From sjkoch at unm.edu Tue Oct 2 14:56:02 2007
From: sjkoch at unm.edu (Steven J. Koch)
Date: Tue, 2 Oct 2007 12:56:02 -0600
Subject: [OWW-SC] Lab Notebook Brainstorming this Friday,
noon EDT: Can someone help me set up telecon?
Message-ID: <00a101c80525$e0de1a00$a29a4e00$@edu>
Dear SC Members,
Except for one person, it looked like Friday noon was the best, and also
this avoids going back to back with SC meeting. I am currently editing the
wiki page
(http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_
Brainstorming) as a page to prepare for the session, then I will send out
email to the main OWW list.
I think people preferred a teleconference, and since the SC uses the wiki
chat + telecom format, that sounds like the best idea. Is it possible for
someone at OWW to set up a similar thing for our Friday session? I am sure
I can also host this here, but likely our technology is clunkier and also I
don't know how to do it. Also, can I "attend" the Thursday SC meeting to
get an idea for how it works?
OK, Thank you and please keep providing any other thoughts and advice!
--Steve
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From wjf42 at MIT.EDU Wed Oct 3 14:15:13 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Wed, 3 Oct 2007 14:15:13 -0400
Subject: [OWW-SC] RSS Extensions available for testing on OpenWetWare.org
Message-ID: <26428aaa0710031115x7d153053v9741b97fa4c5c681@mail.gmail.com>
We've deployed a set of RSS extensions to allow you folks, as well as any
other OpenWetWare users, to include live RSS feeds on any OpenWetWare page.
Here's where you can find out about the extensions:
http://openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS
Examples of how to use each of them are included.
We will eventually move to a single extension for RSS. If there are features
you see in any of the three that appeal to you in particular or problems you
encounter while using them, let me knew.
We will be using RSS as a way to link content from OpenWetWare blogs among
other applications.
We also will provide templates to make the job of using these extensions
easier for all concerned.
Send me email at wjf42 at mit.edu if you have questions or comments or use the
talk page for the RSS extensions. We'll be monitoring the page on a
continual basis.
Thanks.
Bill Flanagan
Openwetware.org
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From jasonk at MIT.EDU Thu Oct 4 01:30:39 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 4 Oct 2007 01:30:39 -0400
Subject: [OWW-SC] Reminder: SC meeting today (TH) at 1pm EST
Message-ID: <7c085c480710032230i4cf1500as556abb666002400d@mail.gmail.com>
Post discussion topics here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting
Also, if you have time please take a look at / try out the new RSS
extensions:
http://openwetware.org/wiki/OpenWetWare:Software/Extensions/RSS
And think about what the "new user experience" should be like now that we
can auto-generate userpages for new users. This is the template for new
userpages at the moment:
http://openwetware.org/wiki/UserPageDefaultContentText
Do we want to make it into a tutorial, etc?
The number is 617-324-7520 and also join the chat (just in the lounge).
Thanks!
jason
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From wjf42 at MIT.EDU Thu Oct 4 08:50:32 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Thu, 4 Oct 2007 08:50:32 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created for
new users autmatically
Message-ID: <26428aaa0710040550o64bde205gfb31da36711be449@mail.gmail.com>
We've recently rolled out a new OpenWetWare feature that we want to let all
of you know about.
When a new user is created, an email message is sent out welcoming the user
to OpenWetWare.org. The email message formerly pointed to the place their
OpenWetWare User: page would be if it had text. They are free to edit and
save the page. This presents a problem for most OpenWetWare.org users:
without having any experience with OpenWetWare or MediaWiki editing, there's
little chance their
User: page would be populated with any information.
The OpenWetWare User Management System (UMS) now will create a default User:
page for all new users. To do this, a standard User: page template has been
created. The information provided by users during registration drives the
content of this page. This page is not a standard MediaWiki template. This
means that future changes to the page will not change existing User: pages.
The information that can be displayed currently includes the new user's
name, email address, reason for joining OpenWetWare, and how they heard
about us.
Since the content is contained in a standard OpenWetWare page, the content
page can be changed. Currently, the display is very basic. If anyone has any
ideas about how this can be enhanced, feel free to contribute.
Look for more detains here:
http://openwetware.org/wiki/OpenWetWare:Software/User_management
Thanks
Bill Flanagan
www.OpenWetWare.org
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From rshetty at MIT.EDU Thu Oct 4 09:10:20 2007
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Thu, 4 Oct 2007 09:10:20 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <26428aaa0710040550o64bde205gfb31da36711be449@mail.gmail.com>
References: <26428aaa0710040550o64bde205gfb31da36711be449@mail.gmail.com>
Message-ID: <6e9f40380710040610r6d0bbae1lefb101dbdc556b99@mail.gmail.com>
Just a quick note that I *believe* that thanks go out to Maureen
Hoatlin for suggesting this feature as a way to get new users more
comfortable with editing the site.
Thanks Maureen! And Bill for implementing it!
-Reshma
On 10/4/07, Bill Flanagan wrote:
> We've recently rolled out a new OpenWetWare feature that we want to let all
> of you know about.
>
> When a new user is created, an email message is sent out welcoming the user
> to OpenWetWare.org. The email message formerly pointed to the place their
> OpenWetWare User: page would be if it had text. They are free to edit and
> save the page. This presents a problem for most OpenWetWare.org users:
> without having any experience with OpenWetWare or MediaWiki editing, there's
> little chance their
> User: page would be populated with any information.
>
> The OpenWetWare User Management System (UMS) now will create a default User:
> page for all new users. To do this, a standard User: page template has been
> created. The information provided by users during registration drives the
> content of this page. This page is not a standard MediaWiki template. This
> means that future changes to the page will not change existing User: pages.
> The information that can be displayed currently includes the new user's
> name, email address, reason for joining OpenWetWare, and how they heard
> about us.
>
> Since the content is contained in a standard OpenWetWare page, the content
> page can be changed. Currently, the display is very basic. If anyone has any
> ideas about how this can be enhanced, feel free to contribute.
>
> Look for more detains here:
>
> http://openwetware.org/wiki/OpenWetWare:Software/User_management
>
> Thanks
>
> Bill Flanagan
> www.OpenWetWare.org
>
>
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
From julius at younglucks.com Thu Oct 4 09:25:27 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Thu, 4 Oct 2007 09:25:27 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <6e9f40380710040610r6d0bbae1lefb101dbdc556b99@mail.gmail.com>
References: <26428aaa0710040550o64bde205gfb31da36711be449@mail.gmail.com>
<6e9f40380710040610r6d0bbae1lefb101dbdc556b99@mail.gmail.com>
Message-ID: <30F220E3-B830-4FD1-9B5A-1C75212ED8A3@younglucks.com>
Great job Bill!
A while ago Vincent and I thought about a similar feature as part of
the outreach effort. There was some discussion of including wiki
tutorial information in the default user page. I think something
along the lines of the 'Welcome!' and 'Basic Wiki Instructions'
sections of
http://openwetware.org/wiki/OpenWetWare:Steering_committee/
Outreach_chairs/mock_home_page
would be extremely useful for new users who are also new to wikis,
and we could easily integrate these sections into your current template.
Any thoughts?
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 4, 2007, at 9:10 AM, Reshma Shetty wrote:
> Just a quick note that I *believe* that thanks go out to Maureen
> Hoatlin for suggesting this feature as a way to get new users more
> comfortable with editing the site.
>
> Thanks Maureen! And Bill for implementing it!
>
> -Reshma
>
> On 10/4/07, Bill Flanagan wrote:
>> We've recently rolled out a new OpenWetWare feature that we want
>> to let all
>> of you know about.
>>
>> When a new user is created, an email message is sent out welcoming
>> the user
>> to OpenWetWare.org. The email message formerly pointed to the
>> place their
>> OpenWetWare User: page would be if it had text. They are free to
>> edit and
>> save the page. This presents a problem for most OpenWetWare.org
>> users:
>> without having any experience with OpenWetWare or MediaWiki
>> editing, there's
>> little chance their
>> User: page would be populated with any information.
>>
>> The OpenWetWare User Management System (UMS) now will create a
>> default User:
>> page for all new users. To do this, a standard User: page template
>> has been
>> created. The information provided by users during registration
>> drives the
>> content of this page. This page is not a standard MediaWiki
>> template. This
>> means that future changes to the page will not change existing
>> User: pages.
>> The information that can be displayed currently includes the new
>> user's
>> name, email address, reason for joining OpenWetWare, and how they
>> heard
>> about us.
>>
>> Since the content is contained in a standard OpenWetWare page, the
>> content
>> page can be changed. Currently, the display is very basic. If
>> anyone has any
>> ideas about how this can be enhanced, feel free to contribute.
>>
>> Look for more detains here:
>>
>> http://openwetware.org/wiki/OpenWetWare:Software/User_management
>>
>> Thanks
>>
>> Bill Flanagan
>> www.OpenWetWare.org
>>
>>
>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
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From austin at csail.mit.edu Thu Oct 4 11:14:25 2007
From: austin at csail.mit.edu (Austin Che)
Date: Thu, 04 Oct 2007 11:14:25 -0400
Subject: [OWW-SC] For MIT people only (SC meeting/SIP)
In-Reply-To: <7c085c480710032230i4cf1500as556abb666002400d@mail.gmail.com>
(Jason Kelly's message of "Thu, 4 Oct 2007 01:30:39 -0400")
References: <7c085c480710032230i4cf1500as556abb666002400d@mail.gmail.com>
Message-ID: <87ejgaykry.fsf@nitsua.mit.edu>
This message is just for the MIT people out there.
MIT now offers personal SIP accounts for everyone including an
incoming number. Just go here to get one:
https://voip.mit.edu/cgi-bin/personal/sipmgr
It takes < 5 minutes to get it activated and working. You can then
use whatever sip client you want (sjphone, gizmo, etc). Your sip
username is your MIT username (i.e. the part before @mit.edu) and
your password is whatever you entered in the above page. You
should be able to dial out on it, such as to the OWW SC
conference. So if you're at MIT and want to call in via SIP, you
should be all set.
--
Austin Che (617)253-5899
From wjf42 at MIT.EDU Thu Oct 4 15:24:47 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Thu, 4 Oct 2007 15:24:47 -0400
Subject: [OWW-SC] Mailing list is now available
Message-ID: <26428aaa0710041224y31a9086m99c96bbf5dccbfc6@mail.gmail.com>
To all,
I've completed an export and a cleanup of the email addresses from
OpenWetWare.
The addresses won't be saved in the OWW wiki for obvious reasons. For now,
I'm creating a database table to contain these records and will hook it to
UMS so that new approved members are automatically added to it. If the
address already is in use, the latest name will be associated with the
address. I may also look at how to update it from OpenWetWare itself so that
address changes will also be added to it. There are a good number of
duplicate emtries that have been removed from the list.I also removed any
entries that didn't have a valid email address.
If anyone wants the stats, let me know.
I can't say that we can do a bulk import into the MIT mailing list manager;
offhand, I'll bet we can, but I'll check. My goal is to have the list
imported into a mailing list manager and ready to send out mailings over the
next week.
Thanks.
Bill Flanagan
www.OpenWetWare.org
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From jasonk at MIT.EDU Thu Oct 4 15:43:52 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 4 Oct 2007 15:43:52 -0400
Subject: [OWW-SC] October SC Meeting Notes
Message-ID: <7c085c480710041243m6467bbe7od32d5766032c04ff@mail.gmail.com>
Hi SC,
Thanks everyone for calling in today. For those who couldn't make it,
notesare here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_October_2007
action list here:
http://openwetware.org/wiki/OpenWetWare:Steering_committee_actions
Reminder that there will be a meeting tomorrow @ Noon EST (call
617-452-2163) to brainstorm lab notebook features. If you can't make it
please post your thoughts here:
http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_Brainstorming
Please add/edit anything I missed.
thanks!
jason
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From bill.altmail at gmail.com Thu Oct 4 18:19:53 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 4 Oct 2007 18:19:53 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
Message-ID: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
Per Reshma's questions,
1. I can add the function call to register the user page in the page change
list. This is a 2 line code change. I'm not implementing it now.
