From jasonk at MIT.EDU Thu Mar 1 11:58:56 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Thu, 1 Mar 2007 11:58:56 -0500 Subject: [OWW-SC] first virtual SC meeting - yikes! Next Friday (3/9) at Noon EST Message-ID: <7c085c480703010858m1f158c7fr677a94e847152f4b@mail.gmail.com> Hi SC, In an effort to speed the transition from an MIT-centered steering committee to one culled from the community at large, we're going to try out an all-virtual SC meeting. this may be a bad idea :) we'll see. We're experimenting with a few options this week on how to do it, more info to follow. We'll likely be calling into a phone system. Also, Austin has been implementing a chat that will be integrated with the wiki, so we can play around with that as well. As a reminder, please help specify SC positions that you think would be useful here: http://openwetware.org/wiki/OpenWetWare:Steering_committee/What_positions_would_be_useful%3F (If you or someone you know would be good for a position, please encourage them to volunteer) Also, add to the agenda here: http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting If you are planning on participating in the meeting, please send me an email. Thanks! jason From austin at csail.mit.edu Thu Mar 1 13:05:30 2007 From: austin at csail.mit.edu (Austin Che) Date: Thu, 01 Mar 2007 13:05:30 -0500 Subject: [OWW-SC] first virtual SC meeting - yikes! Next Friday (3/9) at Noon EST In-Reply-To: <7c085c480703010858m1f158c7fr677a94e847152f4b@mail.gmail.com> (Jason Kelly's message of "Thu, 1 Mar 2007 11:58:56 -0500") References: <7c085c480703010858m1f158c7fr677a94e847152f4b@mail.gmail.com> Message-ID: <877iu0j0ut.fsf@nitsua.mit.edu> > We're experimenting with a few options this week on how to do it, more > info to follow. We'll likely be calling into a phone system. Also, > Austin has been implementing a chat that will be integrated with the > wiki, so we can play around with that as well. I just sent a message to the discuss list about the chat. I would suggest picking a fixed page to use for online sc meetings. The page with the agenda seems good http://openwetware.org/wiki/Special:Chat/OpenWetWare:Steering_committee_next_meeting -- Austin Che (617)253-5899 From skosuri at MIT.EDU Sat Mar 3 19:30:17 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Sat, 3 Mar 2007 19:30:17 -0500 Subject: [OWW-SC] E. coli Wiki Message-ID: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> Hi all, Jim Hu at Texas A&M is involved with the E. coli reannotation efforts and is leading up the wiki efforts. The wiki is still exerimental, but it's pretty cool. Have a look here: http://ecoliwiki.net/colipedia/index.php There are some cool aspects... check out the gene pages here: http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page Let me know if anyone wants access. Sri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070303/2b3ba375/attachment.htm From skosuri at MIT.EDU Sat Mar 3 20:38:26 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Sat, 3 Mar 2007 20:38:26 -0500 Subject: [OWW-SC] The New Science of Sharing Message-ID: <2b0cb7a10703031738o637b894bn66fda4ca386b399a@mail.gmail.com> An articleon from BusinessWeek... there is a favorable mention of OpenWetWare somewhere on the second page: As large-scale scientific collaborations become the norm, scientists will > rely increasingly on distributed methods of collecting data, verifying > discoveries, and testing hypotheses not only to speed things up but to > improve the veracity of scientific knowledge itself. For example, rapid, > iterative, and open-access publishing will engage a much greater proportion > of the scientific community in the peer-review process. Conventional > paper-based scientific journals, meanwhile, will be augmented by dynamic > publishing tools such as blogs, wikis, Web-enabled RSS feeds, and podcasts > that turn scientific publications into living documents. Projects such as > MIT's OpenWetWare are already doing this. > > http://www.businessweek.com/innovate/content/mar2007/id20070302_219704.htm?chan=technology_technology+index+page_more+of+today%27s+top+stories Apparently, we are again an "MIT" project... Apologies to those of you who are not. Sri http://openwetware.org/wiki/Sriram_Kosuri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070303/79ddee5d/attachment.htm From austin at csail.mit.edu Sun Mar 4 17:01:07 2007 From: austin at csail.mit.edu (Austin Che) Date: Sun, 04 Mar 2007 17:01:07 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> (Sri Kosuri's message of "Sat, 3 Mar 2007 19:30:17 -0500") References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> Message-ID: <87tzx0fz30.fsf@nitsua.mit.edu> > There are some cool aspects... check out the gene pages here: > http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page > > Let me know if anyone wants access. A random