From johncumbers at gmail.com Sun Jul 1 12:46:39 2007 From: johncumbers at gmail.com (John Cumbers) Date: Sun, 1 Jul 2007 12:46:39 -0400 Subject: [OWW-Discuss] Open journals' records to give reviewers their due Message-ID: *I missed this earlier, may be of interest, * *cheers,* *John* * * * * *Nature* *447*, 528 (31 May 2007) | doi:10.1038/447528d; Published online 30 May 2007 Open journals' records to give reviewers their due Ariberto Fassati1 1. Wohl Virion Centre and MRC-UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London Medical School, 46 Cleveland Street, London W1T 4JF, UK Sir Sydney Brenner and Richard Robert's request in Correspondence (Nature 446, 725; doi:10.1038/446725a 2007 ) for authors to conserve records of their work and make them freely accessible is of great importance to historians of science. However, unlike an artist's preparatory sketches or a novelist's drafts, scientific papers describing major discoveries have gone through the process of peer review. Reviewers often make significant contributions in shaping discoveries. They suggest new experiments, propose novel interpretations and reject some papers outright. Clearly, this is also important 'behind the scenes' work by scientists usually at the forefront of their discipline, and is an intrinsic part of the scientific process. It is well worth keeping a record of such work, for no history of science will be complete and accurate without it. I therefore propose that journals' records should be made publicly available after an adequate lapse of time, including the names of reviewers and the confidential comments exchanged between editors and reviewers. The Nobel Foundation makes all its records available after 50 years, as do many governmental and other institutions. This delay may be reduced for scientific journals to, perhaps, 15 or 20 years. This is also likely to have a positive impact on the peer-review process itself. The scientific community and future historians will gain from this transparency and from full knowledge of all the events that have contributed to a great discovery. -- John Cumbers, Graduate Student Biology and Medicine Brown University, Box G-W Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070701/4821f9f8/attachment.htm From ilyas at MIT.EDU Tue Jul 10 17:56:20 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Tue, 10 Jul 2007 17:56:20 -0400 Subject: [OWW-Discuss] Assembla Message-ID: <46940084.4060808@mit.edu> An interesting concept for collaboration on distributed software development projects and a potential method to commercialize OWW: http://www.assembla.com/tour From ilyas at MIT.EDU Fri Jul 13 15:48:38 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Fri, 13 Jul 2007 15:48:38 -0400 Subject: [OWW-Discuss] Open Source Day II Message-ID: <4697D716.6090901@mit.edu> May be of interest: "An event targeted at developers and users of open source technology. The focus is on enhancing the technology that supports teaching and learning, including, but not limited to Blackboard Building Blocks and WebCT Powerlinks. In the spirit of Open Space Technology (http://www.openspaceworld.org/) we are soliciting ideas from conference registrants on potential topics to discuss: existing projects, ideas for new projects, building the open source community (social as well as policy, governance, or what's needed on a web site, etc)." http://events.mit.edu/event.html?id=7838784 From ilyas at MIT.EDU Wed Jul 18 14:44:31 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Wed, 18 Jul 2007 14:44:31 -0400 Subject: [OWW-Discuss] How Twitter Creates a Social Sixth Sense Message-ID: <469E5F8F.3070905@mit.edu> http://www.wired.com/techbiz/media/magazine/15-07/st_thompson Could Twitter be useful to the bio community somehow? From tdmckee at alum.mit.edu Tue Jul 24 08:48:18 2007 From: tdmckee at alum.mit.edu (Trevor David McKee) Date: Tue, 24 Jul 2007 08:48:18 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" Message-ID: Hi all, Great site - I've just put my lab's site up in the "labs in development" portion of OWW - and quickly realized I have no clue how to design wiki pages. Any suggestions you could provide on free / inexpensive tutorials on wiki? I know some basic html, but editing wiki pages is sufficienly new for me that I have no clue what all the different formatting rules are, etc. Sorry for the newbie question, and thanks for any help you could provide. Thanks a lot. - Trevor ------------------------------------- Trevor D. McKee, Ph.D. Postdoctoral Fellow Princess Margaret Hospital 610 University Avenue 10th Floor Room 328 Toronto, ON M5G 2M9, Canada tmckee at uhnres.utoronto.ca lab 416-946-4501 x5622 fax 416-946-2984 http://ocipda.googlepages.