2. I like the idea of using the mediawiki email address obfuscation. For
now, you don't need to nclude the emai address. Just omit the UMS_EMAIL tag
in the text of the page to get rid of it. I'll look at the feature you
mentioned and see if I can pass that in rather than the email address.
Per Julian's comments
3. I may go back and comment the wikitext thats' used in the page to
accomplish what I mentioned before: show how tables and tex are formatted as
well as how links are created. This will be the first document new users
will encounter that they will be given the opportunity to modify. We can at
least be clear about how the rather cryptic tags work and provide a little
info on where to get more information about it.
I also send my thanks to Maureen for the suggestion!
Ilya has pointed out that the admin email address isn't showing up in
approval messages. I'm fixing that now and will document any changes related
to it.
Thanks:
I hope you find it useful. Tell us how to make it even MORE useful.
Thanks.
Bill
On 10/4/07, Julius B. Lucks < julius at younglucks.com> wrote:
>
> Great job Bill!
> A while ago Vincent and I thought about a similar feature as part of the
> outreach effort. There was some discussion of including wiki tutorial
> information in the default user page. I think something along the lines of
> the 'Welcome!' and 'Basic Wiki Instructions' sections of
>
> http://openwetware.org/wiki/OpenWetWare:Steering_committee/Outreach_chairs/mock_home_page
>
>
> would be extremely useful for new users who are also new to wikis, and we
> could easily integrate these sections into your current template.
>
> Any thoughts?
>
> Cheers,
>
> Julius
>
>
> ---------------------------------------------------------------------------------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>
> ----------------------------------------------------------------------------------------
>
>
>
> On Oct 4, 2007, at 9:10 AM, Reshma Shetty wrote:
>
> Just a quick note that I *believe* that thanks go out to Maureen
> Hoatlin for suggesting this feature as a way to get new users more
> comfortable with editing the site.
>
> Thanks Maureen! And Bill for implementing it!
>
> -Reshma
>
> On 10/4/07, Bill Flanagan < wjf42 at mit.edu> wrote:
>
> We've recently rolled out a new OpenWetWare feature that we want to let
> all
> of you know about.
>
> When a new user is created, an email message is sent out welcoming the
> user
> to OpenWetWare.org. The email message formerly pointed to the place their
> OpenWetWare User: page would be if it had text. They are free to edit and
> save the page. This presents a problem for most OpenWetWare.org users:
> without having any experience with OpenWetWare or MediaWiki editing,
> there's
> little chance their
> User: page would be populated with any information.
>
> The OpenWetWare User Management System (UMS) now will create a default
> User:
> page for all new users. To do this, a standard User: page template has
> been
> created. The information provided by users during registration drives the
> content of this page. This page is not a standard MediaWiki template. This
> means that future changes to the page will not change existing User:
> pages.
> The information that can be displayed currently includes the new user's
> name, email address, reason for joining OpenWetWare, and how they heard
> about us.
>
> Since the content is contained in a standard OpenWetWare page, the content
> page can be changed. Currently, the display is very basic. If anyone has
> any
> ideas about how this can be enhanced, feel free to contribute.
>
> Look for more detains here:
>
> http://openwetware.org/wiki/OpenWetWare:Software/User_management
>
> Thanks
>
> Bill Flanagan
> www.OpenWetWare.org
>
>
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
>
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From austin at csail.mit.edu Thu Oct 4 18:30:40 2007
From: austin at csail.mit.edu (Austin Che)
Date: Thu, 04 Oct 2007 18:30:40 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
(Bill F.'s message of "Thu, 4 Oct 2007 18:19:53 -0400")
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
Message-ID: <871wcawm0f.fsf@nitsua.mit.edu>
> 1. I can add the function call to register the user page in the page change
> list. This is a 2 line code change. I'm not implementing it now.
I don't know what this is referring to but I think instead of
something showing up as a normal change, a special user creation
log should be added. That way, we know when there are new
users. Otherwise, there's now way for us to know when someone new
is coming on to the site.
--
Austin Che (617)253-5899
From jasonk at MIT.EDU Thu Oct 4 18:43:28 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Thu, 4 Oct 2007 18:43:28 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <871wcawm0f.fsf@nitsua.mit.edu>
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
Message-ID: <7c085c480710041543g4af53c5cl471071b404b80ea2@mail.gmail.com>
That could be a way to help the OWW welcome-wagon (OWWWW) get off the
ground! :)
I've wanted an OWW welcome wagon for awhile, if the new users for the week
were listed somewhere then OWW folks could post a message on their talk page
saying hi to get them started.
thanks,
jason
On 10/4/07, Austin Che wrote:
>
>
> > 1. I can add the function call to register the user page in the page
> change
> > list. This is a 2 line code change. I'm not implementing it now.
>
> I don't know what this is referring to but I think instead of
> something showing up as a normal change, a special user creation
> log should be added. That way, we know when there are new
> users. Otherwise, there's now way for us to know when someone new
> is coming on to the site.
>
> --
> Austin Che (617)253-5899
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
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From bill.altmail at gmail.com Thu Oct 4 18:50:38 2007
From: bill.altmail at gmail.com (Bill F)
Date: Thu, 4 Oct 2007 18:50:38 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <871wcawm0f.fsf@nitsua.mit.edu>
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
Message-ID: <26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
The change I am suggesting is to log to the recent changes list that is
currently used by the system.
The actual time an account is created isn't contained in the table but is
probably available in the MySQL metadata.
Where would you like to see this data? A special page?
On 10/4/07, Austin Che wrote:
>
>
> > 1. I can add the function call to register the user page in the page
> change
> > list. This is a 2 line code change. I'm not implementing it now.
>
> I don't know what this is referring to but I think instead of
> something showing up as a normal change, a special user creation
> log should be added. That way, we know when there are new
> users. Otherwise, there's now way for us to know when someone new
> is coming on to the site.
>
> --
> Austin Che (617)253-5899
>
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From austin at csail.mit.edu Thu Oct 4 18:58:53 2007
From: austin at csail.mit.edu (Austin Che)
Date: Thu, 04 Oct 2007 18:58:53 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
(Bill F.'s message of "Thu, 4 Oct 2007 18:50:38 -0400")
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
Message-ID: <87ve9mv64y.fsf@nitsua.mit.edu>
On the recent changes list but not as a change but as a new log type like:
http://openwetware.org/index.php?title=Special:Recentchanges&filter=n%3DSpecial&limit=100
You can check out the SpecialRenameuser.php for adding a log type
(they add the user rename log).
I'm not sure why you need time metadata. Whenever the UMS creates
an account, it just adds a log entry with the user and timestamp.
> The change I am suggesting is to log to the recent changes list that is
> currently used by the system.
>
> The actual time an account is created isn't contained in the table but is
> probably available in the MySQL metadata.
>
> Where would you like to see this data? A special page?
>
> On 10/4/07, Austin Che wrote:
>>
>>
>> > 1. I can add the function call to register the user page in the page
>> change
>> > list. This is a 2 line code change. I'm not implementing it now.
>>
>> I don't know what this is referring to but I think instead of
>> something showing up as a normal change, a special user creation
>> log should be added. That way, we know when there are new
>> users. Otherwise, there's now way for us to know when someone new
>> is coming on to the site.
>>
>> --
>> Austin Che (617)253-5899
>>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
--
Austin Che (617)253-5899
From bill.altmail at gmail.com Fri Oct 5 11:01:56 2007
From: bill.altmail at gmail.com (Bill F)
Date: Fri, 5 Oct 2007 11:01:56 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <87ve9mv64y.fsf@nitsua.mit.edu>
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
<87ve9mv64y.fsf@nitsua.mit.edu>
Message-ID: <26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
Take a look at this:
http://www.openwetware.org/rss/new_members.xml
This is a simple RSS feed containing the last 5 registered members in the
UMS. I used a feed creation class to make the RSS. The feel can be undated
each time a nw UMS registration is processed.
Using the RSS reader extensions, the new user list can be placed anywhere on
the site.
Any information source from within OpenWetWare can be used to generate RSS
like this or more complicated.
Let me know if there are anythings that you would like to add to the
content.
Thanks.
B.
On 10/4/07, Austin Che wrote:
>
>
> On the recent changes list but not as a change but as a new log type
> like:
> http://openwetware.org/index.php?title=Special:Recentchanges&filter=n%3DSpecial&limit=100
>
>
> You can check out the SpecialRenameuser.php for adding a log type
> (they add the user rename log).
>
> I'm not sure why you need time metadata. Whenever the UMS creates
> an account, it just adds a log entry with the user and timestamp.
>
> > The change I am suggesting is to log to the recent changes list that is
> > currently used by the system.
> >
> > The actual time an account is created isn't contained in the table but
> is
> > probably available in the MySQL metadata.
> >
> > Where would you like to see this data? A special page?
> >
> > On 10/4/07, Austin Che < austin at csail.mit.edu> wrote:
> >>
> >>
> >> > 1. I can add the function call to register the user page in the page
> >> change
> >> > list. This is a 2 line code change. I'm not implementing it now.
> >>
> >> I don't know what this is referring to but I think instead of
> >> something showing up as a normal change, a special user creation
> >> log should be added. That way, we know when there are new
> >> users. Otherwise, there's now way for us to know when someone new
> >> is coming on to the site.
> >>
> >> --
> >> Austin Che (617)253-5899
> >>
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
>
> --
> Austin Che < austin at csail.mit.edu> (617)253-5899
>
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From julius at younglucks.com Fri Oct 5 11:06:47 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Fri, 5 Oct 2007 11:06:47 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
<87ve9mv64y.fsf@nitsua.mit.edu>
<26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
Message-ID: <58D57592-EDDA-4ED6-BBAE-900F00675D1C@younglucks.com>
Hi Bill,
This looks really cool. Could such a system be used to construct
feeds that list 'recent changes' to a set of pages under a common
page name path? For example if there is a series of project pages
[[base_project_page]]
[[base_project_page/day1]]
[[base_project_page/day2]]
could a feed be generated to list the new pages (and their changes)
under [[base_project_page]].
Thanks,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 5, 2007, at 11:01 AM, Bill F wrote:
> Take a look at this:
>
> http://www.openwetware.org/rss/new_members.xml
>
> This is a simple RSS feed containing the last 5 registered members
> in the UMS. I used a feed creation class to make the RSS. The feel
> can be undated each time a nw UMS registration is processed.
>
> Using the RSS reader extensions, the new user list can be placed
> anywhere on the site.
>
> Any information source from within OpenWetWare can be used to
> generate RSS like this or more complicated.
>
> Let me know if there are anythings that you would like to add to
> the content.
>
> Thanks.
>
> B.
>
> On 10/4/07, Austin Che wrote:
>
> On the recent changes list but not as a change but as a new log
> type like:
> http://openwetware.org/index.php?
> title=Special:Recentchanges&filter=n%3DSpecial&limit=100
>
> You can check out the SpecialRenameuser.php for adding a log type
> (they add the user rename log).
>
> I'm not sure why you need time metadata. Whenever the UMS creates
> an account, it just adds a log entry with the user and timestamp.
>
> > The change I am suggesting is to log to the recent changes list
> that is
> > currently used by the system.
> >
> > The actual time an account is created isn't contained in the
> table but is
> > probably available in the MySQL metadata.
> >
> > Where would you like to see this data? A special page?
> >
> > On 10/4/07, Austin Che < austin at csail.mit.edu> wrote:
> >>
> >>
> >> > 1. I can add the function call to register the user page in
> the page
> >> change
> >> > list. This is a 2 line code change. I'm not implementing it now.
> >>
> >> I don't know what this is referring to but I think instead of
> >> something showing up as a normal change, a special user
> creation
> >> log should be added. That way, we know when there are new
> >> users. Otherwise, there's now way for us to know when
> someone new
> >> is coming on to the site.
> >>
> >> --
> >> Austin Che (617)253-5899
> >>
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
>
> --
> Austin Che < austin at csail.mit.edu> (617)253-5899
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
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From tk at csail.mit.edu Fri Oct 5 11:23:26 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Fri, 5 Oct 2007 11:23:26 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <58D57592-EDDA-4ED6-BBAE-900F00675D1C@younglucks.com>
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
<87ve9mv64y.fsf@nitsua.mit.edu>
<26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
<58D57592-EDDA-4ED6-BBAE-900F00675D1C@younglucks.com>
Message-ID: <8d1916ed0b8577e45fa528d99ac408b1@csail.mit.edu>
On Oct 5, 2007, at 11:06 AM, Julius B. Lucks wrote:
> Hi Bill,
>
> This looks really cool.? Could such a system be used to construct
> feeds that list 'recent? changes' to a set of pages under a common
> page name path?? For example if there is a series of project pages
>
> [[base_project_page]]
> [[base_project_page/day1]]
> [[base_project_page/day2]]
>
> could a feed be generated to list the new pages (and their changes)
> under?[[base_project_page]].