thought. As it seems like they don't have a general account management policy yet (or many users), maybe we can convince them to use OpenID and to allow all OWW users to log in? And as it seems like different bio-wikis are popping up all over the place, we can see if we can make OWW a general wiki that can point people to more specific wikis. OWW can handle the general account management for all of these wikis (as we have to do that anyway) and OWW would also provide a large user base for these wikis that get started. -- Austin Che (617)253-5899 From lucks at fas.harvard.edu Sun Mar 4 17:08:05 2007 From: lucks at fas.harvard.edu (Julius Lucks) Date: Sun, 4 Mar 2007 17:08:05 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: <87tzx0fz30.fsf@nitsua.mit.edu> References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> Message-ID: <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> I think this is a great idea. Julius ----------------------------------------------------- http://openwetware.org/wiki/User:Lucks ----------------------------------------------------- On Mar 4, 2007, at 5:01 PM, Austin Che wrote: > >> There are some cool aspects... check out the gene pages here: >> http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page >> >> Let me know if anyone wants access. > > A random thought. As it seems like they don't have a general > account management policy yet (or many users), maybe we can > convince them to use OpenID and to allow all OWW users to log in? > > And as it seems like different bio-wikis are popping up all over > the place, we can see if we can make OWW a general wiki that can > point people to more specific wikis. OWW can handle the general > account management for all of these wikis (as we have to do that > anyway) and OWW would also provide a large user base for these > wikis that get started. > > -- > Austin Che (617)253-5899 > _______________________________________________ > OpenWetWare Steering Committee Mailing List > sc at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-sc -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070304/1008038c/attachment.htm From vincent.rouilly at gmail.com Mon Mar 5 04:51:51 2007 From: vincent.rouilly at gmail.com (Vincent Rouilly) Date: Mon, 5 Mar 2007 09:51:51 +0000 Subject: [OWW-SC] E. coli Wiki In-Reply-To: <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> Message-ID: I also think it is a good idea. As an OWW user, it is true that I would like to be able to contribute to other Bio-Wikis, without the hassle of dealing with multiple accounts and registration processes. But, on the other hand, I am not too sure how happy bio-wikis would be to give up on the control of their own user community. From a technical point of view, would it be possible to offer to bio- wikis a way to combine their own user management with the ability to also authenticate against an OWW OpenID server ? If it is possible, at the end of the day, the only thing you need to convince them is that by default they would trust OWW users. Vincent. On 4 Mar 2007, at 22:08, Julius Lucks wrote: > I think this is a great idea. > > Julius > > ----------------------------------------------------- > http://openwetware.org/wiki/User:Lucks > ----------------------------------------------------- > > > > On Mar 4, 2007, at 5:01 PM, Austin Che wrote: > >> >>> There are some cool aspects... check out the gene pages here: >>> http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page >>> >>> Let me know if anyone wants access. >> >> A random thought. As it seems like they don't have a general >> account management policy yet (or many users), maybe we can >> convince them to use OpenID and to allow all OWW users to log in? >> >> And as it seems like different bio-wikis are popping up all over >> the place, we can see if we can make OWW a general wiki that can >> point people to more specific wikis. OWW can handle the general >> account management for all of these wikis (as we have to do that >> anyway) and OWW would also provide a large user base for these >> wikis that get started. >> >> -- >> Austin Che (617)253-5899 >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070305/67154d1d/attachment.htm From skosuri at MIT.EDU Mon Mar 5 12:54:49 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Mon, 5 Mar 2007 12:54:49 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> Message-ID: <2b0cb7a10703050954g151072c3j9909813854732584@mail.gmail.com> > > From a technical point of view, would it be possible to offer to bio-wikis > a way to combine their own user management with the ability to also > authenticate against an OWW OpenID server ? > If it is possible, at the end of the day, the only thing you need to > convince them is that by default they would trust OWW users. > > Yes, Currently, with the private wiki test, the admins