see it: 
users would report bugs using the form, then Bill/Lorrie would 
prioritize them and enter into the tracking system (may be there's a way 
to make the bugs world-readable too).

Ilya

Bill Flanagan wrote:
> Thanks for the comments. This is great.
> 
> I agree with Tom; I use the link as well. We're very lean re: sidebar 
> links right now. We can add a few more without looking too wordy if we 
> need to.
> 
> Let me try Jason's idea of a box.
> 
> Reporting a problem isn't the same (to me at least) as sending a comment 
> or feedback. Both may send a message or post a db record but this is 
> more an issue of addressing an issue users must be having. Multiplexing 
> a single link with a select page or doing this as a box both make sense: 
> if you want to send a message, is it asking too much to click thru a 
> page to get to it?
> 
> This would mean we can ask more topics over time. To address the issue 
> Julius brought up, we can even have some options disabled unless the 
> client is logged in.
> 
> 
> 
> On Sat, May 17, 2008 at 5:44 PM, Tom Knight <tk at csail.mit.edu 
> <mailto:tk at csail.mit.edu>> wrote:
> 
>     I use the "what links here" all the time.
> 
> 
>     On May 17, 2008, at 3:03 PM, Reshma Shetty wrote:
> 
>         I wonder if we should revamp our toolbox on the bottom lefthand
>         side.
>         My guess is that "Related changes" and "What links here" are rarely
>         used.  We could replace those links with something more useful like
>         "Report a bug".
> 
>         -Reshma
> 
>         On Sat, May 17, 2008 at 2:45 PM, Bill Flanagan
>         <bill.altmail at gmail.com <mailto:bill.altmail at gmail.com>> wrote:
> 
>             We have a page for it here:
> 
>             http://openwetware.org/wiki/OpenWetWare:Software/Bugs
> 
>             Austin started it and I watch it.
> 
>             But there's no easy way for a user to now it's there.
> 
>             Any suggestions on how we should publicize it?
> 
>             Thanks.
> 
> 
>             Bill
> 
> 
>             _______________________________________________
>             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 <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 kanzure at gmail.com  Mon May 19 18:59:29 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Mon, 19 May 2008 17:59:29 -0500
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
Message-ID: <200805191759.29846.kanzure@gmail.com>

On Monday 19 May 2008, Bill Flanagan wrote:
> WetPaint just announced a new feature. Start a wiki at their site and
> WetPaint both allows you and provides to you the hooks needed to
> embed your wiki in pages on other sites.

Hrm. I am suspicious. Especially since I don't see a 'download database' 
link. I know I could always run pywikipediabot or an equivalent, but 
it's always easier to just download a dump.

- Bryan
________________________________________
http://heybryan.org/


From bill.altmail at gmail.com  Mon May 19 20:40:28 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Mon, 19 May 2008 20:40:28 -0400
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <200805191759.29846.kanzure@gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
	<200805191759.29846.kanzure@gmail.com>
Message-ID: <26428aaa0805191740h48232bb2j7d3fb33399d43d66@mail.gmail.com>

Good point.

I'm not advocating wet paint. Frankly, it's tacky. (rimshot!).

"Data checks in but it doesn't check out".

If anyone sees anything useful in the way they're deploying wikis, think
about how it may apply to OWW.

Thanks

B.


t announced a new feature. Start a wiki at their site and
> > WetPaint both allows you and provides to you the hooks needed to
> > embed your wiki in pages on other sites.
>
> Hrm. I am suspicious. Especially since I don't see a 'download database'
> link. I know I could always run pywikipediabot or an equivalent, but
> it's always easier to just download a dump.
>
> - Bryan
> ________________________________________
> http://heybryan.org/
> _______________________________________________
> 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  Mon May 19 21:03:45 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Mon, 19 May 2008 20:03:45 -0500
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <26428aaa0805191740h48232bb2j7d3fb33399d43d66@mail.gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
	<200805191759.29846.kanzure@gmail.com>
	<26428aaa0805191740h48232bb2j7d3fb33399d43d66@mail.gmail.com>
Message-ID: <200805192003.45215.kanzure@gmail.com>

On Monday 19 May 2008, "Bill Flanagan" <bill.altmail at gmail.com> wrote:
> If anyone sees anything useful in the way they're deploying wikis,
> think about how it may apply to OWW.

It would definitely apply if it was more distributed, if the data was 
able to be checked in and out (much like the ikiwiki example (actual 
implementation doesn't matter, ikiwiki is just a good search term)), 
and if then we could aggregate this data on OWW. 

There's certainly times when I want to export content of a wiki to my 
own personal wiki so that I can work on it for a while without 
distracting the typical users. And just to hoard it, too.

- Bryan
________________________________________
http://heybryan.org/


From bill.altmail at gmail.com  Mon May 19 21:26:03 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Mon, 19 May 2008 21:26:03 -0400
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <200805192003.45215.kanzure@gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
	<200805191759.29846.kanzure@gmail.com>
	<26428aaa0805191740h48232bb2j7d3fb33399d43d66@mail.gmail.com>
	<200805192003.45215.kanzure@gmail.com>
Message-ID: <26428aaa0805191826n74b8697cue50f88aaab84d655@mail.gmail.com>

Data portability is typically a non-goal of software companies. One metric
used to be that the market cap of a company was related to how much it would
cost their users to move to another application. It still may be an accurate
measure when I think of it...

So the mediawiki xml export format is a good thing from your perspective.
But what about the wiki text format? Is that a good or a bad thing for you?
You can export the docs but you still have to convert to and from wikitext.
It's an open format but it can be hard to deal with.