>
> Thanks,
>
It would be very useful to have this as a link similar to the "recent
changes" special page. The recent changes list is becoming more and
more unusable as a way to figure out what is going on as the community
becomes more diverse. I'd like a way to prune that list to the recent
changes of interest to me.
From austin at csail.mit.edu Fri Oct 5 11:37:16 2007
From: austin at csail.mit.edu (Austin Che)
Date: Fri, 05 Oct 2007 11:37:16 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <8d1916ed0b8577e45fa528d99ac408b1@csail.mit.edu> (Tom Knight's
message of "Fri, 5 Oct 2007 11:23:26 -0400")
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
<87ve9mv64y.fsf@nitsua.mit.edu>
<26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
<58D57592-EDDA-4ED6-BBAE-900F00675D1C@younglucks.com>
<8d1916ed0b8577e45fa528d99ac408b1@csail.mit.edu>
Message-ID: <87ejg9vahf.fsf@nitsua.mit.edu>
>> This looks really cool.? Could such a system be used to construct
>> feeds that list 'recent? changes' to a set of pages under a common
>> page name path?? For example if there is a series of project pages
>>
>> [[base_project_page]]
>> [[base_project_page/day1]]
>> [[base_project_page/day2]]
>>
>> could a feed be generated to list the new pages (and their changes)
>> under?[[base_project_page]].
>>
>> Thanks,
>>
> It would be very useful to have this as a link similar to the "recent
> changes" special page. The recent changes list is becoming more and
> more unusable as a way to figure out what is going on as the community
> becomes more diverse. I'd like a way to prune that list to the recent
> changes of interest to me.
You can already do this.
Julius, isn't what's on the bottom of
http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_Brainstorming
what you're looking for?
Tom, check out
http://openwetware.org/wiki/User:Austin_J._Che/Extensions/Recentchangesfilter
--
Austin Che (617)253-5899
From austin at csail.mit.edu Fri Oct 5 11:47:09 2007
From: austin at csail.mit.edu (Austin Che)
Date: Fri, 05 Oct 2007 11:47:09 -0400
Subject: [OWW-SC] OpenWetWare User Manaagement System: User Page created
for new users autmatically
In-Reply-To: <87ejg9vahf.fsf@nitsua.mit.edu> (Austin Che's message of "Fri, 05
Oct 2007 11:37:16 -0400")
References: <26428aaa0710041519w5853aca7u448a515944fbdde8@mail.gmail.com>
<871wcawm0f.fsf@nitsua.mit.edu>
<26428aaa0710041550q3ea2d325x1adfae6d31958caf@mail.gmail.com>
<87ve9mv64y.fsf@nitsua.mit.edu>
<26428aaa0710050801g56fb3fcx5aa6f32f8e27bf3a@mail.gmail.com>
<58D57592-EDDA-4ED6-BBAE-900F00675D1C@younglucks.com>
<8d1916ed0b8577e45fa528d99ac408b1@csail.mit.edu>
<87ejg9vahf.fsf@nitsua.mit.edu>
Message-ID: <877im1va0y.fsf@nitsua.mit.edu>
Maybe I should be more specific.
Try these two links. They both filter to pages in the OpenWetWare
namespace. The first is the recent changes to view in the
browser. The second is the rss feed.
http://openwetware.org/wiki/Special:Recentchanges/n=OpenWetWare
http://openwetware.org/index.php?filter=n=OpenWetWare&feed=rss&title=Special:Recentchanges
--
Austin Che (617)253-5899
From jasonk at MIT.EDU Fri Oct 5 14:01:23 2007
From: jasonk at MIT.EDU (Jason Kelly)
Date: Fri, 5 Oct 2007 14:01:23 -0400
Subject: [OWW-SC] Lab Notebook meeting notes
Message-ID: <7c085c480710051101h1155c6b5g2efc8c5437e307ac@mail.gmail.com>
Posted my (messy) meeting notes here:
http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_Brainstorming#Meeting_Notes
thanks everyone who called in and Steve for organizing -- some great ideas
shared.
thanks,
jason
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From sjkoch at unm.edu Fri Oct 5 15:36:43 2007
From: sjkoch at unm.edu (Steven J. Koch)
Date: Fri, 5 Oct 2007 13:36:43 -0600
Subject: [OWW-SC] Lab Notebook meeting notes
In-Reply-To: <7c085c480710051101h1155c6b5g2efc8c5437e307ac@mail.gmail.com>
References: <7c085c480710051101h1155c6b5g2efc8c5437e307ac@mail.gmail.com>
Message-ID: <001601c80787$0f2dfa70$2d89ef50$@edu>
Thanks, Jason! And thanks to everyone for attending the meeting today, I
think it was really productive. I created a table with some of the features
I thought we sort of agreed on, as well as a proposed system for
prioritizing. See:
http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_B
rainstorming#Features_List
I also created sub pages ([[/subpage]]) for about half the features with
quick explanations. If you have time, please take a look and edit / add
features & sub pages, and also vote for your priorities.
--Steve
From: oww-sc-bounces at mit.edu [mailto:oww-sc-bounces at mit.edu] On Behalf Of
Jason Kelly
Sent: Friday, October 05, 2007 12:01 PM
To: oww-sc
Subject: [OWW-SC] Lab Notebook meeting notes
Posted my (messy) meeting notes here:
http://openwetware.org/wiki/OpenWetWare:Feature_list/Lab_notebook/2007_Oct_B
rainstorming#Meeting_Notes
thanks everyone who called in and Steve for organizing -- some great ideas
shared.
thanks,
jason
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From bill.altmail at gmail.com Tue Oct 9 18:55:19 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 9 Oct 2007 18:55:19 -0400
Subject: [OWW-SC] Genbank Accession Number question
Message-ID: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
I'm looking into adding GenBank Accession Number lookup, a feature which has
been mentioned in the past. To do this, I need to know what the set of
information from GenBank would be that people would like to see available.
This is a cop of the the current comment on the Software/Features page:
(http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests)
- Initially, this might be just an extension to Biblio to allow
referencing by accession number. Eventually, this could pull in info from
databases.
- See also
http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_p
NCBI has an example of the full record they maintain:
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
Would a pointer to a similar page for a specific accession number be what's
needed?
The actual accession number for the example record is:
"U49845".
There's an additional version number on he next line:
"U49845.1 GI:1293613".
Does the version number generally get used in citations or is the Accession
Number adequate?
Using the Accession number, I can point the Biblio reference to the NCBI
page (similar to the example) for that particular number. Is the version
number also needed?
Thanks.
Bill Flanagan
OpenWetWare.org
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From tk at csail.mit.edu Tue Oct 9 19:38:08 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Tue, 9 Oct 2007 19:38:08 -0400
Subject: [OWW-SC] Genbank Accession Number question
In-Reply-To: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
Message-ID: <965cc4785f3a8bb0fffccb0c64715f4c@csail.mit.edu>
The accession number is what is normally listed in journal articles.
Version numbers are usually ignored, with the latest version being
accessed.
You probably *do* want to handle genome accession numbers, which have a
different format, such as NC_006055.
We may want support for EMBL and DDBJ numbers as well. What do people
think?
On Oct 9, 2007, at 6:55 PM, Bill F wrote:
> Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
>
> I'm looking into adding GenBank Accession Number lookup, a feature
> which has been mentioned in the past. To do this, I need to know what
> the set of information from GenBank would be that people would like to
> see available.
>
> This is a cop of the the current comment on the Software/Features page:
> (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests )
> ? Initially, this might be just an extension to Biblio to allow
> referencing by accession number. Eventually, this could pull in info
> from databases.
> ? See also
> http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_p
>
> NCBI has an example of the full record they maintain:
>
> ???????????????????????
> http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
>
> Would a pointer to a similar page for a specific accession number be
> what's needed?
>
> The actual accession number for the example record is:
>
> "U49845".
>
> There's an additional version number on he next line:
>
> "U49845.1 GI:1293613".
>
> Does the version number generally get used in citations or is the
> Accession Number adequate?
>
> Using the Accession number, I can point the Biblio reference to the
> NCBI page (similar to the example) for that particular number. Is the
> version number also needed?
>
>
> Thanks.
>
> Bill Flanagan
> OpenWetWare.org
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
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From bill.altmail at gmail.com Tue Oct 9 22:40:55 2007
From: bill.altmail at gmail.com (Bill F)
Date: Tue, 9 Oct 2007 22:40:55 -0400
Subject: [OWW-SC] Genbank Accession Number question
In-Reply-To: <965cc4785f3a8bb0fffccb0c64715f4c@csail.mit.edu>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
<965cc4785f3a8bb0fffccb0c64715f4c@csail.mit.edu>
Message-ID: <26428aaa0710091940h2dc86c17r6731565095f9fcda@mail.gmail.com>
Here's a link to a test page for EMBL's data on the OWW beta server. I'll
add information about the database names, formats, and styles if there's
interest.
http://beta.openwetware.org/oww-dev/embla3.html
I've factored out a simple browser for the databases, styles, and formats
supported via EBML at http://www.ebi.ac.uk:
This page currently will open a new window with the style and format
requested for the database. The browser lists the format supported for each
of the formats. I can build a simplified version of this same query into the
biblio extension.
Let me know about how you folks would like to see the formats and styles
handled. I can default it to one specific set of parameters but allow for
the addition of options if needed.
I'm looking into the DDBJ format as well.
Thanks.
Bill
On 10/9/07, Tom Knight wrote:
>
> The accession number is what is normally listed in journal articles.
> Version numbers are usually ignored, with the latest version being
> accessed.
>
> You probably *do* want to handle genome accession numbers, which have a
> different format, such as NC_006055.
>
> We may want support for EMBL and DDBJ numbers as well. What do people
> think?
>
> On Oct 9, 2007, at 6:55 PM, Bill F wrote:
>
> > Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
> >
> > I'm looking into adding GenBank Accession Number lookup, a feature
> > which has been mentioned in the past. To do this, I need to know what
> > the set of information from GenBank would be that people would like to
> > see available.
> >
> > This is a cop of the the current comment on the Software/Features page:
> > (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests )
> > ? Initially, this might be just an extension to Biblio to
> allow
> > referencing by accession number. Eventually, this could pull in info
> > from databases.
> > ? See also
> > http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_p
> >
> > NCBI has an example of the full record they maintain:
> >
> >
> > http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
> >
> > Would a pointer to a similar page for a specific accession number be
> > what's needed?
> >
> > The actual accession number for the example record is:
> >
> > "U49845".
> >
> > There's an additional version number on he next line:
> >
> > "U49845.1 GI:1293613".
> >
> > Does the version number generally get used in citations or is the
> > Accession Number adequate?
> >
> > Using the Accession number, I can point the Biblio reference to the
> > NCBI page (similar to the example) for that particular number. Is the
> > version number also needed?
> >
> >
> > Thanks.
> >
> > Bill Flanagan
> > OpenWetWare.org
> >
> >
> >
> > _______________________________________________
> > OpenWetWare Steering Committee Mailing List
> > sc at openwetware.org
> > http://mailman.mit.edu/mailman/listinfo/oww-sc
>
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From julius at younglucks.com Wed Oct 10 09:47:31 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 10 Oct 2007 09:47:31 -0400
Subject: [OWW-SC] Genbank Accession Number question
In-Reply-To: <965cc4785f3a8bb0fffccb0c64715f4c@csail.mit.edu>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
<965cc4785f3a8bb0fffccb0c64715f4c@csail.mit.edu>
Message-ID: <150F5D87-9C5F-40EA-BD6A-1415A9357D79@younglucks.com>
I have a use for genome accession numbers as well. How would the
biblio extension work though? The full genome record is obviously
huge - would it display the top few lines of the record, with links
to the full record?