of the private wikis can grant access to whichever OWW users they care to give access to. It's already been implemented. We should definitely continue to approach other wikis, but there are many community annotation wikis that will pop up over the next year or so... E. coli -> as mentioned SGD (yeast) -> moving community efforts to wiki Myxo -> already have community annotation wiki So, we'll see where everything leads... but it seems like a good idea to be offering the service already. Sri On 3/5/07, Vincent Rouilly wrote: > > > I also think it is a good idea. As an OWW user, it is true that I would > like to be able to contribute to other Bio-Wikis, without the hassle of > dealing with multiple accounts and registration processes. > > But, on the other hand, I am not too sure how happy bio-wikis would be to > give up on the control of their own user community. > > From a technical point of view, would it be possible to offer to bio-wikis > a way to combine their own user management with the ability to also > authenticate against an OWW OpenID server ? > If it is possible, at the end of the day, the only thing you need to > convince them is that by default they would trust OWW users. > > Vincent. > > > On 4 Mar 2007, at 22:08, Julius Lucks wrote: > > I think this is a great idea. > Julius > > ----------------------------------------------------- > http://openwetware.org/wiki/User:Lucks > ----------------------------------------------------- > > > > On Mar 4, 2007, at 5:01 PM, Austin Che wrote: > > > There are some cool aspects... check out the gene pages here: > http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page > > Let me know if anyone wants access. > > > A random thought. As it seems like they don't have a general > account management policy yet (or many users), maybe we can > convince them to use OpenID and to allow all OWW users to log in? > > And as it seems like different bio-wikis are popping up all over > the place, we can see if we can make OWW a general wiki that can > point people to more specific wikis. OWW can handle the general > account management for all of these wikis (as we have to do that > anyway) and OWW would also provide a large user base for these > wikis that get started. > > -- > Austin Che (617)253-5899 > _______________________________________________ > 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 > > > > _______________________________________________ > OpenWetWare Steering Committee Mailing List > sc at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-sc > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070305/db5a17ab/attachment.htm From johncumbers at gmail.com Mon Mar 5 16:29:23 2007 From: johncumbers at gmail.com (John Cumbers) Date: Mon, 5 Mar 2007 16:29:23 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: <2b0cb7a10703050954g151072c3j9909813854732584@mail.gmail.com> References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> <2b0cb7a10703050954g151072c3j9909813854732584@mail.gmail.com> Message-ID: so you get a unique id to log in with for openid, e.g (https://johncumbers.myopenid.com/), for oww, currently the equivalent is http://openwetware.org/wiki/User:Johncumbers which is a bit of a mouthful. If we are serious about hosting openID's (which I think we should be) could we look in purchasing www.oww.org from whoever owns it (worth $1000 maybe?) so that we could have something shorter like: http://johncumbers.oww.org or maybe this, (without the new domain) http://Johncumbers.openwetware.org/ not a big deal either way, cheers, John On 3/5/07, Sri Kosuri wrote: > > From a technical point of view, would it be possible to offer to bio-wikis > > a way to combine their own user management with the ability to also > > authenticate against an OWW OpenID server ? > > If it is possible, at the end of the day, the only thing you need to > > convince them is that by default they would trust OWW users. > > > > > Yes, > > Currently, with the private wiki test, the admins of the private wikis can > grant access to whichever OWW users they care to give access to. It's > already been implemented. > > We should definitely continue to approach other wikis, but there are many > community annotation wikis that will pop up over the next year or so... > E. coli -> as mentioned > SGD (yeast) -> moving community efforts to wiki > Myxo -> already have community annotation wiki > > So, we'll see where everything leads... but it seems like a good idea to > be offering the service already. > > Sri > > On 3/5/07, Vincent Rouilly wrote: > > > > > > I also think it is a good idea. As an OWW user, it is true that I would > > like to be able to contribute to other Bio-Wikis, without the hassle of > > dealing with multiple accounts and registration processes. > > > > But, on the other hand, I am not too sure how happy bio-wikis would