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070724/c42e5b5a/attachment.htm From rshetty at MIT.EDU Tue Jul 24 08:52:52 2007 From: rshetty at MIT.EDU (Reshma Shetty) Date: Tue, 24 Jul 2007 08:52:52 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" In-Reply-To: References: Message-ID: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> Hey Trevor, See the help pages at http://openwetware.org/wiki/Help:Contents In particular, these two tutorials might be helpful ... for getting started on OWW http://openwetware.org/wiki/OpenWetWare:Getting_started for starting a lab wiki on OWW http://openwetware.org/wiki/Help:Starting_a_lab_wiki If you have questions beyond this, let us know. Thanks, Reshma On 7/24/07, Trevor David McKee wrote: > Hi all, > > Great site - I've just put my lab's site up in the "labs in development" > portion of OWW - and quickly realized I have no clue how to design wiki > pages. Any suggestions you could provide on free / inexpensive tutorials on > wiki? I know some basic html, but editing wiki pages is sufficienly new for > me that I have no clue what all the different formatting rules are, etc. > Sorry for the newbie question, and thanks for any help you could provide. > > Thanks a lot. > > - Trevor > > ------------------------------------- > Trevor D. McKee, Ph.D. > Postdoctoral Fellow > Princess Margaret Hospital > 610 University Avenue > 10th Floor Room 328 > Toronto, ON M5G 2M9, Canada > tmckee at uhnres.utoronto.ca > lab 416-946-4501 x5622 > fax 416-946-2984 > http://ocipda.googlepages.com/ > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > From skosuri at MIT.EDU Tue Jul 24 09:04:56 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Tue, 24 Jul 2007 09:04:56 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" In-Reply-To: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> References: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> Message-ID: <2b0cb7a10707240604x28e91fbajca85de66d28fbc5d@mail.gmail.com> Hey Trevor, Good to see you on OWW! As for editing wiki pages, the easiest thing to do is to look at another page that has similar formating, and copy and paste the code into your new page. Then you can change the specifics of anything you need. Also, we'll keep a look out for you and help you along the way. Sri On 7/24/07, Reshma Shetty wrote: > > Hey Trevor, > > See the help pages at http://openwetware.org/wiki/Help:Contents > > In particular, these two tutorials might be helpful ... > > for getting started on OWW > http://openwetware.org/wiki/OpenWetWare:Getting_started > > for starting a lab wiki on OWW > http://openwetware.org/wiki/Help:Starting_a_lab_wiki > > If you have questions beyond this, let us know. > > Thanks, > > Reshma > > On 7/24/07, Trevor David McKee wrote: > > Hi all, > > > > Great site - I've just put my lab's site up in the "labs in development" > > portion of OWW - and quickly realized I have no clue how to design wiki > > pages. Any suggestions you could provide on free / inexpensive > tutorials on > > wiki? I know some basic html, but editing wiki pages is sufficienly new > for > > me that I have no clue what all the different formatting rules are, etc. > > Sorry for the newbie question, and thanks for any help you could > provide. > > > > Thanks a lot. > > > > - Trevor > > > > ------------------------------------- > > Trevor D. McKee, Ph.D. > > Postdoctoral Fellow > > Princess Margaret Hospital > > 610 University Avenue > > 10th Floor Room 328 > > Toronto, ON M5G 2M9, Canada > > tmckee at uhnres.utoronto.ca > > lab 416-946-4501 x5622 > > fax 416-946-2984 > > http://ocipda.googlepages.com/ > > > > _______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070724/f3d3c3e9/attachment.htm From trevordmckee at gmail.com Tue Jul 24 09:19:46 2007 From: trevordmckee at gmail.com (Trevor McKee) Date: Tue, 24 Jul 2007 09:19:46 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" In-Reply-To: <2b0cb7a10707240604x28e91fbajca85de66d28fbc5d@mail.gmail.com> References: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> <2b0cb7a10707240604x28e91fbajca85de66d28fbc5d@mail.gmail.com> Message-ID: Great, thanks a lot for the links. Yeah, figured I'd give it a go. I'm not so much a "wetlab" person as I am an imaging person - but OWW is a neat concept, and a little more amenable to editing than our current webpage (which was designed by one of my summer students last year). I'm happy to contribute to any imaging related discussions should you need any particular resources - one very good reference for imaging is ImageJ, the open-source java based image editing and measurement program for science - you can find the program and project page at http://rsb.info.nih.gov/ij/ and you can also find a manual put together by one of the core facilities at our institution: http://www.uhnres.utoronto.ca/facilities/wcif/imagej/ Point me in the right direction and I can stick that info on a page (in case it's not up there already)... Is the oww-discuss list for this kind of stuff, or is the discussion oriented more within the wiki pages? Sorry - I'm a little too old school for all this new fangled web 2.0 stuff - thanks for helping me along. :) Also, I hope to see some of you at the BE / Chem E BBQ next week, as I'm back in town doing some experiments to finish up a (seemingly endless) paper for my former PI there - and if they'll accept crufty alums, I'm down with getting some free Redbones, for old time's sake. :) - Trev On 7/24/07, Sri Kosuri wrote: > > Hey Trevor, > > Good to see you on OWW! As for editing wiki pages, the easiest thing to > do is to look at another page that has similar formating, and copy and paste > the code into your new page. Then you can change the specifics of anything > you need. Also, we'll keep a look out for you and help