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 9, 2007, at 7:38 PM, Tom Knight wrote:
> The accession number is what is normally listed in journal
> articles. Version numbers are usually ignored, with the latest
> version being accessed.
>
> You probably *do* want to handle genome accession numbers, which
> have a different format, such as NC_006055.
>
> We may want support for EMBL and DDBJ numbers as well. What do
> people think?
>
> On Oct 9, 2007, at 6:55 PM, Bill F wrote:
>
>> Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
>>
>> I'm looking into adding GenBank Accession Number lookup, a feature
>> which has been mentioned in the past. To do this, I need to know
>> what the set of information from GenBank would be that people
>> would like to see available.
>>
>> This is a cop of the the current comment on the Software/Features
>> page:
>> (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests )
>> ? Initially, this might be just an extension to Biblio to allow
>> referencing by accession number. Eventually, this could pull in
>> info from databases.
>> ? See also http://blogs.nature.com/wp/nascent/2007/07/
>> scientific_blogging_p
>>
>> NCBI has an example of the full record they maintain:
>>
>> http://www.ncbi.nlm.nih.gov/Sitemap/
>> samplerecord.html
>>
>> Would a pointer to a similar page for a specific accession number
>> be what's needed?
>>
>> The actual accession number for the example record is:
>>
>> "U49845".
>>
>> There's an additional version number on he next line:
>>
>> "U49845.1 GI:1293613".
>>
>> Does the version number generally get used in citations or is the
>> Accession Number adequate?
>>
>> Using the Accession number, I can point the Biblio reference to
>> the NCBI page (similar to the example) for that particular number.
>> Is the version number also needed?
>>
>>
>> Thanks.
>>
>> Bill Flanagan
>> OpenWetWare.org
>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
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From julius at younglucks.com Wed Oct 10 09:57:05 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 10 Oct 2007 09:57:05 -0400
Subject: [OWW-SC] Biblio extension to support arXiv.org e-prints
In-Reply-To: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
Message-ID: <14E69E81-BA67-48CB-80AB-284F783EBDAC@younglucks.com>
Hey Bill,
Do you maintain the biblio extension? As I think I mentioned before,
I am writing an API that gives full programmatic access to all of the
e-prints on arXiv.org. While this has primarily been used as a
physics/math/computer science venue, there is a new, but growing
quantitative biology (q-bio) section. In fact, Nature was recently
inspired by the arXiv.org e-print model to start a similar e-print
service themselves.
In any case, I am certainly an OWW user that links to arXiv e-prints
all the time, and I suspect there will be more and more as time goes
on. The API is simple in design, and I actually used the NCBI APIs
as a starting point, so there should be some similarity. The results
are returned in Atom 1.0 with some extensions for arXiv-specific
metadata.
How easy/hard is it to add support for arXiv e-prints in the biblio
extension? I imagine instead of putting the pmid, you put the
arxivid which looks something like q-bio/0703028 or just 0708.2038
(for the new style id's). The api is in very active development, and
we plan to do an alpha release soon, hopefully within the next couple
of weeks. I can send more details and documentation as well.
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 9, 2007, at 6:55 PM, Bill F wrote:
> Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
>
> I'm looking into adding GenBank Accession Number lookup, a feature
> which has been mentioned in the past. To do this, I need to know
> what the set of information from GenBank would be that people would
> like to see available.
>
> This is a cop of the the current comment on the Software/Features
> page:
> (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests )
> Initially, this might be just an extension to Biblio to allow
> referencing by accession number. Eventually, this could pull in
> info from databases.
> See also http://blogs.nature.com/wp/nascent/2007/07/
> scientific_blogging_p
>
> NCBI has an example of the full record they maintain:
>
> http://www.ncbi.nlm.nih.gov/Sitemap/
> samplerecord.html
>
> Would a pointer to a similar page for a specific accession number
> be what's needed?
>
> The actual accession number for the example record is:
>
> "U49845".
>
> There's an additional version number on he next line:
>
> "U49845.1 GI:1293613".
>
> Does the version number generally get used in citations or is the
> Accession Number adequate?
>
> Using the Accession number, I can point the Biblio reference to the
> NCBI page (similar to the example) for that particular number. Is
> the version number also needed?
>
>
> Thanks.
>
> Bill Flanagan
> OpenWetWare.org
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
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From rshetty at MIT.EDU Wed Oct 10 12:25:55 2007
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Wed, 10 Oct 2007 12:25:55 -0400
Subject: [OWW-SC] Biblio extension to support arXiv.org e-prints
In-Reply-To: <14E69E81-BA67-48CB-80AB-284F783EBDAC@younglucks.com>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
<14E69E81-BA67-48CB-80AB-284F783EBDAC@younglucks.com>
Message-ID: <6e9f40380710100925k3dc120a9kc512792ec8d85bab@mail.gmail.com>
A couple questions
1) Do documents in arXiv.org have DOI's?
2) Are digital objects that have DOI's required to have a certain set
of information associated with them? If yes, is there a way to access
that information (like you can for ISBNs and PubMed ID's)?
If yes to all of the above, would it make more sense to extend Biblio
to support references by DOI's rather just arXiv.org documents ...
i.e. go after the general solution.
Of course, I don't think that Genbank entries have DOI's so we'd still
need a specific solution for those.
-Reshma
On 10/10/07, Julius B. Lucks wrote:
> Hey Bill,
>
> Do you maintain the biblio extension? As I think I mentioned before, I am
> writing an API that gives full programmatic access to all of the e-prints on
> arXiv.org. While this has primarily been used as a physics/math/computer
> science venue, there is a new, but growing quantitative biology (q-bio)
> section. In fact, Nature was recently inspired by the arXiv.org e-print
> model to start a similar e-print service themselves.
>
> In any case, I am certainly an OWW user that links to arXiv e-prints all the
> time, and I suspect there will be more and more as time goes on. The API is
> simple in design, and I actually used the NCBI APIs as a starting point, so
> there should be some similarity. The results are returned in Atom 1.0 with
> some extensions for arXiv-specific metadata.
>
> How easy/hard is it to add support for arXiv e-prints in the biblio
> extension? I imagine instead of putting the pmid, you put the arxivid which
> looks something like q-bio/0703028 or just 0708.2038 (for the new style
> id's). The api is in very active development, and we plan to do an alpha
> release soon, hopefully within the next couple of weeks. I can send more
> details and documentation as well.
>
> Cheers,
>
> Julius
>
>
> ---------------------------------------------------------------------------------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------------------------
>
>
>
>
> On Oct 9, 2007, at 6:55 PM, Bill F wrote:
> Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
>
> I'm looking into adding GenBank Accession Number lookup, a feature which has
> been mentioned in the past. To do this, I need to know what the set of
> information from GenBank would be that people would like to see available.
>
> This is a cop of the the current comment on the Software/Features page:
> (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests
> )
>
> Initially, this might be just an extension to Biblio to allow referencing by
> accession number. Eventually, this could pull in info from databases.
> See also
> http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_p
> NCBI has an example of the full record they maintain:
>
>
> http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
>
> Would a pointer to a similar page for a specific accession number be what's
> needed?
>
> The actual accession number for the example record is:
>
> "U49845".
>
> There's an additional version number on he next line:
>
> "U49845.1 GI:1293613".
>
> Does the version number generally get used in citations or is the Accession
> Number adequate?
>
> Using the Accession number, I can point the Biblio reference to the NCBI
> page (similar to the example) for that particular number. Is the version
> number also needed?
>
>
> Thanks.
>
> Bill Flanagan
> OpenWetWare.org
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
From julius at younglucks.com Wed Oct 10 14:10:44 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 10 Oct 2007 14:10:44 -0400
Subject: [OWW-SC] Biblio extension to support arXiv.org e-prints
In-Reply-To: <6e9f40380710100925k3dc120a9kc512792ec8d85bab@mail.gmail.com>
References: <26428aaa0710091555odab5ca3ra6d8fa579fed246d@mail.gmail.com>
<14E69E81-BA67-48CB-80AB-284F783EBDAC@younglucks.com>
<6e9f40380710100925k3dc120a9kc512792ec8d85bab@mail.gmail.com>
Message-ID: <01EDD17C-0DC3-42A1-9063-99EA20B36FE0@younglucks.com>
Hey Reshma,
Good questions.
>
> 1) Do documents in arXiv.org have DOI's?
>
No they don't. All arXiv documents live on arXiv.org so I imagine
there has been no need to register DOI's with them (since they are
guaranteed not to move around.) (I don't know the official reason why
though - something I should inquire about.)
> 2) Are digital objects that have DOI's required to have a certain set
> of information associated with them? If yes, is there a way to access
> that information (like you can for ISBNs and PubMed ID's)?
I'm pretty sure that DOI's are one way to implement URI's (Universal
Resource Identifiers), and as such are only used to locate
documents. There is I am sure some metadata associated with the DOI
to let resolvers locate it, but I don't think the DOI specification
has anything about actual content.
>
> If yes to all of the above, would it make more sense to extend Biblio
> to support references by DOI's rather just arXiv.org documents ...
> i.e. go after the general solution.
>
The problem is that once the biblio extension locates a resource (via
a DOI, pubmed ID, arXiv ID, ISBN, etc.) it still has to parse out
information about that resource (title, author, etc.). Given that
DOI's can point to many different types of resources (many different
journals with different formats, etc.), there would still have to be
domain-specific code in the extension to digest these different types
of information. Basically until all publishers agree on a common
format, this problem will always persist. This is at least to the
best of my knowledge, but someone probably knows more than me on this
issue.
> Of course, I don't think that Genbank entries have DOI's so we'd still
> need a specific solution for those.
>
You can think of arXiv as pubmed, with a few differences. With both
systems, you can identify a resource via a unique id, and there are
APIs to perform basic searches, and to retrieve related articles.
The key difference is that with arXiv, the full text is ALWAYS
available, while with pubmed not. In this aspect, the arXiv is much
like pubmed central. (And in this case the similarity is not
accidental since the arXiv had a lot to do with the creation of the
latter.)
Cheers,
Julius
> -Reshma
>
> On 10/10/07, Julius B. Lucks wrote:
>> Hey Bill,
>>
>> Do you maintain the biblio extension? As I think I mentioned
>> before, I am
>> writing an API that gives full programmatic access to all of the e-
>> prints on
>> arXiv.org. While this has primarily been used as a physics/math/
>> computer
>> science venue, there is a new, but growing quantitative biology (q-
>> bio)
>> section. In fact, Nature was recently inspired by the arXiv.org e-
>> print
>> model to start a similar e-print service themselves.
>>
>> In any case, I am certainly an OWW user that links to arXiv e-
>> prints all the
>> time, and I suspect there will be more and more as time goes on.
>> The API is
>> simple in design, and I actually used the NCBI APIs as a starting
>> point, so
>> there should be some similarity. The results are returned in Atom
>> 1.0 with
>> some extensions for arXiv-specific metadata.
>>
>> How easy/hard is it to add support for arXiv e-prints in the biblio
>> extension? I imagine instead of putting the pmid, you put the
>> arxivid which
>> looks something like q-bio/0703028 or just 0708.2038 (for the new
>> style
>> id's). The api is in very active development, and we plan to do
>> an alpha
>> release soon, hopefully within the next couple of weeks. I can
>> send more
>> details and documentation as well.
>>
>> Cheers,
>>
>> Julius
>>
>>
>> ---------------------------------------------------------------------
>> ------------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>> ---------------------------------------------------------------------
>> -------------------
>>
>>
>>
>>
>> On Oct 9, 2007, at 6:55 PM, Bill F wrote:
>> Accession Numbers and NCBI Lookup for Biblio Extension to OpenWetWare
>>
>> I'm looking into adding GenBank Accession Number lookup, a feature
>> which has
>> been mentioned in the past. To do this, I need to know what the
>> set of
>> information from GenBank would be that people would like to see
>> available.
>>
>> This is a cop of the the current comment on the Software/Features
>> page:
>> (http://openwetware.org/wiki/OpenWetWare:Software/Feature_requests
>> )
>>
>> Initially, this might be just an extension to Biblio to allow
>> referencing by
>> accession number. Eventually, this could pull in info from databases.