On Mon, May 19, 2008 at 9:03 PM, Bryan Bishop <kanzure at gmail.com> wrote:

> On Monday 19 May 2008, "Bill Flanagan" <bill.altmail at gmail.com> wrote:
> > If anyone sees anything useful in the way they're deploying wikis,
> > think about how it may apply to OWW.
>
> It would definitely apply if it was more distributed, if the data was
> able to be checked in and out (much like the ikiwiki example (actual
> implementation doesn't matter, ikiwiki is just a good search term)),
> and if then we could aggregate this data on OWW.
>
> There's certainly times when I want to export content of a wiki to my
> own personal wiki so that I can work on it for a while without
> distracting the typical users. And just to hoard it, too.
>
> - Bryan
> ________________________________________
> http://heybryan.org/
> _______________________________________________
> 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  Mon May 19 22:07:20 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Mon, 19 May 2008 21:07:20 -0500
Subject: [OWW-Discuss] WetPaint: nex-gen wiki?
In-Reply-To: <26428aaa0805191826n74b8697cue50f88aaab84d655@mail.gmail.com>
References: <26428aaa0805191118p19ba34d8g4a1ec8aa828cdbd0@mail.gmail.com>
	<200805192003.45215.kanzure@gmail.com>
	<26428aaa0805191826n74b8697cue50f88aaab84d655@mail.gmail.com>
Message-ID: <200805192107.20369.kanzure@gmail.com>

On Monday 19 May 2008, "Bill Flanagan" <bill.altmail at gmail.com> wrote:
> So the mediawiki xml export format is a good thing from your
> perspective. But what about the wiki text format? Is that a good or a
> bad thing for you? You can export the docs but you still have to
> convert to and from wikitext. It's an open format but it can be hard
> to deal with.

Yes, it can be difficult at times. I'm alright with it for most of the 
notes that are dumped on wikis, and even some of the content on 
Wikipedia. However, the projects that I have been associating myself 
with recently, such as the manufacturing database, inherently require 
semantics and syntax that the wiki syntax simply can't provide. At the 
same time, it would be nice to have a wiki directly edit that other 
format, some markup language [I am a recent fan of YAML, an object 
serialization format, a brother of RDF and XML and those families].

- Bryan
________________________________________
http://heybryan.org/


From austin at csail.mit.edu  Wed May 21 10:20:25 2008
From: austin at csail.mit.edu (Austin Che)
Date: Wed, 21 May 2008 10:20:25 -0400
Subject: [OWW-Discuss] wiki to pdf books
Message-ID: <87d4nfhh7a.fsf@nitsua.mit.edu>


    I've been notified about this extension that looks useful. It can
    generate a pdf book based on all pages in a category
    http://www.mediawiki.org/wiki/Extension:Pdf_Book
    
    Demo at
    http://www.organicdesign.co.nz/Category:I_am_that
    
    Also single page export as pdf
    http://www.mediawiki.org/wiki/Extension:Pdf_Export
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From austin at csail.mit.edu  Wed May 21 10:25:25 2008
From: austin at csail.mit.edu (Austin Che)
Date: Wed, 21 May 2008 10:25:25 -0400
Subject: [OWW-Discuss] wiki to latex
Message-ID: <877idnhgyy.fsf@nitsua.mit.edu>


    Also, this looks to be extremely nice
    http://www.mediawiki.org/wiki/Extension:Wiki2LaTeX
    It automatically parses mediawiki markup into latex code which can
    then be generated into a pdf or the raw latex code can be edited
    manually, e.g. with LatexDoc.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From rvidal at gmail.com  Wed May 21 11:13:52 2008
From: rvidal at gmail.com (Ricardo Vidal)
Date: Wed, 21 May 2008 11:13:52 -0400
Subject: [OWW-Discuss] wiki to latex
In-Reply-To: <877idnhgyy.fsf@nitsua.mit.edu>
References: <877idnhgyy.fsf@nitsua.mit.edu>
Message-ID: <213fc43b0805210813o62f1d9eaue7193bdd3544eed3@mail.gmail.com>

Also a great feature. Have you tried using it to see how it manages pages
with mixed content (images, tables, links, etc)?

R

On Wed, May 21, 2008 at 10:25 AM, Austin Che <austin at csail.mit.edu> wrote:

>
>    Also, this looks to be extremely nice
>    http://www.mediawiki.org/wiki/Extension:Wiki2LaTeX
>    It automatically parses mediawiki markup into latex code which can
>    then be generated into a pdf or the raw latex code can be edited
>    manually, e.g. with LatexDoc.
>
> --
> 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
>



-- 
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  Wed May 21 11:30:48 2008
From: austin at csail.mit.edu (Austin Che)
Date: Wed, 21 May 2008 11:30:48 -0400
Subject: [OWW-Discuss] wiki to pdf books
In-Reply-To: <6FB03B48-673C-4397-8B2F-ADA0F4B8AB2B@gmail.com> (julius lucks's
	message of "Wed, 21 May 2008 07:56:39 -0700")
References: <87d4nfhh7a.fsf@nitsua.mit.edu>
	<6FB03B48-673C-4397-8B2F-ADA0F4B8AB2B@gmail.com>
Message-ID: <87tzgrfzdj.fsf@nitsua.mit.edu>


> This looks like it could be extremely useful to the open writing
> projects (http://openwetware.org/wiki/Open_writing_projects).  Can we
> try it out?

    There might be some minor technical issues as I was told about
    this extension from someone who said there was a conflict between
    it and the LatexDoc extension. Shouldn't be too difficult to
    figure out. 
    
    Bill, it appears the two extensions don't chain the UnknownAction
    hook properly so only one of the two works depending on which is
    loaded first.
    
-- 
Austin Che           <austin at csail.mit.edu>          (617)253-5899


From bill.altmail at gmail.com  Wed May 21 14:37:07 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Wed, 21 May 2008 14:37:07 -0400
Subject: [OWW-Discuss] wiki to pdf books
In-Reply-To: <87tzgrfzdj.fsf@nitsua.mit.edu>
References: <87d4nfhh7a.fsf@nitsua.mit.edu>
	<6FB03B48-673C-4397-8B2F-ADA0F4B8AB2B@gmail.com>
	<87tzgrfzdj.fsf@nitsua.mit.edu>
Message-ID: <26428aaa0805211137tdc6a6abw9467cebf6f08f3c9@mail.gmail.com>

This isn't a show-stopper but I just noted this comment:

"Interference with Extension:ASHighlight: Export halts on first encountered
<source> tag. Use Extension:SyntaxHighlight GeSHi instead."