you along the way. > > Sri > > On 7/24/07, Reshma Shetty wrote: > > > > Hey Trevor, > > > > See the help pages at http://openwetware.org/wiki/Help:Contents > > > > In particular, these two tutorials might be helpful ... > > > > for getting started on OWW > > http://openwetware.org/wiki/OpenWetWare:Getting_started > > > > for starting a lab wiki on OWW > > http://openwetware.org/wiki/Help:Starting_a_lab_wiki > > > > If you have questions beyond this, let us know. > > > > Thanks, > > > > Reshma > > > > On 7/24/07, Trevor David McKee < tdmckee at alum.mit.edu> wrote: > > > Hi all, > > > > > > Great site - I've just put my lab's site up in the "labs in > > development" > > > portion of OWW - and quickly realized I have no clue how to design > > wiki > > > pages. Any suggestions you could provide on free / inexpensive > > tutorials on > > > wiki? I know some basic html, but editing wiki pages is sufficienly > > new for > > > me that I have no clue what all the different formatting rules are, > > etc. > > > Sorry for the newbie question, and thanks for any help you could > > provide. > > > > > > Thanks a lot. > > > > > > - Trevor > > > > > > ------------------------------------- > > > Trevor D. McKee, Ph.D . > > > Postdoctoral Fellow > > > Princess Margaret Hospital > > > 610 University Avenue > > > 10th Floor Room 328 > > > Toronto, ON M5G 2M9, Canada > > > tmckee at uhnres.utoronto.ca > > > lab 416-946-4501 x5622 > > > fax 416-946-2984 > > > http://ocipda.googlepages.com/ > > > > > > _______________________________________________ > > > OpenWetWare Discussion Mailing List > > > discuss at openwetware.org > > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > > > > _______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070724/0bbec898/attachment.htm From tk at csail.mit.edu Tue Jul 24 11:04:05 2007 From: tk at csail.mit.edu (Tom Knight) Date: Tue, 24 Jul 2007 11:04:05 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" In-Reply-To: References: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> <2b0cb7a10707240604x28e91fbajca85de66d28fbc5d@mail.gmail.com> Message-ID: <965721e5791fbc8600115424d85c752e@csail.mit.edu> We should try to figure out why it was difficult for him to locate these links on his own, and make it easier. On Jul 24, 2007, at 9:19 AM, Trevor McKee wrote: > Great, thanks a lot for the links. > > Yeah, figured I'd give it a go.? I'm not so much a "wetlab" person as > I am an imaging person - but OWW is a neat concept, and a little more > amenable to editing than our current webpage (which was designed by > one of my summer students last year).? I'm happy to contribute to any > imaging related discussions should you need any particular resources - > one very good reference for imaging is ImageJ, the open-source java > based image editing and measurement program for science - you can find > the program and project page at > > http://rsb.info.nih.gov/ij/ > > and you can also find a manual put together by one of the core > facilities at our institution: > > http://www.uhnres.utoronto.ca/facilities/wcif/imagej/ > > Point me in the right direction and I can stick that info on a page > (in case it's not up there already)... > > Is the oww-discuss list for this kind of stuff, or is the discussion > oriented more within the wiki pages?? Sorry - I'm a little too old > school for all this new fangled web 2.0 stuff - thanks for helping me > along.? :) > > Also, I hope to see some of you at the BE / Chem E BBQ next week, as > I'm back in town doing some experiments to finish up a (seemingly > endless) paper for my former PI there - and if they'll accept crufty > alums, I'm down with getting some free Redbones, for old time's sake.? > :) > > - Trev > > > On 7/24/07, Sri Kosuri wrote: >> >> Good to see you on OWW!? As for editing wiki pages, the easiest thing >> to do is to look at another page that has similar formating, and copy >> and paste the code into your new page.? Then you can change the >> specifics of anything you need.? Also, we'll keep a look out for you >> and help you along the way. >> >> Sri >> >> >> On 7/24/07, Reshma Shetty < rshetty at mit.edu> wrote: >>> >>> See the help pages at http://openwetware.org/wiki/Help:Contents >>> >>> In particular, these two tutorials might be helpful ... >>> >>> for getting started on OWW >>> http://openwetware.org/wiki/OpenWetWare:Getting_started >>> >>> for starting a lab wiki on OWW >>> http://openwetware.org/wiki/Help:Starting_a_lab_wiki >>> >>> If you have questions beyond this, let us know. >>> >>> Thanks, >>> >>> Reshma >>> >>> On 7/24/07, Trevor David McKee < tdmckee at alum.mit.edu> wrote: >>> > Hi all, >>> > >>> > Great site - I've just put my lab's site up in the "labs in >>> development" >>> > portion of OWW - and quickly realized I have no clue how to design >>> wiki >>> > pages.??Any suggestions you could provide on free / inexpensive >>> tutorials on >>> > wiki???I know some basic html, but editing wiki pages is >>> sufficienly new for >>> > me that I have no clue what all the different formatting rules >>> are, etc. >>> > Sorry for the newbie question, and thanks for any help you could >>> provide. >>> > >>> > Thanks a lot. >>> > >>> > - Trevor >>> > >>> > ------------------------------------- >>> > Trevor