be > > to give up on the control of their own user community. > > > > From a technical point of view, would it be possible to offer to > > bio-wikis a way to combine their own user management with the ability to > > also authenticate against an OWW OpenID server ? > > If it is possible, at the end of the day, the only thing you need to > > convince them is that by default they would trust OWW users. > > > > Vincent. > > > > > > On 4 Mar 2007, at 22:08, Julius Lucks wrote: > > > > I think this is a great idea. > > Julius > > > > ----------------------------------------------------- > > http://openwetware.org/wiki/User:Lucks > > ----------------------------------------------------- > > > > > > > > On Mar 4, 2007, at 5:01 PM, Austin Che wrote: > > > > > > There are some cool aspects... check out the gene pages here: > > http://ecoliwiki.net/colipedia/index.php/lacI:On_One_Page > > > > Let me know if anyone wants access. > > > > > > A random thought. As it seems like they don't have a general > > account management policy yet (or many users), maybe we can > > convince them to use OpenID and to allow all OWW users to log in? > > > > And as it seems like different bio-wikis are popping up all over > > the place, we can see if we can make OWW a general wiki that can > > point people to more specific wikis. OWW can handle the general > > account management for all of these wikis (as we have to do that > > anyway) and OWW would also provide a large user base for these > > wikis that get started. > > > > -- > > Austin Che (617)253-5899 > > _______________________________________________ > > 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 > > > > > > > > _______________________________________________ > > 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 > > -- John Cumbers, Graduate Student in Computational Biology Brown University, Ecology and Evolutionary Biology, Box G-W 80 Waterman Street, Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070305/3d90cd6c/attachment.htm From austin at csail.mit.edu Mon Mar 5 16:38:41 2007 From: austin at csail.mit.edu (Austin Che) Date: Mon, 05 Mar 2007 16:38:41 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: (John Cumbers's message of "Mon, 5 Mar 2007 16:29:23 -0500") References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> <2b0cb7a10703050954g151072c3j9909813854732584@mail.gmail.com> Message-ID: <87fy8je5ge.fsf@nitsua.mit.edu> > so you get a unique id to log in with for openid, > e.g (https://johncumbers.myopenid.com/), > > for oww, currently the equivalent is > http://openwetware.org/wiki/User:Johncumbers > which is a bit of a mouthful. Not really clear why it matters that it's a mouthful. Who'll be saying it anyway. But I added a redirect so that the following works. Not sure if it's any better. http://openwetware.org/user/Johncumbers > or maybe this, (without the new domain) > http://Johncumbers.openwetware.org/ We're currently using these third level domains for dewikifying and so we'd have to decide what gets priority. Something like foo.user.openwetware.org could work. -- Austin Che (617)253-5899 From tk at csail.mit.edu Mon Mar 5 17:37:06 2007 From: tk at csail.mit.edu (Tom Knight) Date: Mon, 5 Mar 2007 17:37:06 -0500 Subject: [OWW-SC] wikiomics.org Message-ID: <0550f52beb7b7e87d9eef24ed760ebc7@csail.mit.edu> Another biology wiki centered on bioinformatics: http://wikiomics.org -------------- next part -------------- A non-text attachment was scrubbed... Name: smime.p7s Type: application/pkcs7-signature Size: 6620 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-sc/attachments/20070305/24bd5781/attachment.bin From martin_jambon at emailuser.net Mon Mar 5 18:01:17 2007 From: martin_jambon at emailuser.net (Martin Jambon) Date: Mon, 5 Mar 2007 15:01:17 -0800 (PST) Subject: [OWW-SC] wikiomics.org In-Reply-To: <0550f52beb7b7e87d9eef24ed760ebc7@csail.mit.edu> References: <0550f52beb7b7e87d9eef24ed760ebc7@csail.mit.edu> Message-ID: On Mon, 5 Mar 2007, Tom Knight wrote: > Another biology wiki centered on bioinformatics: > > http://wikiomics.org Thanks for noticing! :-) I am currently in charge of maintaining the Wikiomics server and the similarity with OWW is the reason why I am a ((extremely) passive) member of OWW's steering committee. Martin -- Martin Jambon http://martin.jambon.free.fr From johncumbers at gmail.com Mon Mar 5 22:00:17 2007 From: johncumbers at gmail.com (John Cumbers) Date: Mon, 5 Mar 2007 22:00:17 -0500 Subject: [OWW-SC] E. coli Wiki In-Reply-To: <87fy8je5ge.fsf@nitsua.mit.edu> References: <2b0cb7a10703031630g3af24d25pda20b04e78ea1260@mail.gmail.com> <87tzx0fz30.fsf@nitsua.mit.edu> <5D14B059-8A0C-4A0C-8AC2-8E5854BBCD51@fas.harvard.edu> <2b0cb7a10703050954g151072c3j9909813854732584@mail.gmail.com> <87fy8je5ge.fsf@nitsua.mit.edu> Message-ID: you'd just be typing it to log-in to other places, so