>> See also
>> http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_p
>> NCBI has an example of the full record they maintain:
>>
>>
>> http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
>>
>> Would a pointer to a similar page for a specific accession number
>> be what's
>> needed?
>>
>> The actual accession number for the example record is:
>>
>> "U49845".
>>
>> There's an additional version number on he next line:
>>
>> "U49845.1 GI:1293613".
>>
>> Does the version number generally get used in citations or is the
>> Accession
>> Number adequate?
>>
>> Using the Accession number, I can point the Biblio reference to
>> the NCBI
>> page (similar to the example) for that particular number. Is the
>> version
>> number also needed?
>>
>>
>> Thanks.
>>
>> Bill Flanagan
>> OpenWetWare.org
>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>>
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From lucks at fas.harvard.edu Wed Oct 10 19:00:24 2007
From: lucks at fas.harvard.edu (Julius Lucks)
Date: Wed, 10 Oct 2007 19:00:24 -0400
Subject: [OWW-SC] Fwd: publishing conference
References:
Message-ID: <23C9E980-AFC4-482D-A5D2-3DE99777D5BD@fas.harvard.edu>
FYI - November 9 Publishing Conference at Harvard Med School.
Julius
------------------------------------------------------------------------
---
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
---
Begin forwarded message:
> From: Bodo Stern
> Date: October 10, 2007 6:24:27 PM EDT
> To: CGRGT at LISTSERV.CGR.HARVARD.EDU
> Subject: publishing conference
> Reply-To: bstern at CGR.HARVARD.EDU
>
>
>
> What's the impact of the "impact factor"?
> Do you believe that more journals should adopt open-access policies?
> Are you satisfied with the current scientific publishing process?
> Will the internet revolutionize publishing?
>>>
> If you have thoughts or questions about the future or scientific
> publishing (and who doesn't?), please join us at:
>
> "Publishing in the New Millennium: A Forum on Publishing in the
> Biosciences"
> Friday, November 9, 1:00 - 6:00 pm
> TMEC Walter Amphitheater, Harvard Medical School
> 260 Longwood Ave, Boston, MA 02115
> www.harvardpublishingforum.com www.harvardpublishingforum.com/>
> This is a student-organized conference that will convene experts
> from across the world to discuss the state of publishing in the
> biological sciences.
>
> KEYNOTE ADDRESS:
> Harold Varmus, M.D.
> Nobel-Laureate and Co-founder of PLoS, former Director of the NIH,
> and CEO of Memorial-Sloan Kettering Cancer Center
> Dr. Varmus will draw on his experience as Director of the NIH and
> as a co-founder of the Public Library of Science to reflect on the
> current and future state of scientific publishing.
>
> PANELS:
> The State of Publishing will critically assess the impact that
> scientific publishing has on scientific research.
> Panelists include:
> ? Robert Kiley, Head of e-Strategy, Wellcome Library,
> Wellcome Trust
> ? Isaac Kohane, Director, Countway Library, Harvard
> University [tentative]
> ? Emilie Marcus, Editor-in-Chief, Cell Press and Editor, Cell
> ? Stuart Shieber, Professor, Harvard University
>
> Publishing 2.0 will examine the future of publishing in an
> increasingly digital world.
> Panelists include:
> ? Moshe Pritsker, Editor-in-Chief and Founder, Journal of
> Visualized Experiments
> ? Hilary Spencer, Product Manager, Nature Precedings
> ? John Wilbanks, Executive Director, Science Commons
> ? Bora Zivkovic, Community Manager, PLoS ONE
>
> We also want to know what you think! Please take a moment to
> complete a brief online poll at www.harvardpublishingforum.com
> and register (optional,
> but strongly encouraged) for this half-day event.
>
> A reception, sponsored in part by the Nature Publishing Group/
> Nature Network, will follow the forum.
>
> This student-organized forum is generously sponsored by the Harvard
> Biophysics Program and the Harvard Integrated Life Sciences (HILS)
> Program. Questions? Contact Kishore Kuchibhotla
> [kuchibh at fas.harvard.edu] or Zeba Wunderlich
> [ wunderl at fas.harvard.edu ].
>
> All are invited so please forward widely!
>
>
>
> ------ End of Forwarded Message
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From julius at younglucks.com Thu Oct 11 18:36:13 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Thu, 11 Oct 2007 18:36:13 -0400
Subject: [OWW-SC] Content for Seeding User Pages
Message-ID:
Hi SC,
To follow up on Bills work creating the ability to seed new user
pages with content (and upon Jason's suggestion), I have created a
proposed default user page at
http://openwetware.org/wiki/OpenWetWare_talk:UserPageDefaultContentText
The page contains a brief tutorial on how to edit the User page, and
encourages the new member to add more information to the page as well
as contribute to the OWW wiki in general.
Please take a minute to have a look at the page, and edit/comment as
you see fit. Hopefully we can finalize this soon so that we can
encourage new users to start making contributions to OWW.
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
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From julius at younglucks.com Sun Oct 14 11:59:38 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Sun, 14 Oct 2007 11:59:38 -0400
Subject: [OWW-SC] User Page Default Content Live
Message-ID:
Hi SC,
Thanks for all the comments on the default user page contents. It
looks like we have stabilized on
http://openwetware.org/index.php?
title=OpenWetWare:UserPageDefaultContentText
which I think is excellent. I have gone ahead and made these changes
to the page that is used for the live user page creation.
I think the next step is to tweak the welcoming email a little bit to
encourage users to look at their newly created user page, and maybe
even shorten it a bit. (Ideally it would contain a single link to
their new user page.)
Reshma, I remember you putting up a page about the content of the
email - can you point that out to me so we can start discussing its
content?
Thanks a bunch,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
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From rshetty at MIT.EDU Sun Oct 14 12:16:52 2007
From: rshetty at MIT.EDU (Reshma Shetty)
Date: Sun, 14 Oct 2007 12:16:52 -0400
Subject: [OWW-SC] User Page Default Content Live
In-Reply-To:
References:
Message-ID: <6e9f40380710140916p4a4ad0b3gad6f4220ab270e59@mail.gmail.com>
http://openwetware.org/wiki/OpenWetWare:Welcome_email
-Reshma
On 10/14/07, Julius B. Lucks wrote:
> Hi SC,
>
> Thanks for all the comments on the default user page contents. It looks
> like we have stabilized on
>
> http://openwetware.org/index.php?title=OpenWetWare:UserPageDefaultContentText
>
> which I think is excellent. I have gone ahead and made these changes to the
> page that is used for the live user page creation.
>
> I think the next step is to tweak the welcoming email a little bit to
> encourage users to look at their newly created user page, and maybe even
> shorten it a bit. (Ideally it would contain a single link to their new user
> page.)
>
> Reshma, I remember you putting up a page about the content of the email -
> can you point that out to me so we can start discussing its content?
>
>
> Thanks a bunch,
>
> Julius
>
> ---------------------------------------------------------------------------------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------------------------
>
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
>
From julius at younglucks.com Sun Oct 14 12:25:48 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Sun, 14 Oct 2007 12:25:48 -0400
Subject: [OWW-SC] User Page Default Content Live
In-Reply-To: <6e9f40380710140916p4a4ad0b3gad6f4220ab270e59@mail.gmail.com>
References:
<6e9f40380710140916p4a4ad0b3gad6f4220ab270e59@mail.gmail.com>
Message-ID: <1BF95084-44B4-4946-84D2-6CE37EFA8DC8@younglucks.com>
Thanks Reshma,
I have put an adjusted draft of the intro email up on the talk page
http://openwetware.org/wiki/OpenWetWare_talk:Welcome_email
I would like to make the email as short and sweet as possible, and
draw attention to the new user pages. Your feedback is much
appreciated!!!!
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 14, 2007, at 12:16 PM, Reshma Shetty wrote:
> http://openwetware.org/wiki/OpenWetWare:Welcome_email
>
> -Reshma
>
> On 10/14/07, Julius B. Lucks wrote:
>> Hi SC,
>>
>> Thanks for all the comments on the default user page contents. It
>> looks
>> like we have stabilized on
>>
>> http://openwetware.org/index.php?
>> title=OpenWetWare:UserPageDefaultContentText
>>
>> which I think is excellent. I have gone ahead and made these
>> changes to the
>> page that is used for the live user page creation.
>>
>> I think the next step is to tweak the welcoming email a little bit to
>> encourage users to look at their newly created user page, and
>> maybe even
>> shorten it a bit. (Ideally it would contain a single link to their
>> new user
>> page.)
>>
>> Reshma, I remember you putting up a page about the content of the
>> email -
>> can you point that out to me so we can start discussing its content?
>>
>>
>> Thanks a bunch,
>>
>> Julius
>>
>> ---------------------------------------------------------------------
>> ------------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>> ---------------------------------------------------------------------
>> -------------------
>>
>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>>
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From wjf42 at MIT.EDU Tue Oct 16 18:19:45 2007
From: wjf42 at MIT.EDU (Bill Flanagan)
Date: Tue, 16 Oct 2007 18:19:45 -0400
Subject: [OWW-SC] USB Label Printers
Message-ID: <26428aaa0710161519j16e76554vcbb5c7e989b49c6b@mail.gmail.com>
Tom Knight mentioned label printer support as a useful OWW feature to
consider.
Does anyone currently use a computer-connected label printers in your lab?
In our lab, we have an old Brother P-Touch connected to one researcher's
Mac. I have an old one at home as well. If anyone is using any of these
devices, please let me know the following:
1. How you're using them.
2. What kind of label printer you have.
- Manufacturer
- Model
- Computer-OS
I'd also like to know is what kind of data you would like to print and
correlate from OWW.
Thanks.
Bill Flanagan
Technical Developer
OpenWetWare.org
Endy Lab
Department of Biology, MIT
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From tk at csail.mit.edu Tue Oct 16 18:40:57 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Tue, 16 Oct 2007 18:40:57 -0400
Subject: [OWW-SC] USB Label Printers
In-Reply-To: <26428aaa0710161519j16e76554vcbb5c7e989b49c6b@mail.gmail.com>
References: <26428aaa0710161519j16e76554vcbb5c7e989b49c6b@mail.gmail.com>
Message-ID:
We use Brother P-touch labels, primarily black on white 3/4" wide
(TZ-241 tape). This has shown to be stable both during autoclaving and
-80 freezing.
The labels I make have initials in the lower left corner and an
automatically created date in the lower right corner. The rest is a
centered free-text label. I have templates for three sizes -- one for
large bottles, one for cryotubes and eppendorfs, and a third for slim
tubes such as screw cap tubes.
I like to print an extra copy labels that I make to paste into the
notebook.
Eventually, bar codes will be important.
I run it from a Mac, but the same label maker works on PCs as well.
The model I use is the P-Touch Pro-XL, but they all work essentially
the same.
On Oct 16, 2007, at 6:19 PM, Bill Flanagan wrote:
> Tom Knight mentioned label printer support as a useful OWW feature to
> consider.
> ?
> Does anyone currently use a computer-connected label printers in your
> lab? In our lab, we have an old Brother P-Touch connected to one
> researcher's Mac. I have an old one at home as well. If anyone is
> using any of these devices, please let me know the following:
>
> 1. How you're using them.
> 2. What kind of label printer you have.
> ?? - Manufacturer
> ?? - Model
> ?? - Computer-OS?
>
> I'd also like to know is what kind of data you would like to print and
> correlate from OWW.
>
>
> Thanks.
>
>
> Bill Flanagan
> Technical Developer
> OpenWetWare.org
> Endy Lab
> Department of Biology, MIT
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
From tk at csail.mit.edu Mon Oct 22 14:35:18 2007
From: tk at csail.mit.edu (Tom Knight)
Date: Mon, 22 Oct 2007 14:35:18 -0400
Subject: [OWW-SC] Senate considers open access amendments TODAY
Message-ID: <328812382a07cc97d205f1184e007548@csail.mit.edu>
You might consider writing your senator (from your home state, which
would make it broader support) to recommend rejection of the amendments
gutting the NIH requirement for open access publication of government
supported work. See Jonathan Eisen's blog here:
http://phylogenomics.blogspot.com/
From austin at csail.mit.edu Mon Oct 29 14:04:37 2007
From: austin at csail.mit.edu (Austin Che)
Date: Mon, 29 Oct 2007 14:04:37 -0400
Subject: [OWW-SC] Open Science Talk Nov 4 by Cameron Neylon
Message-ID: <873avt23wq.fsf@nitsua.mit.edu>
Please let whoever you think might be interested know about the
following. It will be a 30 minute talk followed by 30 minutes of
discussion about openness in general.