D. McKee, Ph.D . >>> > Postdoctoral Fellow >>> > Princess Margaret Hospital >>> > 610 University Avenue >>> > 10th Floor Room 328 >>> > Toronto, ON M5G 2M9, Canada >>> > tmckee at uhnres.utoronto.ca >>> > lab??416-946-4501 x5622 >>> > fax??416-946-2984 >>> > http://ocipda.googlepages.com/ >>> > >>> > _______________________________________________ >>> > OpenWetWare Discussion Mailing List >>> > discuss at openwetware.org >>> > http://mailman.mit.edu/mailman/listinfo/oww-discuss >>> > >>> > >>> _______________________________________________ >>> OpenWetWare Discussion Mailing List >>> discuss at openwetware.org >>> http://mailman.mit.edu/mailman/listinfo/oww-discuss >> > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 4422 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070724/cac0a40e/attachment.bin From jasonk at MIT.EDU Tue Jul 24 21:53:00 2007 From: jasonk at MIT.EDU (Jason Kelly) Date: Tue, 24 Jul 2007 21:53:00 -0400 Subject: [OWW-Discuss] question - pointers to wiki design "for dummies" In-Reply-To: <965721e5791fbc8600115424d85c752e@csail.mit.edu> References: <6e9f40380707240552s3c2ef3b9hcf8be866fad7a20f@mail.gmail.com> <2b0cb7a10707240604x28e91fbajca85de66d28fbc5d@mail.gmail.com> <965721e5791fbc8600115424d85c752e@csail.mit.edu> Message-ID: <7c085c480707241853i38a4fd1ave8c638bb993fad67@mail.gmail.com> > We should try to figure out why it was difficult for him to locate > these links on his own, and make it easier. Yeah, agreed. Part of the problem is that there isn't really a big 'imaging' area on OWW at the moment, so he'd have to start a section. And I think the barrier is still pretty high to starting a new topic area on the site, new community members seem to be a lot more comfortable adding to existing resources than starting new ones. Maybe we should make the process of starting "topic portals" more turnkey, or have a page dedicated to them? I think they are currently in the 'Reference Materials' column of the Resources page: http://openwetware.org/wiki/Resources We do a better job aggregating and explaining how to add protocols and lab homepages, which is why I think we get more of those. As for the 'getting started' pages, we email the links in the welcome email and the help button is on the homepage and the toolbar. Reshma also just added an icon to the help button on the labs page which should make it more noticeable: http://openwetware.org/wiki/Labs any other suggestions welcome, or other problems that people have had in finding particular types of information on the site. thanks, jason On 7/24/07, Tom Knight wrote: > We should try to figure out why it was difficult for him to locate > these links on his own, and make it easier. > > On Jul 24, 2007, at 9:19 AM, Trevor McKee wrote: > > > Great, thanks a lot for the links. > > > > Yeah, figured I'd give it a go. I'm not so much a "wetlab" person as > > I am an imaging person - but OWW is a neat concept, and a little more > > amenable to editing than our current webpage (which was designed by > > one of my summer students last year). I'm happy to contribute to any > > imaging related discussions should you need any particular resources - > > one very good reference for imaging is ImageJ, the open-source java > > based image editing and measurement program for science - you can find > > the program and project page at > > > > http://rsb.info.nih.gov/ij/ > > > > and you can also find a manual put together by one of the core > > facilities at our institution: > > > > http://www.uhnres.utoronto.ca/facilities/wcif/imagej/ > > > > Point me in the right direction and I can stick that info on a page > > (in case it's not up there already)... > > > > Is the oww-discuss list for this kind of stuff, or is the discussion > > oriented more within the wiki pages? Sorry - I'm a little too old > > school for all this new fangled web 2.0 stuff - thanks for helping me > > along. :) > > > > Also, I hope to see some of you at the BE / Chem E BBQ next week, as > > I'm back in town doing some experiments to finish up a (seemingly > > endless) paper for my former PI there - and if they'll accept crufty > > alums, I'm down with getting some free Redbones, for old time's sake. > > :) > > > > - Trev > > > > > > On 7/24/07, Sri Kosuri wrote: > >> > >> Good to see you on OWW! As for editing wiki pages, the easiest thing > >> to do is to look at another page that has similar formating, and copy > >> and paste the code into your new page. Then you can change the > >> specifics of anything you need. Also, we'll keep a look out for you > >> and help you along the way. > >> > >> Sri > >> > >> > >> On 7/24/07, Reshma Shetty < rshetty at mit.edu> wrote: > >>> > >>> See the help pages at http://openwetware.org/wiki/Help:Contents > >>> > >>> In particular, these two tutorials might be helpful ... > >>> > >>> for getting started on OWW > >>> http://openwetware.org/wiki/OpenWetWare:Getting_started > >>> > >>> for starting a lab wiki on OWW > >>> http://openwetware.org/wiki/Help:Starting_a_lab_wiki > >>> > >>> If you have questions beyond this, let us know. > >>> > >>> Thanks, > >>> > >>> Reshma > >>> > >>> On 7/24/07, Trevor David McKee < tdmckee at alum.mit.edu> wrote: > >>> > Hi all, > >>> > > >>> > Great site - I've just put my