the shorter the better no? John On 3/5/07, Austin Che wrote: > > > > so you get a unique id to log in with for openid, > > e.g (https://johncumbers.myopenid.com/), > > > > for oww, currently the equivalent is > > http://openwetware.org/wiki/User:Johncumbers > > which is a bit of a mouthful. > > Not really clear why it matters that it's a mouthful. Who'll be > saying it anyway. But I added a redirect so that the following > works. Not sure if it's any better. > http://openwetware.org/user/Johncumbers > > > or maybe this, (without the new domain) > > http://Johncumbers.openwetware.org/ > > We're currently using these third level domains for dewikifying > and so we'd have to decide what gets priority. Something like > foo.user.openwetware.org could work. > > -- > Austin Che (617)253-5899 > -- John Cumbers, Graduate Student in Computational Biology Brown University, Ecology and Evolutionary Biology, Box G-W 80 Waterman Street, Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070305/d12c9a6b/attachment.htm From jasonk at MIT.EDU Wed Mar 7 08:21:59 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 7 Mar 2007 08:21:59 -0500 Subject: [OWW-SC] SC Meeting Friday @ Noon in CYBERSPACE ;) Message-ID: <7c085c480703070521x118524fds2c41f58a8fdfd760@mail.gmail.com> Hi Folks, Just a reminder that the SC meeting will be Friday at Noon EST, and everyone will be calling in (including the MIT folks). Some rules to make this more likely to succeed: 1. No cellphones 2. Use headphones or a handset --> no speakers as they produce an echo 3. Mute mike when not talking to keep down background noise We'll also be using the new OWW chat function, so please enable chat in your preferences. My Preferences-->Misc-->Enable wiki chat. That chat page will be: http://openwetware.org/wiki/Special:Chat/OpenWetWare:Steering_committee/Meeting_-_March_2007 We'll be calling into the MIT conf call system since that worked pretty well last time, the number will be: 617-324-7520 Please call in at 11:55 if possible so we can iron out the kinks... The agenda is here, please add/edit: http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting Thanks! jason From endy at MIT.EDU Wed Mar 7 14:28:07 2007 From: endy at MIT.EDU (Drew Endy) Date: Wed, 7 Mar 2007 14:28:07 -0500 Subject: [OWW-SC] quick question Message-ID: <07C553CA-2E9A-4002-A1ED-AF19A5610DF6@mit.edu> Can anybody give a quick estimate of current number of labs and users on OWW? Thanks! Drew From endy at MIT.EDU Wed Mar 7 14:51:44 2007 From: endy at MIT.EDU (Drew Endy) Date: Wed, 7 Mar 2007 14:51:44 -0500 Subject: [OWW-SC] quick question In-Reply-To: <6e9f40380703071149p23e7bb7as5b14068384b84c4b@mail.gmail.com> References: <07C553CA-2E9A-4002-A1ED-AF19A5610DF6@mit.edu> <6e9f40380703071149p23e7bb7as5b14068384b84c4b@mail.gmail.com> Message-ID: <33FC5778-B42E-405E-9CB7-2569748783F7@mit.edu> thank you! On Mar 7, 2007, at 2:49 PM, Reshma Shetty wrote: > 2368 users and ~90 labs. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070307/9eacdcb6/attachment.htm From skosuri at MIT.EDU Wed Mar 7 15:09:40 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Wed, 7 Mar 2007 15:09:40 -0500 Subject: [OWW-SC] quick question In-Reply-To: <07C553CA-2E9A-4002-A1ED-AF19A5610DF6@mit.edu> References: <07C553CA-2E9A-4002-A1ED-AF19A5610DF6@mit.edu> Message-ID: <2b0cb7a10703071209sae46b14ybfb80c8c6aa54a0@mail.gmail.com> 2368 Users 95 Labs listed on Labs page (probably more) ~40,000 pageviews & 7000 visits / day Sri On 3/7/07, Drew Endy wrote: > > Can anybody give a quick estimate of current number of labs and users > on OWW? > > Thanks! > Drew > _______________________________________________ > OpenWetWare Steering Committee Mailing List > sc at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-sc > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070307/f526ac93/attachment.htm From austin at csail.mit.edu Thu Mar 8 22:08:43 2007 From: austin at csail.mit.edu (Austin Che) Date: Thu, 08 Mar 2007 22:08:43 -0500 Subject: [OWW-SC] SC Meeting Friday @ Noon in CYBERSPACE ;) In-Reply-To: <7c085c480703070521x118524fds2c41f58a8fdfd760@mail.gmail.com> (Jason Kelly's message of "Wed, 7 Mar 2007 08:21:59 -0500") References: <7c085c480703070521x118524fds2c41f58a8fdfd760@mail.gmail.com> Message-ID: <87vehbi05g.fsf@nitsua.mit.edu> > We'll be calling into the MIT conf call system since that worked > pretty well last time, the number will be: > 617-324-7520 I've set up an experimental voip bridge so people can call in for free from their computers. If you dial 16173247520 at asterisk.austinche.name using any SIP softphone, you should get in to the above system. If you want to test it out beforehand, you can also try calling any other MIT number. 