I'll load it up to check it out this week. Interesting.

B.


On Wed, May 21, 2008 at 11:30 AM, Austin Che <austin at csail.mit.edu> wrote:

>
> > This looks like it could be extremely useful to the open writing
> > projects (http://openwetware.org/wiki/Open_writing_projects).  Can we
> > try it out?
>
>    There might be some minor technical issues as I was told about
>    this extension from someone who said there was a conflict between
>    it and the LatexDoc extension. Shouldn't be too difficult to
>    figure out.
>
>    Bill, it appears the two extensions don't chain the UnknownAction
>    hook properly so only one of the two works depending on which is
>    loaded first.
>
> --
> Austin Che           <austin at csail.mit.edu>          (617)253-5899
>
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From rvidal at gmail.com  Thu May 22 00:00:54 2008
From: rvidal at gmail.com (Ricardo Vidal)
Date: Thu, 22 May 2008 00:00:54 -0400
Subject: [OWW-Discuss] wiki to pdf books
In-Reply-To: <26428aaa0805211137tdc6a6abw9467cebf6f08f3c9@mail.gmail.com>
References: <87d4nfhh7a.fsf@nitsua.mit.edu>
	<6FB03B48-673C-4397-8B2F-ADA0F4B8AB2B@gmail.com>
	<87tzgrfzdj.fsf@nitsua.mit.edu>
	<26428aaa0805211137tdc6a6abw9467cebf6f08f3c9@mail.gmail.com>
Message-ID: <213fc43b0805212100h61773300h5038d372cf6dc890@mail.gmail.com>

I'd be interested to see this work. It's a nice feature that I assume some
folks would like to see.

R

On Wed, May 21, 2008 at 2:37 PM, Bill Flanagan <bill.altmail at gmail.com>
wrote:

> This isn't a show-stopper but I just noted this comment:
>
> "Interference with Extension:ASHighlight: Export halts on first encountered
> <source> tag. Use Extension:SyntaxHighlight GeSHi instead."
>
> I'll load it up to check it out this week. Interesting.
>
> B.
>
>
>
> On Wed, May 21, 2008 at 11:30 AM, Austin Che <austin at csail.mit.edu> wrote:
>
>>
>> > This looks like it could be extremely useful to the open writing
>> > projects (http://openwetware.org/wiki/Open_writing_projects).  Can we
>> > try it out?
>>
>>    There might be some minor technical issues as I was told about
>>    this extension from someone who said there was a conflict between
>>    it and the LatexDoc extension. Shouldn't be too difficult to
>>    figure out.
>>
>>    Bill, it appears the two extensions don't chain the UnknownAction
>>    hook properly so only one of the two works depending on which is
>>    loaded first.
>>
>> --
>> 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
>
>


-- 
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  Thu May 22 11:15:11 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Thu, 22 May 2008 11:15:11 -0400
Subject: [OWW-Discuss] wiki to pdf books
In-Reply-To: <213fc43b0805212100h61773300h5038d372cf6dc890@mail.gmail.com>
References: <87d4nfhh7a.fsf@nitsua.mit.edu>
	<6FB03B48-673C-4397-8B2F-ADA0F4B8AB2B@gmail.com>
	<87tzgrfzdj.fsf@nitsua.mit.edu>
	<26428aaa0805211137tdc6a6abw9467cebf6f08f3c9@mail.gmail.com>
	<213fc43b0805212100h61773300h5038d372cf6dc890@mail.gmail.com>
Message-ID: <26428aaa0805220815x165cf23ewebc9d7b26282190f@mail.gmail.com>

Cool. It installs without any problem. There are a few templates used with
it to actually product the book. I'll load it up over the next few days in
OWW.

On Thu, May 22, 2008 at 12:00 AM, Ricardo Vidal <rvidal at gmail.com> wrote:

> I'd be interested to see this work. It's a nice feature that I assume some
> folks would like to see.
>
> R
>
> On Wed, May 21, 2008 at 2:37 PM, Bill Flanagan <bill.altmail at gmail.com>
> wrote:
>
>> This isn't a show-stopper but I just noted this comment:
>>
>> "Interference with Extension:ASHighlight: Export halts on first
>> encountered <source> tag. Use Extension:SyntaxHighlight GeSHi instead."
>>
>> I'll load it up to check it out this week. Interesting.
>>
>> B.
>>
>>
>>
>> On Wed, May 21, 2008 at 11:30 AM, Austin Che <austin at csail.mit.edu>
>> wrote:
>>
>>>
>>> > This looks like it could be extremely useful to the open writing
>>> > projects (http://openwetware.org/wiki/Open_writing_projects).  Can we
>>> > try it out?
>>>
>>>    There might be some minor technical issues as I was told about
>>>    this extension from someone who said there was a conflict between
>>>    it and the LatexDoc extension. Shouldn't be too difficult to
>>>    figure out.
>>>
>>>    Bill, it appears the two extensions don't chain the UnknownAction
>>>    hook properly so only one of the two works depending on which is
>>>    loaded first.
>>>
>>> --
>>> 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
>>
>>
>
>
> --
> Ricardo Vidal
> rvidal at gmail.com | http://my.biotechlife.net
> http://www.openwetware.org - Share your Science
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From hackdna at gmail.com  Thu May 22 19:06:50 2008
From: hackdna at gmail.com (hackdna)
Date: Thu, 22 May 2008 16:06:50 -0700
Subject: [OWW-Discuss] Jun  3,
	2008: Science Social Media Breakfast at Channel Cafe
Message-ID: <0016e64135bcbada23044dd9c413@google.com>

May be of interest. I've heard Channel Cafe is a nice spot :)

Ilya

Sent to you by hackdna via Google Reader: Jun 3, 2008: Science Social
Media Breakfast at Channel Cafe via Upcoming: Boston Events on 5/20/08
Join Elio Schaechter of Small Things Considered and Chris Condayan from
the MicrobeWorld Radio and Video podcasts for a lively breakfast
discussion about using new media for science communication. All
attendees are encouraged to share their experiences in using new media,
such as blogs, social networks, video and audio podcasts, and wikis, to
promote the life sciences or for use in educational settings.