lab's site up in the "labs in > >>> development" > >>> > portion of OWW - and quickly realized I have no clue how to design > >>> wiki > >>> > pages.Any suggestions you could provide on free / inexpensive > >>> tutorials on > >>> > wiki?I know some basic html, but editing wiki pages is > >>> sufficienly new for > >>> > me that I have no clue what all the different formatting rules > >>> are, etc. > >>> > Sorry for the newbie question, and thanks for any help you could > >>> provide. > >>> > > >>> > Thanks a lot. > >>> > > >>> > - Trevor > >>> > > >>> > ------------------------------------- > >>> > Trevor D. McKee, Ph.D . > >>> > Postdoctoral Fellow > >>> > Princess Margaret Hospital > >>> > 610 University Avenue > >>> > 10th Floor Room 328 > >>> > Toronto, ON M5G 2M9, Canada > >>> > tmckee at uhnres.utoronto.ca > >>> > lab416-946-4501 x5622 > >>> > fax416-946-2984 > >>> > http://ocipda.googlepages.com/ > >>> > > >>> > _______________________________________________ > >>> > OpenWetWare Discussion Mailing List > >>> > discuss at openwetware.org > >>> > http://mailman.mit.edu/mailman/listinfo/oww-discuss > >>> > > >>> > > >>> _______________________________________________ > >>> OpenWetWare Discussion Mailing List > >>> discuss at openwetware.org > >>> http://mailman.mit.edu/mailman/listinfo/oww-discuss > >> > > _______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > From trevordmckee at gmail.com Wed Jul 25 16:27:36 2007 From: trevordmckee at gmail.com (Trevor McKee) Date: Wed, 25 Jul 2007 16:27:36 -0400 Subject: [OWW-Discuss] Microscopy question: follow up Message-ID: Just a quick e-mail to clarify the issue: I was able to find the Protocols:Other protocols:Microscopy section OK, I guess my thoughts were more of a confusion as to whether to put microscopy and image analysis under Protocols:Other protocols:Microscopy, Protocols:in silico, or Resources:Microscopy. I guess since it's a wiki, I could put it somewhere, and then let someone else edit it to another location afterwards - is that the idea? I'd be happy to start an imaging section, if you could tell me which of those major webpages / categories it would fall under. I agree that some sort of topics portal would be nice from a new user's perspective, because especially for those new to wiki's, the whole process of editing the front page or some major page (i.e. Resources, Protocols, etc.) to start a new section is somewhat intimidating (i.e. i don't want to muck up the site, having just started to use it) Thanks again for your help, Trevor > > We should try to figure out why it was difficult for him to locate > > these links on his own, and make it easier. > > Yeah, agreed. > > Part of the problem is that there isn't really a big 'imaging' area on > OWW at the moment, so he'd have to start a section. And I think the > barrier is still pretty high to starting a new topic area on the site, > new community members seem to be a lot more comfortable adding to > existing resources than starting new ones. Maybe we should make the > process of starting "topic portals" more turnkey, or have a page > dedicated to them? I think they are currently in the 'Reference > Materials' column of the Resources page: > http://openwetware.org/wiki/Resources > > We do a better job aggregating and explaining how to add protocols and > lab homepages, which is why I think we get more of those. > > As for the 'getting started' pages, we email the links in the welcome > email and the help button is on the homepage and the toolbar. Reshma > also just added an icon to the help button on the labs page which > should make it more noticeable: > http://openwetware.org/wiki/Labs > > any other suggestions welcome, or other problems that people have had > in finding particular types of information on the site. > > thanks, > jason > > On 7/24/07, Tom Knight wrote: > > We should try to figure out why it was difficult for him to locate > > these links on his own, and make it easier. > > > > On Jul 24, 2007, at 9:19 AM, Trevor McKee wrote: > > > > > Great, thanks a lot for the links. > > > > > > Yeah, figured I'd give it a go. I'm not so much a "wetlab" person as > > > I am an imaging person - but OWW is a neat concept, and a little more > > > amenable to editing than our current webpage (which was designed by > > > one of my summer students last year). I'm happy to contribute to any > > > imaging related discussions should you need any particular resources - > > > one very good reference for imaging is ImageJ, the open-source java > > > based image editing and measurement program for science - you can find > > > the program and project page at > > > > > > http://rsb.info.nih.gov/ij/ > > > > > > and you can also find a manual put together by one of the core > > > facilities at our institution: > > > > > > http://www.uhnres.utoronto.ca/facilities/wcif/imagej/ > > > > > > Point me in the right direction and I can stick that info on a page > > > (in case it's not up there already)... > > > > > > Is the oww-discuss list for this kind of stuff, or is the discussion > > > oriented more within the wiki pages? Sorry - I'm a little too old > > > school for all this new fangled web 2.0 stuff - thanks for helping me > > > along. :) > > > > > > Also, I hope to see