16172535899 at asterisk.austinche.name should call my office. For more fun, call 16172533696 at asterisk.austinche.name to get the MIT's automated information line. It should let you know whether your software/the system is working. I would guess any SIP softphone client should work http://en.wikipedia.org/wiki/List_of_SIP_software#SIP_clients I think the sjphone client or the gizmo project should work fine, but not tested by me... You shouldn't need to register with anyhwere. Just dial the above number. Update: I just did a test and it works fine except right now it seems that the MIT VoIP system only allows one outbound call at a time. I'm going to try to set up a conference bridge on my own system so that multiple people can call in but if that doesn't work, whoever calls the conference number first tomorrow wins :) Again, dial this number for tomorrow: 16173247520 at asterisk.austinche.name -- Austin Che (617)253-5899 From austin at csail.mit.edu Fri Mar 9 10:30:04 2007 From: austin at csail.mit.edu (Austin Che) Date: Fri, 09 Mar 2007 10:30:04 -0500 Subject: [OWW-SC] SC Meeting Friday @ Noon in CYBERSPACE ;) In-Reply-To: <87vehbi05g.fsf@nitsua.mit.edu> (Austin Che's message of "Thu, 08 Mar 2007 22:08:43 -0500") References: <7c085c480703070521x118524fds2c41f58a8fdfd760@mail.gmail.com> <87vehbi05g.fsf@nitsua.mit.edu> Message-ID: <87zm6m77ur.fsf@nitsua.mit.edu> In case anyone was confused, you can either call into the meeting via a normal phone line at 617-324-7520 OR if you are in front a Internet connected computer and don't want to pay any phone charges (such as for Skype), I've set up a voip conference bridge. I've now set it up so an unlimited number of people can connect. Just call oww at asterisk.austinche.name at any time via any sip client (we've tested with Gizmo, twinkle, firefly). You'll be automatically be put into a conference room with everyone else calling this sip number. At the appropriate time, I'll call 6173247520 and bridge everyone who calls in via sip to those who call in via the phone line. -- Austin Che (617)253-5899 From jasonk at MIT.EDU Mon Mar 12 16:04:46 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Mon, 12 Mar 2007 16:04:46 -0400 Subject: [OWW-SC] March meeting notes + please sign up for meeting time! Message-ID: <7c085c480703121304h301a4bbhe20b8c1474efe969@mail.gmail.com> Hi SC, Well, the virtual meeting went quite well -- thanks John for suggesting it! We decided to stick with it in the future. There is a chat transcript and an mp3 recording of the conference call for those of you that missed it, it's thrilling listening I'm sure :) They can be found here along with meeting notes: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_March_2007 We had some people volunteer for SC chairs, you can find them here: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Chairs Not all the positions are filled, and anyone can sign up who is interested -- so take a look and and sign up! The SC chairs will be responsible for writing up a brief report on their area 2 days before the SC meeting on the notes page here: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_April_2007 They will also bring up any issues for discussion during the SC meeting in their area. Hopefully this makes the meetings more efficient. Finally, with the new virtual SC meeting we can choose a new date / time, so that everyone can make it, please sign up for the time that works best for you here: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_time Thanks! jason From macowell at gmail.com Tue Mar 13 15:04:53 2007 From: macowell at gmail.com (Mackenzie Cowell) Date: Tue, 13 Mar 2007 15:04:53 -0400 Subject: [OWW-SC] Fwd: [fc-boston] Talk on Open Access/Public Library of Science Wed, 7:30, Harvard U. In-Reply-To: <55bea5620703121838m7b314afakbcb738538d3f29da@mail.gmail.com> References: <55bea5620703121833y3185db89w9dcb3cac7aac0318@mail.gmail.com> <55bea5620703121838m7b314afakbcb738538d3f29da@mail.gmail.com> Message-ID: <54746a3f0703131204r1ae2da22n82269ee22afb0c21@mail.gmail.com> *Gavin Yamey on "Opening Up to Open Access: What can other disciplines learn from the Sciences?" *FYI: "Gavin Yamey MD, Senior Editor of PLoS Medicine ( http://www.plosmedicine.org) and Consulting Editor of PLoS Neglected Tropical Diseases (http://www.plosntds.org), shares his experiences in the open access movement and explores possible avenues for its expansion to other fields, with a focus on the social sciences and humanities." details below. ---------- Forwarded message ---------- From: Elizabeth Stark < estark at law.harvard.edu> Date: Mar 12, 2007 9:38 PM Subject: [fc-boston] Talk on Open Access/Public Library of Science Wed, 7:30, Harvard U. To: freeculture-boston at hcs.harvard.edu Hey Boston Free Culture Folks, Thought you might be interested in coming to this event on Wednesday. Also, we haven't forgotten about you-- we're planning a BFC digital music event for April and a meetup in the near future. Details to come. Elizabeth -------------------------------------------* Gavin Yamey on "Opening Up to Open Access: What can other disciplines learn from the Sciences?"