News team: we might want to have a news highlight about this on
the front page.
----
http://openwetware.org/wiki/Seminar_Series/Cameron_Neylon
3:30pm, Sunday November 4th, 2007
MIT Stata Center, 32-155
Organized in conjunction with iGEM
Speaker: Cameron Neylon
Title: A Beginner's Guide to Open Science (not for beginners but by
beginners)
Abstract:
The modern biochemistry or molecular biology laboratory generates
large quantities of data that are generally stored across multiple
computers attached to multiple instruments. Much of this data is
never published and the majority languishes on old computers and
is ultimately lost. At a local level this is a frustration for
investigators who will often struggle to obtain specific pieces of
data produced in their own laboratory. On a larger scale this is
becoming a much more serious issue with the obligation of
researchers to funding bodies to both preserve research data and
make it available to other users increasingly becoming a formal a
condition of publicly funded grants. Systems are required that can
capture and preserve data along with sufficient information and
metadata to make it possible for others to use this data.
In parallel with this a movement is growing within the research
community that advocates greater openness in providing both the
raw data from published studies as well as making available the
large quantities of data that are never published. The logical
extreme of this approach is Open Notebook Science [1], pioneered
at Drexel University [2], where the researcher's laboratory
notebook is made available on the internet as it is
recorded. Achieving the aims of Open Notebook Science also
requires systems which can capture data and provide it in a useful
format. In addition these systems must make the data visible to
relevant online searches.
We are developing and using an electronic laboratory notebook
based on a Blog format to capture experimental data in a
biochemistry laboratory [3,4]. Within the system each sample is
recorded in a single post. Analysis and manipulations of the
sample are recorded in separate posts with links back to the input
sample and forward to any products. All the information is made
immediately available on the Web as it is recorded. The Blog
engine has been specially built in house and has a number of
features designed to enable and encourage the effective capture of
data and metadata in the environment of a biochemistry
laboratory. I will describe the Blog system and our evolving
approach to capturing metadata as well as the process of
integrating this with other web services to provide an open
environment for recording work in the laboratory, laboratory
materials, and validated procedures. The challenges and problems
encountered in reconciling the twin aims of capturing data and
making it available and readable will also be discussed along with
the similarities and differences emerging between different
approaches to Open Notebook Science [2,5,6].
[1] http://drexel-coas-elearning.blogspot.com/2006/09/open-notebook-science.html
[2] http://usefulchem.wikispaces.com/
[3] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/10
[4] http://chemtools.chem.soton.ac.uk/projects/blog/blogs.php/blog_id/13
[5] http://www.jeremiahfaith.com/open_notebook_science/
[6] http://www.michaelbarton.me.uk/
Biography:
Cameron studied for a first degree in Biochemistry at the
University of Western Australia before moving to the Research
School of Chemistry at the Australian National University to study
for a PhD in protein chemistry and molecular biology. After his
doctoral studies he moved to the United Kingdom to take up a
Wellcome Trust International Travelling Fellowship at the
University of Bath to develop a library of constrained peptides as
potential activators of 7-transmembrane receptors.
In 2001 he moved to the School of Chemistry at the University of
Southampton as Lecturer in Chemical Biology and in 2005 he took up
a joint appointment as Senior Scientist in Biomolecular Sciences
at the ISIS Neutron Scattering Facility located within the STFC
Rutherford Appleton Laboratory. Current areas of research include
the development of new methods for protein labelling and the
synthesis of protein conjugates, experimental and computational
approaches studies of high throughout nucleic acid sequence
analysis, and the the development of complementary analytical
methods for probing the structure and dynamics of proteins and
protein-ligand complexes in solution. In addition to these
experimental studies the combination of high throughput
methodology and working on two sites has led to a developing
interest in open approaches to science and electronic lab
notebooks being developed in collaboration with the group of
Professor Jeremy Frey.
From julius at younglucks.com Wed Oct 31 11:04:40 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 31 Oct 2007 11:04:40 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
Message-ID: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
Hi Bill and John (and SC),
I just had this idea so please excuse its half-bakedness. What about
promoting 'publishing' of oww materials on arXiv.org?
arXiv.org already has a quantitative biology section (http://
arxiv.org/list/q-bio/new), and I am willing to bet that essentially
all papers coming out of the OWW community could fit into this
section. The arXiv allows you to post paper pre-prints online for
free, and it is completely open access. Every e-print has associated
with it a unique id, that is completely referenceable in papers,
etc. In addition, if you do publish your paper in a journal, you can
update arXiv e-print metadata with the journal reference, or a DOI of
the journal article.
Compared to an alliance with Nature or some other body, promoting
'publishing' on the arXiv has many advantages:
1.) It already exists and no agreement or negotiations need to be
made to use it. There is a very mild form of control in that people
that are new to the arXiv system must be 'endorsed' by existing
people, but this can be gotten around until enough OWW people are
themselves endorsers.
2.) It provides all the functionality we want - some sort of official
stamp on an OWW document in the form of an e-print that is completely
referenceable and is more like a paper than a wiki page. In fact,
the arXiv supports the notion of versions, so that you can always
submit a newer version of a resource, keeping complete access to
older versions.
3.) There are many tools already in place, or being developed that we
can integrate the arXiv with OWW. As Bill knows, the arXiv already
has an API that allows you to pull content from the arXiv into OWW
trivially (by just specifying e-print id). In addition, this API
supplies journal references and DOI's if they are present, so it
would be very easy to create references in the biblio extension for
both the e-print and the published version. Also, there is an ingest
API in active development (and soon to be released) with which we
could easily create our long-dreamed-of 'publish' button on OWW that
could automatically publish an OWW page.
4.) Journals will accept papers that have been posted on the arXiv
already. In particular, Nature has committed to this as is evident
on the Nature Proceedings page (http://precedings.nature.com/
about#journal-submissions)
"Nature Precedings hosts manuscripts that may be submitted to any
journal of any publisher. Nature and all Nature journals have a
policy that permits such posts on recognized pre- or e-print servers
such as Nature Precedings and arXiv without affecting their
eligibility for publication, whether or not such postings result in
discussion on other sites and in the media. We cannot take
responsibility for the possibility of scooping by competitors.
Authors submitting to other journals are advised to check their
policies about prior postings before sending manuscripts to Nature
Precedings."
(In fact, Nature Precedings was heavily inspired by the arXiv.)
5.) If the quantitative biology community grows and needs more of a
refined categorization (such as synthetic biology, etc.), the arXiv
can expand its categorization scheme (which is how the q-bio section
started in the first place).
6.) Integrating with the arXiv integrates what OWW is doing with the
physics, math and computer science communities.
This is juts a brainstorm, but it seems to me like the arXiv could
provide the avenue that we have been thinking about in the OWW
publishing arena.
Any thoughts?
Cheers,
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
From endy at MIT.EDU Wed Oct 31 11:15:21 2007
From: endy at MIT.EDU (Drew Endy)
Date: Wed, 31 Oct 2007 11:15:21 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
In-Reply-To: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
References: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
Message-ID:
I think that this is a good idea. Either we need to do this, or
something equivalent ourselves. Drew
On Oct 31, 2007, at 11:04 AM, Julius B. Lucks wrote:
> Hi Bill and John (and SC),
>
> I just had this idea so please excuse its half-bakedness. What about
> promoting 'publishing' of oww materials on arXiv.org?
>
> arXiv.org already has a quantitative biology section (http://
> arxiv.org/list/q-bio/new), and I am willing to bet that essentially
> all papers coming out of the OWW community could fit into this
> section. The arXiv allows you to post paper pre-prints online for
> free, and it is completely open access. Every e-print has associated
> with it a unique id, that is completely referenceable in papers,
> etc. In addition, if you do publish your paper in a journal, you can
> update arXiv e-print metadata with the journal reference, or a DOI of
> the journal article.
>
> Compared to an alliance with Nature or some other body, promoting
> 'publishing' on the arXiv has many advantages:
>
> 1.) It already exists and no agreement or negotiations need to be
> made to use it. There is a very mild form of control in that people
> that are new to the arXiv system must be 'endorsed' by existing
> people, but this can be gotten around until enough OWW people are
> themselves endorsers.
>
> 2.) It provides all the functionality we want - some sort of official
> stamp on an OWW document in the form of an e-print that is completely
> referenceable and is more like a paper than a wiki page. In fact,
> the arXiv supports the notion of versions, so that you can always
> submit a newer version of a resource, keeping complete access to
> older versions.
>
> 3.) There are many tools already in place, or being developed that we
> can integrate the arXiv with OWW. As Bill knows, the arXiv already
> has an API that allows you to pull content from the arXiv into OWW
> trivially (by just specifying e-print id). In addition, this API
> supplies journal references and DOI's if they are present, so it
> would be very easy to create references in the biblio extension for
> both the e-print and the published version. Also, there is an ingest
> API in active development (and soon to be released) with which we
> could easily create our long-dreamed-of 'publish' button on OWW that
> could automatically publish an OWW page.
>
> 4.) Journals will accept papers that have been posted on the arXiv
> already. In particular, Nature has committed to this as is evident
> on the Nature Proceedings page (http://precedings.nature.com/
> about#journal-submissions)
>
> "Nature Precedings hosts manuscripts that may be submitted to any
> journal of any publisher. Nature and all Nature journals have a
> policy that permits such posts on recognized pre- or e-print servers
> such as Nature Precedings and arXiv without affecting their
> eligibility for publication, whether or not such postings result in
> discussion on other sites and in the media. We cannot take
> responsibility for the possibility of scooping by competitors.
> Authors submitting to other journals are advised to check their
> policies about prior postings before sending manuscripts to Nature
> Precedings."
>
> (In fact, Nature Precedings was heavily inspired by the arXiv.)
>
> 5.) If the quantitative biology community grows and needs more of a
> refined categorization (such as synthetic biology, etc.), the arXiv
> can expand its categorization scheme (which is how the q-bio section
> started in the first place).
>
> 6.) Integrating with the arXiv integrates what OWW is doing with the
> physics, math and computer science communities.
>
> This is juts a brainstorm, but it seems to me like the arXiv could
> provide the avenue that we have been thinking about in the OWW
> publishing arena.
>
> Any thoughts?
>
> Cheers,
>
> Julius
>
>
> ----------------------------------------------------------------------
> --
> ---------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------
> --
> ----------------
>
>
>
>
>
>
>
> _______________________________________________
> OpenWetWare Steering Committee Mailing List
> sc at openwetware.org
> http://mailman.mit.edu/mailman/listinfo/oww-sc
From julius at younglucks.com Wed Oct 31 11:26:23 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 31 Oct 2007 11:26:23 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
In-Reply-To:
References: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
Message-ID: <0DF8B7A0-F576-41C2-BE79-343F4A86D04A@younglucks.com>
The only thing that really has to be facilitated is the endorsement
system for new arXiv users. The current procedure is that if you are
not an endorser yourself, you need to be endorsed by several
endorsers. I will talk to Paul Ginsparg about this and ask if we
could at least seed the system with a few endorsers from OWW to start
the chain going.
The advantage to going with the arXiv with respect to rolling out
something ourselves is that:
1.) The arXiv has been around since 1991 and they are very good at
what they do. They also are supported by Cornell, and will be around
for a long time to come. They also have huge recognition within the
open access community, and are unaffiliated with publishers.
2.) Having worked at the arXiv, it is actually a complicated beast
beneath the surface. I don't think we would want to get into this
arena quite yet. We can always try things out on the arXiv, and if
it is a real hit and the arXiv does not provide the flexibility we
want, we can make our own system and import our old arXiv postings.
And one more previous point I forgot to add on the previous list:
7.) There are a bunch of 'overlay' journals built on top of the arXiv
already. Basically editors use the arXiv as their whole submission
system, put papers through peer review of some sort, then create
their journal as a series of links to arXiv posts. It would be
completely natural for OWW to create something like this if we ever
wanted to get into the publishing arena ourselves. There is a lot of
flexibility with this.