some of you at the BE / Chem E BBQ next week, as > > > I'm back in town doing some experiments to finish up a (seemingly > > > endless) paper for my former PI there - and if they'll accept crufty > > > alums, I'm down with getting some free Redbones, for old time's sake. > > > :) > > > > > > - Trev > > > > > > > > > On 7/24/07, Sri Kosuri wrote: > > >> > > >> Good to see you on OWW! As for editing wiki pages, the easiest thing > > >> to do is to look at another page that has similar formating, and copy > > >> and paste the code into your new page. Then you can change the > > >> specifics of anything you need. Also, we'll keep a look out for you > > >> and help you along the way. > > >> > > >> Sri > > >> > > >> > > >> On 7/24/07, Reshma Shetty < rshetty at mit.edu> wrote: > > >>> > > >>> See the help pages at http://openwetware.org/wiki/Help:Contents > > >>> > > >>> In particular, these two tutorials might be helpful ... > > >>> > > >>> for getting started on OWW > > >>> http://openwetware.org/wiki/OpenWetWare:Getting_started > > >>> > > >>> for starting a lab wiki on OWW > > >>> http://openwetware.org/wiki/Help:Starting_a_lab_wiki > > >>> > > >>> If you have questions beyond this, let us know. > > >>> > > >>> Thanks, > > >>> > > >>> Reshma > > >>> > > >>> On 7/24/07, Trevor David McKee < tdmckee at alum.mit.edu> wrote: > > >>> > Hi all, > > >>> > > > >>> > Great site - I've just put my lab's site up in the "labs in > > >>> development" > > >>> > portion of OWW - and quickly realized I have no clue how to design > > >>> wiki > > >>> > pages.Any suggestions you could provide on free / inexpensive > > >>> tutorials on > > >>> > wiki?I know some basic html, but editing wiki pages is > > >>> sufficienly new for > > >>> > me that I have no clue what all the different formatting rules > > >>> are, etc. > > >>> > Sorry for the newbie question, and thanks for any help you could > > >>> provide. > > >>> > > > >>> > Thanks a lot. > > >>> > > > >>> > - Trevor > > >>> > > > >>> > ------------------------------------- > > >>> > Trevor D. McKee, Ph.D . > > >>> > Postdoctoral Fellow > > >>> > Princess Margaret Hospital > > >>> > 610 University Avenue > > >>> > 10th Floor Room 328 > > >>> > Toronto, ON M5G 2M9, Canada > > >>> > tmckee at uhnres.utoronto.ca > > >>> > lab416-946-4501 x5622 > > >>> > fax416-946-2984 > > >>> > http://ocipda.googlepages.com/ > > >>> > > > >>> > _______________________________________________ > > >>> > OpenWetWare Discussion Mailing List > > >>> > discuss at openwetware.org > > >>> > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > >>> > > > >>> > > > >>> _______________________________________________ > > >>> OpenWetWare Discussion Mailing List > > >>> discuss at openwetware.org > > >>> http://mailman.mit.edu/mailman/listinfo/oww-discuss > > >> > > > _______________________________________________ > > > OpenWetWare Discussion Mailing List > > > discuss at openwetware.org > > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > _______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > > > ------------------------------ > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > End of Oww-discuss Digest, Vol 11, Issue 7 > ****************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070725/b1de3540/attachment.htm From marceaug at aei.ca Wed Jul 25 12:37:37 2007 From: marceaug at aei.ca (Gabriel Marceau) Date: Wed, 25 Jul 2007 12:37:37 -0400 Subject: [OWW-Discuss] Contents of Oww-discuss digest... In-Reply-To: References: Message-ID: <46A77C51.2080900@aei.ca> I think the comment was about finding why the originator of this thread could not easily find out the pages giving instructions on how to write in "Wiki". The links are on the main page under the "Help: Step by step tutorials" button, I think it cannot be easier to find. On the comment about the news pages the real easy solution would be for someone to create "stub" pages. You simply create the topic and enter a temp code that designates the page as a stub inviting people to expand it. For an example see: http://openwetware.org/wiki/Measures_and_Models_of_T7_Gene_Expression For the template: http://openwetware.org/wiki/Template:Stub If people want to suggests new stubs they could either make a list to send to this mailing list and I or someone else could create them or they can write their suggestion on the "Ideas" page of the "Community" section or we can create a dedicated page about "wanted" stubs. Gabriel From rshetty at MIT.EDU Thu Jul 26 11:47:04 2007 From: rshetty at MIT.EDU (Reshma Shetty) Date: Thu, 26 Jul 2007 11:47:04 -0400 Subject: [OWW-Discuss] Microscopy question: follow up In-Reply-To: References: Message-ID: <6e9f40380707260847hc3aa1cbidf1bb910cf6137d9@mail.gmail.com> Hey Trevor, Thanks for your email. Your confusion about where to put stuff is totally understandable. We're still struggling to figure out how to best organize information on OpenWetWare. You are totally right that the best thing to do is to just post information and then it can be reorganized by others as needed. For the sake of answering your question, the best place to put information depends on what information you want to post. If you just want to add a link to a webpage or a quick note, people generally add it to