* * Wednesday, March 14, 7:30pm* Harvard University Sever Hall Room 202 Map: http://map.harvard.edu/level3.cfm?mapname=camb_allston&tile=F7&quadrant=B&series=W What can academics do to ensure that their research results are included in the growing "knowledge commons?" Gavin Yamey MD, Senior Editor of PLoS Medicine (http://www.plosmedicine.org) and Consulting Editor of PLoS Neglected Tropical Diseases (http://www.plosntds.org), shares his experiences in the open access movement and explores possible avenues for its expansion to other fields, with a focus on the social sciences and humanities. The Public Library of Science (http://www.plos.org), an international non-profit grassroots movement of scientists and physicians, is working to change the status quo by campaigning to make the biomedical literature a freely available global public good. PLoS now publishes 7 open access journals, and is urging traditional biomedical publishers to adopt more socially responsive practices. Will other fields follow in their footsteps? Dessert will be served. Sponsored by the Berkman Center ( http://cyber.law.harvard.edu ) and Harvard College Free Culture ( http://hcs.harvard.edu/freeculture). This is a lead up event to the 2007 Internet & Society Conference ( http://www.is2k7.org), which will be held on the Harvard Campus on June 1, 2007. _______________________________________________ Freeculture-boston mailing list Freeculture-boston at lists.hcs.harvard.edu http://lists.hcs.harvard.edu/mailman/listinfo/freeculture-boston -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20070313/63c61943/attachment.htm From austin at csail.mit.edu Thu Mar 15 14:00:12 2007 From: austin at csail.mit.edu (Austin Che) Date: Thu, 15 Mar 2007 14:00:12 -0400 Subject: [OWW-SC] wikipedia summer of code Message-ID: <87mz2ewfo3.fsf@nitsua.mit.edu> If anyone has code ideas that would also apply to wikipedia, this is your chance to get someone to work on it for Google's summer of code: http://meta.wikimedia.org/wiki/Summer_of_Code_2007 -- Austin Che (617)253-5899 From endy at MIT.EDU Fri Mar 16 00:55:56 2007 From: endy at MIT.EDU (Drew Endy) Date: Fri, 16 Mar 2007 00:55:56 -0400 Subject: [OWW-SC] Fwd: [PLoSONE Advisory Board] PLoS ONE papers scheduled for 14th March References: <43EF8742E13BC7439F70B5F101449F04B006AF@SFEXCH01.plos.org> Message-ID: <73C7E3E0-5BA5-482D-9CE6-A51637CCA5BD@MIT.EDU> Folks, Chris Surridge at PLoS One has an interesting article coming out that I thought might be of sufficient interest to some or all of us that we may be willing to provide some comments on it (for the PLoS One website (we could even do this somehow via a coupling to OWW). Here's the abstract. Please send me an email if you want the full PDF ahead of its release and might be interested in jotting your thoughts down for comments (good, bad, or suggestive) online... Sharing Detailed Research Data Is Associated with Increased Citation Rate Heather A. Piwowar*, Roger S. Day, Douglas B. Fridsma Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America Background. Sharing research data provides benefit to the general scientific community, but the benefit is less obvious for the investigator who makes his or her data available. Principal Findings. We examined the citation history of 85 cancer microarray clinical trial publications with respect to the availability of their data. The 48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression. Significance. This correlation between publicly available data and increased literature impact may further motivate investigators to share their detailed research data. Thanks, Drew Begin forwarded message: > From: "Chris Surridge" > Date: March 15, 2007 6:36:06 AM EDT > To: "Drew Endy" > Subject: RE: [PLoSONE Advisory Board] PLoS ONE papers scheduled for > 14th March > > Drew, > > Thanks. Anything I can do to cement ties with OWW is great. This > one is > published on the 21st March. > > > Chris > > -----Original Message----- > From: Drew Endy [mailto:endy at MIT.EDU] > Sent: 10 March 2007 19:27 > To: Chris Surridge > Subject: Re: [PLoSONE Advisory Board] PLoS ONE papers scheduled for > 14th > March > > Chris, > > Can you send me this article (below). The folks behind OWW would > likely be very interested in providing detailed comments. > > Thanks / hope that you are great. > Drew > > > On Mar 8, 2007, at 10:00 AM, Chris Surridge wrote: > >> Sharing Detailed Research Data Is Associated with Increased >> Citation Rate >> >> Piwowar >> >> 10.1371/journal.pone.0000308 > From jcbraff at MIT.EDU Wed Mar 21 16:45:48 2007 From: jcbraff at MIT.EDU (Jennifer Braff) Date: Wed, 21 Mar 2007 13:45:48 -0700 Subject: [OWW-SC] oww news and highlights