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 31, 2007, at 11:15 AM, Drew Endy wrote:
> I think that this is a good idea. Either we need to do this, or
> something equivalent ourselves. Drew
>
>
> On Oct 31, 2007, at 11:04 AM, Julius B. Lucks wrote:
>
>> Hi Bill and John (and SC),
>>
>> I just had this idea so please excuse its half-bakedness. What about
>> promoting 'publishing' of oww materials on arXiv.org?
>>
>> arXiv.org already has a quantitative biology section (http://
>> arxiv.org/list/q-bio/new), and I am willing to bet that essentially
>> all papers coming out of the OWW community could fit into this
>> section. The arXiv allows you to post paper pre-prints online for
>> free, and it is completely open access. Every e-print has associated
>> with it a unique id, that is completely referenceable in papers,
>> etc. In addition, if you do publish your paper in a journal, you can
>> update arXiv e-print metadata with the journal reference, or a DOI of
>> the journal article.
>>
>> Compared to an alliance with Nature or some other body, promoting
>> 'publishing' on the arXiv has many advantages:
>>
>> 1.) It already exists and no agreement or negotiations need to be
>> made to use it. There is a very mild form of control in that people
>> that are new to the arXiv system must be 'endorsed' by existing
>> people, but this can be gotten around until enough OWW people are
>> themselves endorsers.
>>
>> 2.) It provides all the functionality we want - some sort of official
>> stamp on an OWW document in the form of an e-print that is completely
>> referenceable and is more like a paper than a wiki page. In fact,
>> the arXiv supports the notion of versions, so that you can always
>> submit a newer version of a resource, keeping complete access to
>> older versions.
>>
>> 3.) There are many tools already in place, or being developed that we
>> can integrate the arXiv with OWW. As Bill knows, the arXiv already
>> has an API that allows you to pull content from the arXiv into OWW
>> trivially (by just specifying e-print id). In addition, this API
>> supplies journal references and DOI's if they are present, so it
>> would be very easy to create references in the biblio extension for
>> both the e-print and the published version. Also, there is an ingest
>> API in active development (and soon to be released) with which we
>> could easily create our long-dreamed-of 'publish' button on OWW that
>> could automatically publish an OWW page.
>>
>> 4.) Journals will accept papers that have been posted on the arXiv
>> already. In particular, Nature has committed to this as is evident
>> on the Nature Proceedings page (http://precedings.nature.com/
>> about#journal-submissions)
>>
>> "Nature Precedings hosts manuscripts that may be submitted to any
>> journal of any publisher. Nature and all Nature journals have a
>> policy that permits such posts on recognized pre- or e-print servers
>> such as Nature Precedings and arXiv without affecting their
>> eligibility for publication, whether or not such postings result in
>> discussion on other sites and in the media. We cannot take
>> responsibility for the possibility of scooping by competitors.
>> Authors submitting to other journals are advised to check their
>> policies about prior postings before sending manuscripts to Nature
>> Precedings."
>>
>> (In fact, Nature Precedings was heavily inspired by the arXiv.)
>>
>> 5.) If the quantitative biology community grows and needs more of a
>> refined categorization (such as synthetic biology, etc.), the arXiv
>> can expand its categorization scheme (which is how the q-bio section
>> started in the first place).
>>
>> 6.) Integrating with the arXiv integrates what OWW is doing with the
>> physics, math and computer science communities.
>>
>> This is juts a brainstorm, but it seems to me like the arXiv could
>> provide the avenue that we have been thinking about in the OWW
>> publishing arena.
>>
>> Any thoughts?
>>
>> Cheers,
>>
>> Julius
>>
>>
>> ---------------------------------------------------------------------
>> ---
>> ---------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>> ---------------------------------------------------------------------
>> ---
>> ----------------
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> OpenWetWare Steering Committee Mailing List
>> sc at openwetware.org
>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>
From endy at MIT.EDU Wed Oct 31 11:30:25 2007
From: endy at MIT.EDU (Drew Endy)
Date: Wed, 31 Oct 2007 11:30:25 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
In-Reply-To: <0DF8B7A0-F576-41C2-BE79-343F4A86D04A@younglucks.com>
References: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
<0DF8B7A0-F576-41C2-BE79-343F4A86D04A@younglucks.com>
Message-ID:
We would need to have a conversation with arXiv leadership before
making a decision.
On Oct 31, 2007, at 11:26 AM, Julius B. Lucks wrote:
> The only thing that really has to be facilitated is the endorsement
> system for new arXiv users. The current procedure is that if you
> are not an endorser yourself, you need to be endorsed by several
> endorsers. I will talk to Paul Ginsparg about this and ask if we
> could at least seed the system with a few endorsers from OWW to
> start the chain going.
>
> The advantage to going with the arXiv with respect to rolling out
> something ourselves is that:
>
> 1.) The arXiv has been around since 1991 and they are very good at
> what they do. They also are supported by Cornell, and will be
> around for a long time to come. They also have huge recognition
> within the open access community, and are unaffiliated with
> publishers.
>
> 2.) Having worked at the arXiv, it is actually a complicated beast
> beneath the surface. I don't think we would want to get into this
> arena quite yet. We can always try things out on the arXiv, and if
> it is a real hit and the arXiv does not provide the flexibility we
> want, we can make our own system and import our old arXiv postings.
>
> And one more previous point I forgot to add on the previous list:
>
> 7.) There are a bunch of 'overlay' journals built on top of the
> arXiv already. Basically editors use the arXiv as their whole
> submission system, put papers through peer review of some sort,
> then create their journal as a series of links to arXiv posts. It
> would be completely natural for OWW to create something like this
> if we ever wanted to get into the publishing arena ourselves.
> There is a lot of flexibility with this.
>
> ----------------------------------------------------------------------
> -----------------
> Please Reply to My Permanent Address: julius at younglucks.com
> http://www.openwetware.org/wiki/User:Julius_B._Lucks
> ----------------------------------------------------------------------
> ------------------
>
>
>
> On Oct 31, 2007, at 11:15 AM, Drew Endy wrote:
>
>> I think that this is a good idea. Either we need to do this, or
>> something equivalent ourselves. Drew
>>
>>
>> On Oct 31, 2007, at 11:04 AM, Julius B. Lucks wrote:
>>
>>> Hi Bill and John (and SC),
>>>
>>> I just had this idea so please excuse its half-bakedness. What
>>> about
>>> promoting 'publishing' of oww materials on arXiv.org?
>>>
>>> arXiv.org already has a quantitative biology section (http://
>>> arxiv.org/list/q-bio/new), and I am willing to bet that essentially
>>> all papers coming out of the OWW community could fit into this
>>> section. The arXiv allows you to post paper pre-prints online for
>>> free, and it is completely open access. Every e-print has
>>> associated
>>> with it a unique id, that is completely referenceable in papers,
>>> etc. In addition, if you do publish your paper in a journal, you
>>> can
>>> update arXiv e-print metadata with the journal reference, or a
>>> DOI of
>>> the journal article.
>>>
>>> Compared to an alliance with Nature or some other body, promoting
>>> 'publishing' on the arXiv has many advantages:
>>>
>>> 1.) It already exists and no agreement or negotiations need to be
>>> made to use it. There is a very mild form of control in that people
>>> that are new to the arXiv system must be 'endorsed' by existing
>>> people, but this can be gotten around until enough OWW people are
>>> themselves endorsers.
>>>
>>> 2.) It provides all the functionality we want - some sort of
>>> official
>>> stamp on an OWW document in the form of an e-print that is
>>> completely
>>> referenceable and is more like a paper than a wiki page. In fact,
>>> the arXiv supports the notion of versions, so that you can always
>>> submit a newer version of a resource, keeping complete access to
>>> older versions.
>>>
>>> 3.) There are many tools already in place, or being developed
>>> that we
>>> can integrate the arXiv with OWW. As Bill knows, the arXiv already
>>> has an API that allows you to pull content from the arXiv into OWW
>>> trivially (by just specifying e-print id). In addition, this API
>>> supplies journal references and DOI's if they are present, so it
>>> would be very easy to create references in the biblio extension for
>>> both the e-print and the published version. Also, there is an
>>> ingest
>>> API in active development (and soon to be released) with which we
>>> could easily create our long-dreamed-of 'publish' button on OWW that
>>> could automatically publish an OWW page.
>>>
>>> 4.) Journals will accept papers that have been posted on the arXiv
>>> already. In particular, Nature has committed to this as is evident
>>> on the Nature Proceedings page (http://precedings.nature.com/
>>> about#journal-submissions)
>>>
>>> "Nature Precedings hosts manuscripts that may be submitted to any
>>> journal of any publisher. Nature and all Nature journals have a
>>> policy that permits such posts on recognized pre- or e-print servers
>>> such as Nature Precedings and arXiv without affecting their
>>> eligibility for publication, whether or not such postings result in
>>> discussion on other sites and in the media. We cannot take
>>> responsibility for the possibility of scooping by competitors.
>>> Authors submitting to other journals are advised to check their
>>> policies about prior postings before sending manuscripts to Nature
>>> Precedings."
>>>
>>> (In fact, Nature Precedings was heavily inspired by the arXiv.)
>>>
>>> 5.) If the quantitative biology community grows and needs more of a
>>> refined categorization (such as synthetic biology, etc.), the arXiv
>>> can expand its categorization scheme (which is how the q-bio section
>>> started in the first place).
>>>
>>> 6.) Integrating with the arXiv integrates what OWW is doing with the
>>> physics, math and computer science communities.
>>>
>>> This is juts a brainstorm, but it seems to me like the arXiv could
>>> provide the avenue that we have been thinking about in the OWW
>>> publishing arena.
>>>
>>> Any thoughts?
>>>
>>> Cheers,
>>>
>>> Julius
>>>
>>>
>>> --------------------------------------------------------------------
>>> ----
>>> ---------------
>>> Please Reply to My Permanent Address: julius at younglucks.com
>>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>>> --------------------------------------------------------------------
>>> ----
>>> ----------------
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> OpenWetWare Steering Committee Mailing List
>>> sc at openwetware.org
>>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>
>
>
>
From julius at younglucks.com Wed Oct 31 11:52:30 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 31 Oct 2007 11:52:30 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
In-Reply-To:
References: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
<0DF8B7A0-F576-41C2-BE79-343F4A86D04A@younglucks.com>
Message-ID: <7EB82180-21FE-4A7F-966F-53E67C188377@younglucks.com>
I agree that we should have a conversation. The arXiv is pretty
hands off in general, and various communities have built resources
around the arXiv as the communities have seen fit. But it would be
good to talk about it so the arXiv has some ideas of our plans.
I am happy to write Paul Ginsparg an email, or chat with him in
person about this. I'll do this informally at first, and suggest a
conference call with OWW board/steering committee members.
How does this sound?
Julius
------------------------------------------------------------------------
---------------
Please Reply to My Permanent Address: julius at younglucks.com
http://www.openwetware.org/wiki/User:Julius_B._Lucks
------------------------------------------------------------------------
----------------
On Oct 31, 2007, at 11:30 AM, Drew Endy wrote:
> We would need to have a conversation with arXiv leadership before
> making a decision.
>
>
> On Oct 31, 2007, at 11:26 AM, Julius B. Lucks wrote:
>
>> The only thing that really has to be facilitated is the
>> endorsement system for new arXiv users. The current procedure is
>> that if you are not an endorser yourself, you need to be endorsed
>> by several endorsers. I will talk to Paul Ginsparg about this and
>> ask if we could at least seed the system with a few endorsers from
>> OWW to start the chain going.
>>
>> The advantage to going with the arXiv with respect to rolling out
>> something ourselves is that:
>>
>> 1.) The arXiv has been around since 1991 and they are very good at
>> what they do. They also are supported by Cornell, and will be
>> around for a long time to come. They also have huge recognition
>> within the open access community, and are unaffiliated with
>> publishers.
>>
>> 2.) Having worked at the arXiv, it is actually a complicated beast
>> beneath the surface. I don't think we would want to get into this
>> arena quite yet. We can always try things out on the arXiv, and
>> if it is a real hit and the arXiv does not provide the flexibility
>> we want, we can make our own system and import our old arXiv
>> postings.