an existing page. Like http://openwetware.org/wiki/Microscopy This page is intended to be a portal to anything having to do with Microscopy on OpenWetWare. If you are interested in adding say a whole new protocol having to do with imaging or microscopy, then you could just start a new page and put the following line at the bottom ... [[Category:Microscopy]] [[Category:Protocol]] This will make the a link to that page show up both on http://openwetware.org/wiki/Protocols under Other protocols:Microscopy and on the page http://openwetware.org/wiki/Microscopy. (Both pages autogenerate links to anything tagged with the Categories "Microscopy" and "Protocol".) If you wanted to start a whole new page on a protocol having to do with software for microscopy image analysis. Then you could add the line [[Category:Microscopy]] [[Category:Protocol]] [[Category:In silico]] to the bottom of the page. This will make the page show up both on the page http://openwetware.org/wiki/Protocols under the topic Other protocols:Microscopy AND the topic In silico. And again, it will also show up on http://openwetware.org/wiki/Microscopy. Basically, we're trying to give people as many ways as possible to find the relevant info. Let me know if this makes sense or is just totally confusing. Also, more generally, it would be great to be talking about how to best organize information on OWW so that it can be found easily and people can post easily. Thanks to Trevor for highlighting this issues with OWW. If people have ideas or feedback, please send them to the list or to me. Thanks, Reshma On 7/25/07, Trevor McKee wrote: > Just a quick e-mail to clarify the issue: > > I was able to find the Protocols:Other protocols:Microscopy section OK, I > guess my thoughts were more of a confusion as to whether to put microscopy > and image analysis under Protocols:Other protocols:Microscopy, Protocols:in > silico, or Resources:Microscopy. I guess since it's a wiki, I could put it > somewhere, and then let someone else edit it to another location afterwards > - is that the idea? > > I'd be happy to start an imaging section, if you could tell me which of > those major webpages / categories it would fall under. I agree that some > sort of topics portal would be nice from a new user's perspective, because > especially for those new to wiki's, the whole process of editing the front > page or some major page ( i.e. Resources, Protocols, etc.) to start a new > section is somewhat intimidating (i.e. i don't want to muck up the site, > having just started to use it) > > Thanks again for your help, > Trevor > > > > > We should try to figure out why it was difficult for him to locate > > > these links on his own, and make it easier. > > > > Yeah, agreed. > > > > Part of the problem is that there isn't really a big 'imaging' area on > > OWW at the moment, so he'd have to start a section. And I think the > > barrier is still pretty high to starting a new topic area on the site, > > new community members seem to be a lot more comfortable adding to > > existing resources than starting new ones. Maybe we should make the > > process of starting "topic portals" more turnkey, or have a page > > dedicated to them? I think they are currently in the 'Reference > > Materials' column of the Resources page: > > http://openwetware.org/wiki/Resources > > > > We do a better job aggregating and explaining how to add protocols and > > lab homepages, which is why I think we get more of those. > > > > As for the 'getting started' pages, we email the links in the welcome > > email and the help button is on the homepage and the toolbar. Reshma > > also just added an icon to the help button on the labs page which > > should make it more noticeable: > > http://openwetware.org/wiki/Labs > > > > any other suggestions welcome, or other problems that people have had > > in finding particular types of information on the site. > > > > thanks, > > jason > > > > On 7/24/07, Tom Knight wrote: > > > We should try to figure out why it was difficult for him to locate > > > these links on his own, and make it easier. > > > > > > On Jul 24, 2007, at 9:19 AM, Trevor McKee wrote: > > > > > > > Great, thanks a lot for the links. > > > > > > > > Yeah, figured I'd give it a go. I'm not so much a "wetlab" person as > > > > I am an imaging person - but OWW is a neat concept, and a little more > > > > amenable to editing than our current webpage (which was designed by > > > > one of my summer students last year). I'm happy to contribute to any > > > > imaging related discussions should you need any particular resources - > > > > one very good reference for imaging is ImageJ, the open-source java > > > > based image editing and measurement program for science - you can find > > > > the program and project page at > > > > > > > > http://rsb.info.nih.gov/ij/ > > > > > > > > and you can also find a manual put together by one of the core > > > > facilities at our institution: > > > > > > > > > http://www.uhnres.utoronto.ca/facilities/wcif/imagej/ > > > > > > > > Point me in the right direction and I can stick that info on a page > > > > (in case it's not up there already)... > > > > > > > > Is the oww-discuss list for this kind of stuff, or is the discussion > > > > oriented