Message-ID: I've been thinking about the format and organization for OWW News and Highlights and am hoping to get some more input before the next sc meeting. Ideally I think we'd like: (1) to encourage input from a wide OWW user base (2) to have a straightforward protocol for contributing news and videos, as well as suggesting labs or events to be highlighted (3) to keep news and announcements current and make sure that highlights and videos are swapped out regularly (4) to maintain a cool-looking front page yet avoid discouraging OWW users from contributing due to formatting concerns or (understandable) reluctance to remove others' contributions (5) to make sure that news and highlights that are swapped out are archived appropriately Please edit and add to this list at: http://openwetware.org/wiki/OpenWetWare:Steering_committee/ News_and_highlights_chairs The best solution I have come up with thus far is to have News and Highlights curated (by myself and/or others), with an invitation on the front page to send news items and highlights contributions/nominations to the News and Highlights Chair(s). It does not strike me as ideal for the front page of OWW to be "curated," but, since it is currently locked to general editing anyway, at least this option encourages community contribution and seems to up the odds that news and highlights will be swapped out and archived in a timely fashion. If people have ideas for different ways of accomplishing this, please suggest them! Thanks, Jen From ilyas at MIT.EDU Wed Mar 21 15:28:09 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Wed, 21 Mar 2007 15:28:09 -0400 Subject: [OWW-SC] help wanted page Message-ID: <46018749.1010202@mit.edu> Should we start a common "help wanted" page or a category? A quick search shows some interest in the community: http://openwetware.org/wiki/Silver:_Open_Positions http://openwetware.org/wiki/Kafatos:Positions http://openwetware.org/wiki/Crisanti:Positions http://openwetware.org/wiki/Yu_Lab:Jobs http://openwetware.org/wiki/OpenWetWare:Jobs Ilya From jasonk at MIT.EDU Thu Mar 22 00:06:13 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 21 Mar 2007 23:06:13 -0500 Subject: [OWW-SC] help wanted page In-Reply-To: <46018749.1010202@mit.edu> References: <46018749.1010202@mit.edu> Message-ID: <7c085c480703212106x18d0fa76se18f9da8d9690aee@mail.gmail.com> Sounds like a good idea. On 3/21/07, Ilya Sytchev wrote: > Should we start a common "help wanted" page or a category? A quick > search shows some interest in the community: > > http://openwetware.org/wiki/Silver:_Open_Positions > http://openwetware.org/wiki/Kafatos:Positions > http://openwetware.org/wiki/Crisanti:Positions > http://openwetware.org/wiki/Yu_Lab:Jobs > http://openwetware.org/wiki/OpenWetWare:Jobs > > Ilya > _______________________________________________ > OpenWetWare Steering Committee Mailing List > sc at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-sc > From ilyas at MIT.EDU Fri Mar 23 19:22:54 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Fri, 23 Mar 2007 19:22:54 -0400 Subject: [OWW-SC] help wanted page In-Reply-To: <7c085c480703212106x18d0fa76se18f9da8d9690aee@mail.gmail.com> References: <46018749.1010202@mit.edu> <7c085c480703212106x18d0fa76se18f9da8d9690aee@mail.gmail.com> Message-ID: <4604614E.3090600@mit.edu> OK, I've started a draft page here: http://openwetware.org/wiki/Jobs Ilya Jason Kelly wrote: > Sounds like a good idea. > > On 3/21/07, Ilya Sytchev wrote: >> Should we start a common "help wanted" page or a category? A quick >> search shows some interest in the community: >> >> http://openwetware.org/wiki/Silver:_Open_Positions >> http://openwetware.org/wiki/Kafatos:Positions >> http://openwetware.org/wiki/Crisanti:Positions >> http://openwetware.org/wiki/Yu_Lab:Jobs >> http://openwetware.org/wiki/OpenWetWare:Jobs >> >> Ilya >> _______________________________________________ >> OpenWetWare Steering Committee Mailing List >> sc at openwetware.org >> http://mailman.mit.edu/mailman/listinfo/oww-sc >> From jasonk at MIT.EDU Wed Mar 28 02:21:03 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 28 Mar 2007 02:21:03 -0400 Subject: [OWW-SC] next SC meeting April 4 at Noon EST Message-ID: <7c085c480703272321p6de4fbealca08f76c302a15a9@mail.gmail.com> Hi SC, Thanks everyone for posting your scheduling availability -- It looks like the best time for SC meetings is the first wednesday of the month at Noon EST. So our next meeting will be next wednesday, April 4. SC chairs remember to post summaries here at least 2 days before the meeting: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_April_2007 Also, if you have suggested items for discussion, please add them here: http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting Meeting will be virtual, details on the conference call number, etc, to follow. Thanks! jason