This event coincides with American Society for Microbiology's 108th
General Meeting in Boston, Massachusetts from Sunday, June 1 to
Thursday, June 5, 2008.

Please note that The Science Social Media Breakfast is not directly
associated with ASM's General Meeting and is therefore open to anyone
in the Boston Metro Area to attend.

Attendance is free, but space is limited. Register online at
http://ssmb.eventbrite.com

Date
Tuesday, June 3, 2008

Time
8:00 am ET - 10:00 am ET

Location
The Channel Cafe
300 Summer Street
Boston, MA 02210

Things you can do from here:
- Subscribe to Upcoming: Boston Events using Google Reader
- Get started using Google Reader to easily keep up with all your
favorite sites
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From Torsten.Waldminghaus at rr-research.no  Fri May 23 08:14:40 2008
From: Torsten.Waldminghaus at rr-research.no (Torsten Waldminghaus)
Date: Fri, 23 May 2008 14:14:40 +0200
Subject: [OWW-Discuss] lab page set up
Message-ID: <AFE5B2464F1EB547BBACE62CCE8E402001B52B8F@mr3k6001.ad.medicalresearch.no>

I was trying to set up a lab page on OWW and became aware of some possible mistakes on the help page http://openwetware.org/wiki/Help:Starting_a_lab_wiki 

In the chapter ?Set up your main lab page? there is a link to the page ?Labname? in the sentence ??  First, go to the generic lab wiki page <http://openwetware.org/wiki/LabName>  (open it in a new browser window if you want to keep reading this text).?

However the page ?Labname? does not exist but instead is derefered to ?Template:Labname?.  If one further follows the description one is asked to ?Replace every instance of {{Template:LabName}} with {{Template:<Your PI's last name>}}.?, but this is not contained in the Template:Labname page. 

I would really want to fix this but first I do not know how and second I could not exclude that it is me being wrong and not the page.

I appreciate any help. Have a nice weekend,

Torsten

 

 

 

Torsten Waldminghaus

Department of Cell Biology

Institute for Cancer Research

Rikshospitalet-Radiumhospitalet-HF

Ullernchaussen 70

0310 Oslo

tel: 47-22935973

fax: 47-22934580

e-mail: Torsten.Waldminghaus at rr-research.no

 

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From bill.altmail at gmail.com  Fri May 23 11:36:47 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Fri, 23 May 2008 11:36:47 -0400
Subject: [OWW-Discuss] lab page set up
In-Reply-To: <AFE5B2464F1EB547BBACE62CCE8E402001B52B8F@mr3k6001.ad.medicalresearch.no>
References: <AFE5B2464F1EB547BBACE62CCE8E402001B52B8F@mr3k6001.ad.medicalresearch.no>
Message-ID: <26428aaa0805230836r35f4ff3fi7c11464b33da7f0e@mail.gmail.com>

Torsten,

I'm sorry for the inconvenience. Let me take a look at it now. I'll get
right back to you.

B.


On Fri, May 23, 2008 at 8:14 AM, Torsten Waldminghaus <
Torsten.Waldminghaus at rr-research.no> wrote:

>  I was trying to set up a lab page on OWW and became aware of some
> possible mistakes on the help page
> http://openwetware.org/wiki/Help:Starting_a_lab_wiki
>
> In the chapter '*Set up your main lab page' there is a link to the page
> 'Labname' in the sentence '*?  First, go to the generic lab wiki page<http://openwetware.org/wiki/LabName>(open it in a new browser window if you want to keep reading this text).'
>
> However the page 'Labname' does not exist but instead is derefered to
> 'Template:Labname'.  If one further follows the description one is asked to
> 'Replace every instance of {{Template:LabName}} with {{Template:<Your PI's
> last name>}}.', but this is not contained in the Template:Labname page.
>
> I would really want to fix this but first I do not know how and second I
> could not exclude that it is me being wrong and not the page.
>
> I appreciate any help. Have a nice weekend,
>
> Torsten
>
> * *
>
>
>
>
>
> Torsten Waldminghaus
>
> Department of Cell Biology
>
> Institute for Cancer Research
>
> Rikshospitalet-Radiumhospitalet-HF
>
> Ullernchaussen 70
>
> 0310 Oslo
>
> tel: 47-22935973
>
> fax: 47-22934580
>
> e-mail: Torsten.Waldminghaus at rr-research.no
>
>
>
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>
>
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From rvidal at gmail.com  Fri May 23 13:06:17 2008
From: rvidal at gmail.com (Ricardo Vidal)
Date: Fri, 23 May 2008 13:06:17 -0400
Subject: [OWW-Discuss] lab page set up
In-Reply-To: <26428aaa0805230836r35f4ff3fi7c11464b33da7f0e@mail.gmail.com>
References: <AFE5B2464F1EB547BBACE62CCE8E402001B52B8F@mr3k6001.ad.medicalresearch.no>
	<26428aaa0805230836r35f4ff3fi7c11464b33da7f0e@mail.gmail.com>
Message-ID: <213fc43b0805231006n130d3cf9k1ab7d5e35043fdb2@mail.gmail.com>

I'll give this a look too. Nice digging Torsten! :)

R

On Fri, May 23, 2008 at 11:36 AM, Bill Flanagan <bill.altmail at gmail.com>
wrote:

> Torsten,
>
> I'm sorry for the inconvenience. Let me take a look at it now. I'll get
> right back to you.
>
> B.
>
>
> On Fri, May 23, 2008 at 8:14 AM, Torsten Waldminghaus <
> Torsten.Waldminghaus at rr-research.no> wrote:
>
>>  I was trying to set up a lab page on OWW and became aware of some
>> possible mistakes on the help page
>> http://openwetware.org/wiki/Help:Starting_a_lab_wiki
>>
>> In the chapter '*Set up your main lab page' there is a link to the page
>> 'Labname' in the sentence '*?  First, go to the generic lab wiki page<http://openwetware.org/wiki/LabName>(open it in a new browser window if you want to keep reading this text).'
>>
>> However the page 'Labname' does not exist but instead is derefered to
>> 'Template:Labname'.  If one further follows the description one is asked to
>> 'Replace every instance of {{Template:LabName}} with {{Template:<Your
>> PI's last name>}}.', but this is not contained in the Template:Labname
>> page.
>>
>> I would really want to fix this but first I do not know how and second I
>> could not exclude that it is me being wrong and not the page.
>>
>> I appreciate any help. Have a nice weekend,
>>
>> Torsten
>>
>> * *
>>
>>
>>
>>
>>
>> Torsten Waldminghaus
>>
>> Department of Cell Biology
>>
>> Institute for Cancer Research
>>
>> Rikshospitalet-Radiumhospitalet-HF
>>
>> Ullernchaussen 70
>>
>> 0310 Oslo
>>
>> tel: 47-22935973
>>
>> fax: 47-22934580
>>
>> e-mail: Torsten.Waldminghaus at rr-research.no
>>
>>
>>
>> _______________________________________________
>> 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
>
>


-- 
Ricardo Vidal
rvidal at gmail.com | http://my.biotechlife.net
http://www.openwetware.org - Share your Science
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From ilyas at MIT.EDU  Sun May 25 13:46:55 2008
From: ilyas at MIT.EDU (Ilya Sytchev)
Date: Sun, 25 May 2008 13:46:55 -0400
Subject: [OWW-Discuss] RISDpedia
Message-ID: <4839A60F.9040600@mit.edu>

They have an interesting interface for adding a new page and a few other 
features:

http://risdpedia.net/


From hoatlinm at ohsu.edu  Mon May 26 14:01:01 2008
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 May 2008 11:01:01 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
Message-ID: <C46048ED.FD3C%hoatlinm@ohsu.edu>

Hi All,

I suggest that OWW get a group designation on LinkedIn (professional
networking) and Facebook (social networking). It might help get more
exposure if the OWW badge were displayed on our pages. What do you think?

-Maureen





From johncumbers at gmail.com  Mon May 26 14:09:26 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 26 May 2008 11:09:26 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <C46048ED.FD3C%hoatlinm@ohsu.edu>
References: <C46048ED.FD3C%hoatlinm@ohsu.edu>
Message-ID: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>

Hi Maureen,
I thought that there was a facebook group, but I can't see it, anyone else
remember?
I think I'd be in favor of starting a new social network rather than trying
to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
Open Social?

also, (btw Maureen, try this list discuss at openwetware.org instead in the
future, as we're fazing out the sc list)
cheers,
John

On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:

> Hi All,
>
> I suggest that OWW get a group designation on LinkedIn (professional
> networking) and Facebook (social networking). It might help get more
> exposure if the OWW badge were displayed on our pages. What do you think?
>
> -Maureen
>
>
>
> _______________________________________________
> 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

NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371
Moffett Field, CA 94035
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From johncumbers at gmail.com  Mon May 26 14:09:26 2008
From: johncumbers at gmail.com (John Cumbers)
Date: Mon, 26 May 2008 11:09:26 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <C46048ED.FD3C%hoatlinm@ohsu.edu>
References: <C46048ED.FD3C%hoatlinm@ohsu.edu>
Message-ID: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>

Hi Maureen,
I thought that there was a facebook group, but I can't see it, anyone else
remember?
I think I'd be in favor of starting a new social network rather than trying
to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
Open Social?

also, (btw Maureen, try this list discuss at openwetware.org instead in the
future, as we're fazing out the sc list)
cheers,
John

On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:

> Hi All,
>
> I suggest that OWW get a group designation on LinkedIn (professional
> networking) and Facebook (social networking). It might help get more
> exposure if the OWW badge were displayed on our pages. What do you think?
>
> -Maureen
>
>
>
> _______________________________________________
> 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

NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371
Moffett Field, CA 94035
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From sjkoch at unm.edu  Mon May 26 14:18:22 2008
From: sjkoch at unm.edu (Steven J. Koch)
Date: Mon, 26 May 2008 12:18:22 -0600
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
References: <C46048ED.FD3C%hoatlinm@ohsu.edu>
	<cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
Message-ID: <004201c8bf5c$e1c10940$a5431bc0$@edu>

I'm in favor of OWW group on LinkedIn (facebook too, though I haven't gotten
around to using that yet).  I think LinkedIn is a valuable network for
academic labs, since it connects graduate students and postdocs to industry
and the venture capital world.  This is good, because many students will
move on from academia, into networks that are difficult to grow from
scientific meetings alone.  I don't know what Open Social is, but I'm
guessing that LinkedIn is better developed for the purpose I'm talking
about.

 

From: oww-discuss-bounces at mit.edu [mailto:oww-discuss-bounces at mit.edu] On
Behalf Of John Cumbers
Sent: Monday, May 26, 2008 12:09 PM
To: Maureen Hoatlin
Cc: oww-sc; Ricardo Vidal; discuss at openwetware.org
Subject: Re: [OWW-Discuss] OWW logo on facebook and LinkedIn

 

Hi Maureen, 
I thought that there was a facebook group, but I can't see it, anyone else
remember?  
I think I'd be in favor of starting a new social network rather than trying
to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
Open Social?
 
also, (btw Maureen, try this list discuss at openwetware.org instead in the
future, as we're fazing out the sc list)
cheers, 
John

On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:

Hi All,

I suggest that OWW get a group designation on LinkedIn (professional
networking) and Facebook (social networking). It might help get more
exposure if the OWW badge were displayed on our pages. What do you think?