more within the wiki pages? Sorry - I'm a little too old > > > > school for all this new fangled web 2.0 stuff - thanks for helping me > > > > along. :) > > > > > > > > Also, I hope to see some of you at the BE / Chem E BBQ next week, as > > > > I'm back in town doing some experiments to finish up a (seemingly > > > > endless) paper for my former PI there - and if they'll accept crufty > > > > alums, I'm down with getting some free Redbones, for old time's sake. > > > > :) > > > > > > > > - Trev > > > > > > > > > > > > On 7/24/07, Sri Kosuri wrote: > > > >> > > > >> Good to see you on OWW! As for editing wiki pages, the easiest thing > > > >> to do is to look at another page that has similar formating, and copy > > > >> and paste the code into your new page. Then you can change the > > > >> specifics of anything you need. Also, we'll keep a look out for you > > > >> and help you along the way. > > > >> > > > >> Sri > > > >> > > > >> > > > >> On 7/24/07, Reshma Shetty < rshetty at mit.edu> wrote: > > > >>> > > > >>> See the help pages at > http://openwetware.org/wiki/Help:Contents > > > >>> > > > >>> In particular, these two tutorials might be helpful ... > > > >>> > > > >>> for getting started on OWW > > > >>> > http://openwetware.org/wiki/OpenWetWare:Getting_started > > > >>> > > > >>> for starting a lab wiki on OWW > > > >>> > http://openwetware.org/wiki/Help:Starting_a_lab_wiki > > > >>> > > > >>> If you have questions beyond this, let us know. > > > >>> > > > >>> Thanks, > > > >>> > > > >>> Reshma > > > >>> > > > >>> On 7/24/07, Trevor David McKee < tdmckee at alum.mit.edu > wrote: > > > >>> > Hi all, > > > >>> > > > > >>> > Great site - I've just put my lab's site up in the "labs in > > > >>> development" > > > >>> > portion of OWW - and quickly realized I have no clue how to design > > > >>> wiki > > > >>> > pages.Any suggestions you could provide on free / inexpensive > > > >>> tutorials on > > > >>> > wiki?I know some basic html, but editing wiki pages is > > > >>> sufficienly new for > > > >>> > me that I have no clue what all the different formatting rules > > > >>> are, etc. > > > >>> > Sorry for the newbie question, and thanks for any help you could > > > >>> provide. > > > >>> > > > > >>> > Thanks a lot. > > > >>> > > > > >>> > - Trevor > > > >>> > > > > >>> > ------------------------------------- > > > >>> > Trevor D. McKee, Ph.D . > > > >>> > Postdoctoral Fellow > > > >>> > Princess Margaret Hospital > > > >>> > 610 University Avenue > > > >>> > 10th Floor Room 328 > > > >>> > Toronto, ON M5G 2M9, Canada > > > >>> > tmckee at uhnres.utoronto.ca > > > >>> > lab416-946-4501 x5622 > > > >>> > fax416-946-2984 > > > >>> > http://ocipda.googlepages.com/ > > > >>> > > > > >>> > _______________________________________________ > > > >>> > OpenWetWare Discussion Mailing List > > > >>> > discuss at openwetware.org > > > >>> > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > >>> > > > > >>> > > > > >>> _______________________________________________ > > > >>> OpenWetWare Discussion Mailing List > > > >>> discuss at openwetware.org > > > >>> > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > >> > > > > _______________________________________________ > > > > OpenWetWare Discussion Mailing List > > > > discuss at openwetware.org > > > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > > _______________________________________________ > > > OpenWetWare Discussion Mailing List > > > discuss at openwetware.org > > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > > > > > > > > ------------------------------ > > > > _______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > > End of Oww-discuss Digest, Vol 11, Issue 7 > > ****************************************** > > > > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > From ilyas at MIT.EDU Mon Jul 30 17:26:48 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Mon, 30 Jul 2007 17:26:48 -0400 Subject: [OWW-Discuss] Now THAT's What I'm Talking About! Message-ID: <46AE5798.3060004@mit.edu> A blog post that tells about interesting ways one advertising company (http://www.avenuea-razorfish.com/) is using Web 2.0: "AARF employees have learned to add the tag 'AARF' when they come across a web page (using del.icio.us), a photo (Flickr), or a news story (Digg) that they think will be of interest to their colleagues. Shortly after they add this tag, the bookmark (look at the top of the box), thumbnail of the photo (middle) or headline and description of the story (bottom) show up within the AARF E2.0 Intranet." http://blog.hbs.edu/faculty/amcafee/index.php/faculty_amcafee_v3/now_thats_what_im_talking_about/ OWW users could tag web pages or papers of interest which then would show up on the Reviews page (http://openwetware.org/wiki/Reviews), for example? From johncumbers at gmail.com Mon Jul 30 18:20:48 2007 From: johncumbers at gmail.com (John Cumbers) Date: Mon, 30 Jul 2007 18:20:48 -0400 Subject: [OWW-Discuss] http://www.myresearchspace.com/ Message-ID: a little painful to read, but this looks interesting, http://www.myresearchspace.com/ cheers, John -- John Cumbers, Graduate Student Biology and Medicine Brown University, Box G-W Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070730/ae7f1280/attachment.htm