>>
>> And one more previous point I forgot to add on the previous list:
>>
>> 7.) There are a bunch of 'overlay' journals built on top of the
>> arXiv already. Basically editors use the arXiv as their whole
>> submission system, put papers through peer review of some sort,
>> then create their journal as a series of links to arXiv posts. It
>> would be completely natural for OWW to create something like this
>> if we ever wanted to get into the publishing arena ourselves.
>> There is a lot of flexibility with this.
>>
>> ---------------------------------------------------------------------
>> ------------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>> ---------------------------------------------------------------------
>> -------------------
>>
>>
>>
>> On Oct 31, 2007, at 11:15 AM, Drew Endy wrote:
>>
>>> I think that this is a good idea. Either we need to do this, or
>>> something equivalent ourselves. Drew
>>>
>>>
>>> On Oct 31, 2007, at 11:04 AM, Julius B. Lucks wrote:
>>>
>>>> Hi Bill and John (and SC),
>>>>
>>>> I just had this idea so please excuse its half-bakedness. What
>>>> about
>>>> promoting 'publishing' of oww materials on arXiv.org?
>>>>
>>>> arXiv.org already has a quantitative biology section (http://
>>>> arxiv.org/list/q-bio/new), and I am willing to bet that essentially
>>>> all papers coming out of the OWW community could fit into this
>>>> section. The arXiv allows you to post paper pre-prints online for
>>>> free, and it is completely open access. Every e-print has
>>>> associated
>>>> with it a unique id, that is completely referenceable in papers,
>>>> etc. In addition, if you do publish your paper in a journal,
>>>> you can
>>>> update arXiv e-print metadata with the journal reference, or a
>>>> DOI of
>>>> the journal article.
>>>>
>>>> Compared to an alliance with Nature or some other body, promoting
>>>> 'publishing' on the arXiv has many advantages:
>>>>
>>>> 1.) It already exists and no agreement or negotiations need to be
>>>> made to use it. There is a very mild form of control in that
>>>> people
>>>> that are new to the arXiv system must be 'endorsed' by existing
>>>> people, but this can be gotten around until enough OWW people are
>>>> themselves endorsers.
>>>>
>>>> 2.) It provides all the functionality we want - some sort of
>>>> official
>>>> stamp on an OWW document in the form of an e-print that is
>>>> completely
>>>> referenceable and is more like a paper than a wiki page. In fact,
>>>> the arXiv supports the notion of versions, so that you can always
>>>> submit a newer version of a resource, keeping complete access to
>>>> older versions.
>>>>
>>>> 3.) There are many tools already in place, or being developed
>>>> that we
>>>> can integrate the arXiv with OWW. As Bill knows, the arXiv already
>>>> has an API that allows you to pull content from the arXiv into OWW
>>>> trivially (by just specifying e-print id). In addition, this API
>>>> supplies journal references and DOI's if they are present, so it
>>>> would be very easy to create references in the biblio extension for
>>>> both the e-print and the published version. Also, there is an
>>>> ingest
>>>> API in active development (and soon to be released) with which we
>>>> could easily create our long-dreamed-of 'publish' button on OWW
>>>> that
>>>> could automatically publish an OWW page.
>>>>
>>>> 4.) Journals will accept papers that have been posted on the arXiv
>>>> already. In particular, Nature has committed to this as is evident
>>>> on the Nature Proceedings page (http://precedings.nature.com/
>>>> about#journal-submissions)
>>>>
>>>> "Nature Precedings hosts manuscripts that may be submitted to any
>>>> journal of any publisher. Nature and all Nature journals have a
>>>> policy that permits such posts on recognized pre- or e-print
>>>> servers
>>>> such as Nature Precedings and arXiv without affecting their
>>>> eligibility for publication, whether or not such postings result in
>>>> discussion on other sites and in the media. We cannot take
>>>> responsibility for the possibility of scooping by competitors.
>>>> Authors submitting to other journals are advised to check their
>>>> policies about prior postings before sending manuscripts to Nature
>>>> Precedings."
>>>>
>>>> (In fact, Nature Precedings was heavily inspired by the arXiv.)
>>>>
>>>> 5.) If the quantitative biology community grows and needs more of a
>>>> refined categorization (such as synthetic biology, etc.), the arXiv
>>>> can expand its categorization scheme (which is how the q-bio
>>>> section
>>>> started in the first place).
>>>>
>>>> 6.) Integrating with the arXiv integrates what OWW is doing with
>>>> the
>>>> physics, math and computer science communities.
>>>>
>>>> This is juts a brainstorm, but it seems to me like the arXiv could
>>>> provide the avenue that we have been thinking about in the OWW
>>>> publishing arena.
>>>>
>>>> Any thoughts?
>>>>
>>>> Cheers,
>>>>
>>>> Julius
>>>>
>>>>
>>>> -------------------------------------------------------------------
>>>> -----
>>>> ---------------
>>>> Please Reply to My Permanent Address: julius at younglucks.com
>>>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>>>> -------------------------------------------------------------------
>>>> -----
>>>> ----------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> OpenWetWare Steering Committee Mailing List
>>>> sc at openwetware.org
>>>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>>
>>
>>
>>
>
-------------- next part --------------
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From julius at younglucks.com Wed Oct 31 16:37:52 2007
From: julius at younglucks.com (Julius B. Lucks)
Date: Wed, 31 Oct 2007 16:37:52 -0400
Subject: [OWW-SC] OWW Publishing with arXiv.org
In-Reply-To:
References: <4AC31555-3E65-41C6-AD83-BB690C9E5D45@younglucks.com>
<0DF8B7A0-F576-41C2-BE79-343F4A86D04A@younglucks.com>
Message-ID: <1AFBE400-6B3D-46A4-9FC3-9044C34052F1@younglucks.com>
Hi Drew,
I just spoke to Paul Ginsparg and he said it makes perfect sense.
There is not even an endorsement issue if the e-prints are submitted
with email addresses from academic institutions.
So it is really up to the OWW community as to how best use arXiv as a
resource.
Cheers,
Julius
On Oct 31, 2007, at 11:30 AM, Drew Endy wrote:
> We would need to have a conversation with arXiv leadership before
> making a decision.
>
>
> On Oct 31, 2007, at 11:26 AM, Julius B. Lucks wrote:
>
>> The only thing that really has to be facilitated is the
>> endorsement system for new arXiv users. The current procedure is
>> that if you are not an endorser yourself, you need to be endorsed
>> by several endorsers. I will talk to Paul Ginsparg about this and
>> ask if we could at least seed the system with a few endorsers from
>> OWW to start the chain going.
>>
>> The advantage to going with the arXiv with respect to rolling out
>> something ourselves is that:
>>
>> 1.) The arXiv has been around since 1991 and they are very good at
>> what they do. They also are supported by Cornell, and will be
>> around for a long time to come. They also have huge recognition
>> within the open access community, and are unaffiliated with
>> publishers.
>>
>> 2.) Having worked at the arXiv, it is actually a complicated beast
>> beneath the surface. I don't think we would want to get into this
>> arena quite yet. We can always try things out on the arXiv, and
>> if it is a real hit and the arXiv does not provide the flexibility
>> we want, we can make our own system and import our old arXiv
>> postings.
>>
>> And one more previous point I forgot to add on the previous list:
>>
>> 7.) There are a bunch of 'overlay' journals built on top of the
>> arXiv already. Basically editors use the arXiv as their whole
>> submission system, put papers through peer review of some sort,
>> then create their journal as a series of links to arXiv posts. It
>> would be completely natural for OWW to create something like this
>> if we ever wanted to get into the publishing arena ourselves.
>> There is a lot of flexibility with this.
>>
>> ---------------------------------------------------------------------
>> ------------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>> ---------------------------------------------------------------------
>> -------------------
>>
>>
>>
>> On Oct 31, 2007, at 11:15 AM, Drew Endy wrote:
>>
>>> I think that this is a good idea. Either we need to do this, or
>>> something equivalent ourselves. Drew
>>>
>>>
>>> On Oct 31, 2007, at 11:04 AM, Julius B. Lucks wrote:
>>>
>>>> Hi Bill and John (and SC),
>>>>
>>>> I just had this idea so please excuse its half-bakedness. What
>>>> about
>>>> promoting 'publishing' of oww materials on arXiv.org?
>>>>
>>>> arXiv.org already has a quantitative biology section (http://
>>>> arxiv.org/list/q-bio/new), and I am willing to bet that essentially
>>>> all papers coming out of the OWW community could fit into this
>>>> section. The arXiv allows you to post paper pre-prints online for
>>>> free, and it is completely open access. Every e-print has
>>>> associated
>>>> with it a unique id, that is completely referenceable in papers,
>>>> etc. In addition, if you do publish your paper in a journal,
>>>> you can
>>>> update arXiv e-print metadata with the journal reference, or a
>>>> DOI of
>>>> the journal article.
>>>>
>>>> Compared to an alliance with Nature or some other body, promoting
>>>> 'publishing' on the arXiv has many advantages:
>>>>
>>>> 1.) It already exists and no agreement or negotiations need to be
>>>> made to use it. There is a very mild form of control in that
>>>> people
>>>> that are new to the arXiv system must be 'endorsed' by existing
>>>> people, but this can be gotten around until enough OWW people are
>>>> themselves endorsers.
>>>>
>>>> 2.) It provides all the functionality we want - some sort of
>>>> official
>>>> stamp on an OWW document in the form of an e-print that is
>>>> completely
>>>> referenceable and is more like a paper than a wiki page. In fact,
>>>> the arXiv supports the notion of versions, so that you can always
>>>> submit a newer version of a resource, keeping complete access to
>>>> older versions.
>>>>
>>>> 3.) There are many tools already in place, or being developed
>>>> that we
>>>> can integrate the arXiv with OWW. As Bill knows, the arXiv already
>>>> has an API that allows you to pull content from the arXiv into OWW
>>>> trivially (by just specifying e-print id). In addition, this API
>>>> supplies journal references and DOI's if they are present, so it
>>>> would be very easy to create references in the biblio extension for
>>>> both the e-print and the published version. Also, there is an
>>>> ingest
>>>> API in active development (and soon to be released) with which we
>>>> could easily create our long-dreamed-of 'publish' button on OWW
>>>> that
>>>> could automatically publish an OWW page.
>>>>
>>>> 4.) Journals will accept papers that have been posted on the arXiv
>>>> already. In particular, Nature has committed to this as is evident
>>>> on the Nature Proceedings page (http://precedings.nature.com/
>>>> about#journal-submissions)
>>>>
>>>> "Nature Precedings hosts manuscripts that may be submitted to any
>>>> journal of any publisher. Nature and all Nature journals have a
>>>> policy that permits such posts on recognized pre- or e-print
>>>> servers
>>>> such as Nature Precedings and arXiv without affecting their
>>>> eligibility for publication, whether or not such postings result in
>>>> discussion on other sites and in the media. We cannot take
>>>> responsibility for the possibility of scooping by competitors.
>>>> Authors submitting to other journals are advised to check their
>>>> policies about prior postings before sending manuscripts to Nature
>>>> Precedings."
>>>>
>>>> (In fact, Nature Precedings was heavily inspired by the arXiv.)
>>>>
>>>> 5.) If the quantitative biology community grows and needs more of a
>>>> refined categorization (such as synthetic biology, etc.), the arXiv
>>>> can expand its categorization scheme (which is how the q-bio
>>>> section
>>>> started in the first place).
>>>>
>>>> 6.) Integrating with the arXiv integrates what OWW is doing with
>>>> the
>>>> physics, math and computer science communities.
>>>>
>>>> This is juts a brainstorm, but it seems to me like the arXiv could
>>>> provide the avenue that we have been thinking about in the OWW
>>>> publishing arena.
>>>>
>>>> Any thoughts?
>>>>
>>>> Cheers,
>>>>
>>>> Julius
>>>>
>>>>
>>>> -------------------------------------------------------------------
>>>> -----
>>>> ---------------
>>>> Please Reply to My Permanent Address: julius at younglucks.com
>>>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>>>> -------------------------------------------------------------------
>>>> -----
>>>> ----------------
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> OpenWetWare Steering Committee Mailing List
>>>> sc at openwetware.org
>>>> http://mailman.mit.edu/mailman/listinfo/oww-sc
>>>
>>
>>
>>
>