-Maureen



_______________________________________________
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

NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371 
Moffett Field, CA 94035

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From hoatlinm at ohsu.edu  Mon May 26 14:32:13 2008
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 May 2008 11:32:13 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
Message-ID: <C460503D.FD48%hoatlinm@ohsu.edu>

I looked for a facebook OWW but didn?t find one. The OWW group decal on
LinkedIn would serve mainly to link all those using this network and to
increase OWW visibility. More of an enhancement rather than network
duplication I think.
Also, in addition to Steve?s points, it may be useful for labs who are
trying to establish collaborations with industry.
-M


On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:

> Hi Maureen, 
> I thought that there was a facebook group, but I can't see it, anyone else
> remember?  
> I think I'd be in favor of starting a new social network rather than trying to
> create duplicate networks  elsewhere,  Ricardo, what 's the deal with Open
> Social?
>  
> also, (btw Maureen, try this list discuss at openwetware.org instead in the
> future, as we're fazing out the sc list)
> cheers, 
> John
> 
> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> Hi All,
>> 
>> I suggest that OWW get a group designation on LinkedIn (professional
>> networking) and Facebook (social networking). It might help get more
>> exposure if the OWW badge were displayed on our pages. What do you think?
>> 
>> -Maureen
>> 
>> 
>> 
>> _______________________________________________
>> OpenWetWare Discussion Mailing List
>> discuss at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
> 
> 


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From hoatlinm at ohsu.edu  Mon May 26 14:32:13 2008
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 May 2008 11:32:13 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
Message-ID: <C460503D.FD48%hoatlinm@ohsu.edu>

I looked for a facebook OWW but didn?t find one. The OWW group decal on
LinkedIn would serve mainly to link all those using this network and to
increase OWW visibility. More of an enhancement rather than network
duplication I think.
Also, in addition to Steve?s points, it may be useful for labs who are
trying to establish collaborations with industry.
-M


On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:

> Hi Maureen, 
> I thought that there was a facebook group, but I can't see it, anyone else
> remember?  
> I think I'd be in favor of starting a new social network rather than trying to
> create duplicate networks  elsewhere,  Ricardo, what 's the deal with Open
> Social?
>  
> also, (btw Maureen, try this list discuss at openwetware.org instead in the
> future, as we're fazing out the sc list)
> cheers, 
> John
> 
> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> Hi All,
>> 
>> I suggest that OWW get a group designation on LinkedIn (professional
>> networking) and Facebook (social networking). It might help get more
>> exposure if the OWW badge were displayed on our pages. What do you think?
>> 
>> -Maureen
>> 
>> 
>> 
>> _______________________________________________
>> OpenWetWare Discussion Mailing List
>> discuss at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-discuss
> 
> 


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From jasonk at MIT.EDU  Mon May 26 16:39:23 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 26 May 2008 16:39:23 -0400
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <C460503D.FD48%hoatlinm@ohsu.edu>
References: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
	<C460503D.FD48%hoatlinm@ohsu.edu>
Message-ID: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com>

There is a facebook group -- Maureen you're in it ;)  not sure if this
link will work but it's here:
http://www.facebook.com/group.php?gid=2235655118

if you search for openwetware in facebook, it should come up -- it has
62 members at the moment.

I agree with Steve about LinkedIn, we may as well get a group set up
so I submitted one of those too -- will send out a link when LinkedIN
approves it (takes a couple days, apparently).

I think we can think about what kind of "social networking" would be
useful to people on OWW.  OpenSocial is just a technical protocol from
Google allowing for 'distributed' social networking -- the real
question is what would we want out of home-grown network?  if we
figured that out, then we could decide the best technology for
implementing it.

thanks,
jason


On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
> I looked for a facebook OWW but didn't find one. The OWW group decal on
> LinkedIn would serve mainly to link all those using this network and to
> increase OWW visibility. More of an enhancement rather than network
> duplication I think.
> Also, in addition to Steve's points, it may be useful for labs who are
> trying to establish collaborations with industry.
> -M
>
>
> On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:
>
> Hi Maureen,
> I thought that there was a facebook group, but I can't see it, anyone else
> remember?
> I think I'd be in favor of starting a new social network rather than trying
> to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
> Open Social?
>
> also, (btw Maureen, try this list discuss at openwetware.org instead in the
> future, as we're fazing out the sc list)
> cheers,
> John
>
> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>
> Hi All,
>
> I suggest that OWW get a group designation on LinkedIn (professional
> networking) and Facebook (social networking). It might help get more
> exposure if the OWW badge were displayed on our pages. What do you think?
>
> -Maureen
>
>
>
> _______________________________________________
> 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
>
>


From jasonk at MIT.EDU  Mon May 26 16:39:23 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Mon, 26 May 2008 16:39:23 -0400
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <C460503D.FD48%hoatlinm@ohsu.edu>
References: <cfd758050805261109x67eae55nf18b2a1f16d447b0@mail.gmail.com>
	<C460503D.FD48%hoatlinm@ohsu.edu>
Message-ID: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com>

There is a facebook group -- Maureen you're in it ;)  not sure if this
link will work but it's here:
http://www.facebook.com/group.php?gid=2235655118

if you search for openwetware in facebook, it should come up -- it has
62 members at the moment.

I agree with Steve about LinkedIn, we may as well get a group set up
so I submitted one of those too -- will send out a link when LinkedIN
approves it (takes a couple days, apparently).

I think we can think about what kind of "social networking" would be
useful to people on OWW.  OpenSocial is just a technical protocol from
Google allowing for 'distributed' social networking -- the real
question is what would we want out of home-grown network?  if we
figured that out, then we could decide the best technology for
implementing it.

thanks,
jason


On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
> I looked for a facebook OWW but didn't find one. The OWW group decal on
> LinkedIn would serve mainly to link all those using this network and to
> increase OWW visibility. More of an enhancement rather than network
> duplication I think.
> Also, in addition to Steve's points, it may be useful for labs who are
> trying to establish collaborations with industry.
> -M
>
>
> On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:
>
> Hi Maureen,
> I thought that there was a facebook group, but I can't see it, anyone else
> remember?
> I think I'd be in favor of starting a new social network rather than trying
> to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
> Open Social?
>
> also, (btw Maureen, try this list discuss at openwetware.org instead in the
> future, as we're fazing out the sc list)
> cheers,
> John
>
> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>
> Hi All,
>
> I suggest that OWW get a group designation on LinkedIn (professional
> networking) and Facebook (social networking). It might help get more
> exposure if the OWW badge were displayed on our pages. What do you think?
>
> -Maureen
>
>
>
> _______________________________________________
> 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
>
>


From hoatlinm at ohsu.edu  Mon May 26 19:26:00 2008
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 May 2008 16:26:00 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com>
Message-ID: <C4609518.FD5E%hoatlinm@ohsu.edu>

Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a
OWW group on facebook! I use the mobile version my iPhone so much (which
doesn't list groups) that I forgot. Pathetic.
-Maureen



Maureen E. Hoatlin, PhD.
Biochemistry and Molecular Biology & Molecular and Medical Genetics
Hematologic Malignancies Program, Oregon Cancer Institute
Program in Molecular & Cellular Biosciences
Oregon Health & Science University
3181 S.W. Sam Jackson Pk. Rd.
Medical Research Building, Rm 518
Mailcode L224
Portland, OR 97239
Office: 503-494-1123
Mobile: 503-805-6816
Lab: 503-494-5427
FAX: 503-494--8393
Departmental phone: 503-494-7781
Email: hoatlinm at OHSU.edu
Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab
LinkedIn Profile: http://www.linkedin.com/in/hoatlin






On 5/26/08 1:39 PM, "Jason Kelly" <jasonk at mit.edu> wrote:

> There is a facebook group -- Maureen you're in it ;)  not sure if this
> link will work but it's here:
> http://www.facebook.com/group.php?gid=2235655118
> 
> if you search for openwetware in facebook, it should come up -- it has
> 62 members at the moment.
> 
> I agree with Steve about LinkedIn, we may as well get a group set up
> so I submitted one of those too -- will send out a link when LinkedIN
> approves it (takes a couple days, apparently).
> 
> I think we can think about what kind of "social networking" would be
> useful to people on OWW.  OpenSocial is just a technical protocol from
> Google allowing for 'distributed' social networking -- the real
> question is what would we want out of home-grown network?  if we
> figured that out, then we could decide the best technology for
> implementing it.
> 
> thanks,
> jason
> 
> 
> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> I looked for a facebook OWW but didn't find one. The OWW group decal on
>> LinkedIn would serve mainly to link all those using this network and to
>> increase OWW visibility. More of an enhancement rather than network
>> duplication I think.
>> Also, in addition to Steve's points, it may be useful for labs who are
>> trying to establish collaborations with industry.
>> -M
>> 
>> 
>> On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:
>> 
>> Hi Maureen,
>> I thought that there was a facebook group, but I can't see it, anyone else
>> remember?
>> I think I'd be in favor of starting a new social network rather than trying
>> to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
>> Open Social?
>> 
>> also, (btw Maureen, try this list discuss at openwetware.org instead in the
>> future, as we're fazing out the sc list)
>> cheers,
>> John
>> 
>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> 
>> Hi All,
>> 
>> I suggest that OWW get a group designation on LinkedIn (professional
>> networking) and Facebook (social networking). It might help get more
>> exposure if the OWW badge were displayed on our pages. What do you think?
>> 
>> -Maureen
>> 
>> 
>> 
>> _______________________________________________
>> 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
>> 
>> 




From hoatlinm at ohsu.edu  Mon May 26 19:26:00 2008
From: hoatlinm at ohsu.edu (Maureen Hoatlin)
Date: Mon, 26 May 2008 16:26:00 -0700
Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn
In-Reply-To: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com>
Message-ID: <C4609518.FD5E%hoatlinm@ohsu.edu>

Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a
OWW group on facebook! I use the mobile version my iPhone so much (which
doesn't list groups) that I forgot. Pathetic.
-Maureen



Maureen E. Hoatlin, PhD.
Biochemistry and Molecular Biology & Molecular and Medical Genetics
Hematologic Malignancies Program, Oregon Cancer Institute
Program in Molecular & Cellular Biosciences
Oregon Health & Science University
3181 S.W. Sam Jackson Pk. Rd.
Medical Research Building, Rm 518
Mailcode L224
Portland, OR 97239
Office: 503-494-1123
Mobile: 503-805-6816
Lab: 503-494-5427
FAX: 503-494--8393
Departmental phone: 503-494-7781
Email: hoatlinm at OHSU.edu
Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab
LinkedIn Profile: http://www.linkedin.com/in/hoatlin






On 5/26/08 1:39 PM, "Jason Kelly" <jasonk at mit.edu> wrote:

> There is a facebook group -- Maureen you're in it ;)  not sure if this
> link will work but it's here:
> http://www.facebook.com/group.php?gid=2235655118
> 
> if you search for openwetware in facebook, it should come up -- it has
> 62 members at the moment.
> 
> I agree with Steve about LinkedIn, we may as well get a group set up
> so I submitted one of those too -- will send out a link when LinkedIN
> approves it (takes a couple days, apparently).
> 
> I think we can think about what kind of "social networking" would be
> useful to people on OWW.  OpenSocial is just a technical protocol from
> Google allowing for 'distributed' social networking -- the real
> question is what would we want out of home-grown network?  if we
> figured that out, then we could decide the best technology for
> implementing it.
> 
> thanks,
> jason
> 
> 
> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> I looked for a facebook OWW but didn't find one. The OWW group decal on
>> LinkedIn would serve mainly to link all those using this network and to
>> increase OWW visibility. More of an enhancement rather than network
>> duplication I think.
>> Also, in addition to Steve's points, it may be useful for labs who are
>> trying to establish collaborations with industry.
>> -M
>> 
>> 
>> On 5/26/08 11:09 AM, "John Cumbers" <johncumbers at gmail.com> wrote:
>> 
>> Hi Maureen,
>> I thought that there was a facebook group, but I can't see it, anyone else
>> remember?
>> I think I'd be in favor of starting a new social network rather than trying
>> to create duplicate networks  elsewhere,  Ricardo, what 's the deal with
>> Open Social?
>> 
>> also, (btw Maureen, try this list discuss at openwetware.org instead in the
>> future, as we're fazing out the sc list)
>> cheers,
>> John
>> 
>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin <hoatlinm at ohsu.edu> wrote:
>> 
>> Hi All,
>> 
>> I suggest that OWW get a group designation on LinkedIn (professional
>> networking) and Facebook (social networking). It might help get more
>> exposure if the OWW badge were displayed on our pages. What do you think?
>> 
>> -Maureen
>> 
>> 
>> 
>> _______________________________________________
>> 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
>> 
>> 




From jasonk at MIT.EDU  Tue May 27 08:51:45 2008
From: jasonk at MIT.EDU (Jason Kelly)
Date: Tue, 27 May 2008 08:51:45 -0400
Subject: [OWW-Discuss] RISDpedia
In-Reply-To: <4839A60F.9040600@mit.edu>
References: <4839A60F.9040600@mit.edu>
Message-ID: <7c085c480805270551x5b971070i1bc1a5b6caa30c6f@mail.gmail.com>

Yeah, thats pretty cool.  We might consider having something like the
"add a page" for protocols.  Would be particularly useful if it could
check for 'similar' pages.  E.g. you want to add a protocol for
"Miller Assay" and it finds the OWW page:
http://openwetware.org/wiki/Beta-Galactosidase_Assay_%28A_better_Miller%29

and suggests you add your variant there.  this would help to rally
people around sharing/improving the same protocol page.

jason

On Sun, May 25, 2008 at 1:46 PM, Ilya Sytchev <ilyas at mit.edu> wrote:
> They have an interesting interface for adding a new page and a few other
> features:
>
> http://risdpedia.net/
> _______________________________________________
> OpenWetWare Discussion Mailing List
> discuss at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-discuss
>


From bill.altmail at gmail.com  Tue May 27 11:02:11 2008
From: bill.altmail at gmail.com (Bill Flanagan)
Date: Tue, 27 May 2008 11:02:11 -0400
Subject: [OWW-Discuss] Facebook heading for the open (source) road?
Message-ID: <26428aaa0805270802t79fdc5abk55cf7050d5fb31a8@mail.gmail.com>

This is cool. I think...

http://news.cnet.com/8301-13577_3-9952311-36.html

"Facebook will reportedly open-source the code for its application platform,
according to TechCrunch. The announcement may be just days away.

"Facebook representatives did not immediately respond to requests for
comment."
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From suckale at mpi-cbg.de  Wed May 28 11:02:18 2008
From: suckale at mpi-cbg.de (Jakob Suckale)
Date: Wed, 28 May 2008 17:02:18 +0200
Subject: [OWW-Discuss] Fwd: Launch of WikiProfessional
In-Reply-To: <042f01c8c01e$f6fe1e20$0202a8c0@Jacintha>
References: <042f01c8c01e$f6fe1e20$0202a8c0@Jacintha>
Message-ID: <918eed010805280802y2707db92n87c83660305e48ed@mail.gmail.com>

WikiProfessional, the Dutch semantic wiki, is about to start its beta
test phase. See their message below and the Wikipedia article about
the web site - http://en.wikipedia.org/wiki/Wikiprofessional

Best, Jakob



---------- Forwarded message ----------
From: WikiProfessional Consortium <info at wikiprofessional.org>
Date: Tue, May 27, 2008 at 7:27 PM
Subject: Launch of WikiProfessional
To: WikiProfessional  <info at wikiprofessional.org>


Dear Sir, Madam,

We are delighted to give you advance notice of the announcement that
WikiProfessional will launch later this week. Please see the press
release attached. If you would like to forward the press release to
friends and colleagues, please feel free to do so. If you would like
to put it on a blog or web site, it is highly appreciated if you
adhere to the embargo.

Thank you for your kind attention.

Sincerely,
The WikiProfessional Consortium Team



If you no longer would like to be kept informed about
WikiProfessional, please let us know by sending an email to
remove at wikiprofessional.org.
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From kanzure at gmail.com  Wed May 28 11:50:23 2008
From: kanzure at gmail.com (Bryan Bishop)
Date: Wed, 28 May 2008 10:50:23 -0500
Subject: [OWW-Discuss] Fwd: Launch of WikiProfessional
In-Reply-To: <918eed010805280802y2707db92n87c83660305e48ed@mail.gmail.com>
References: <042f01c8c01e$f6fe1e20$0202a8c0@Jacintha>
	<918eed010805280802y2707db92n87c83660305e48ed@mail.gmail.com>
Message-ID: <200805281050.23797.kanzure@gmail.com>

On Wednesday 28 May 2008, Jakob Suckale wrote:
> WikiProfessional, the Dutch semantic wiki, is about to start its beta
> test phase. See their message below and the Wikipedia article about
> the web site - http://en.wikipedia.org/wiki/Wikiprofessional

>From the page:
> When data is entered, the system semantically analyzes and recognizes
> co-occurrences between different entities. The results are visualized
> through a Knowlet, which is a visual representation of semantic
> distance between associated entities. This Knowlet is then used to
> notify persons that have subscribed to these entities, enabling a
> rapid data interchange between collaborators.

Hrm. This would be a really, really good use for the SKDB project I was 
proposing. Otherwise all of that information is going to be stuck in a 
wiki format and not be entirely functional. Just need to write a few 
python classes to represent the different types of entities, and then 
write up the protocols in a standardized language so that the parts can 
be fabricated, or otherwise strung together, for a physical, actual 
project [none of us want the data to just 'sit there' being dead].

- Bryan
________________________________________
http://heybryan.org/