From skosuri at MIT.EDU Mon Oct 2 14:44:39 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Mon, 2 Oct 2006 14:44:39 -0400 Subject: [OWW-SC] Peer review article in AP Message-ID: <2b0cb7a10610021144k3892b6a9m97e53ea128365bbe@mail.gmail.com> http://news.yahoo.com/s/ap/20061001/ap_on_sc/peer_review_science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061002/bde33110/attachment.htm From skosuri at MIT.EDU Mon Oct 2 15:07:24 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Mon, 2 Oct 2006 15:07:24 -0400 Subject: [OWW-SC] free university wiki hosting Message-ID: <2b0cb7a10610021207vec0c128i8c1811516331b3b0@mail.gmail.com> Wikia is offering public and private wiki hosting for universities. I'm not completely sure of the details, but check it out here: http://students.wikia.com/ sri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061002/fc32f332/attachment.htm From jasonk at MIT.EDU Wed Oct 4 11:33:56 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 4 Oct 2006 11:33:56 -0400 Subject: [OWW-SC] Fwd: Postgenomic + OWW In-Reply-To: References: <7c085c480609272126y722a8fc1sd1eebe2ad70c700e@mail.gmail.com> Message-ID: <7c085c480610040833h3d09e98g5348dbba6778bfb8@mail.gmail.com> from postgenomic... ---------- Forwarded message ---------- From: Adie, Euan Date: Oct 4, 2006 8:33 AM Subject: Re: Postgenomic + OWW To: Jason Kelly Hi Jason, The short answer is yes - I'm definitely interested. :) I think that at the very least it'd be cool to link papers already in the Postgenomic database to the wiki pages that cite them - we do something similar already with Faculty of 1000 reviews. As you say, this sort of thing is currently outside of the current paper-cites-paper referencing system. Technically speaking, ideally there'd be a feed of recently modified pages that included the full text of the page (not just the edit): if you're using the MediaWiki citation plugin (?) then we could get everything else by looking for that markup... I don't know how feasible that is on your end: I don't really know an awful lot about the MediaWiki internals, unfortunately. :( Anyway, thanks for your mail, Cheers, Euan On 28/9/06 05:26, "Jason Kelly" wrote: > > (1) Commentary about a particular paper (e.g. a summary or critique) - > this most closely resembles the blog-type content that postgenomic > currently aggregates. > http://openwetware.org/wiki/Stephanopoulos:Literature_Reviewed > > (2) Reference to a paper in a protocol, material description (e.g. > media recipe), etc. > http://openwetware.org/wiki/Bacterial_Transformation#References > > (3) Reference to a paper in a research project description (e.g. > referencing it as prior work) > http://openwetware.org/wiki/Reshma_Shetty/Thesis_research > > What's interesting about the last 2 types is that they are analogous > to references in a typical peer-reviewed publication. However, since > OWW falls outside the normal referencing system, author's aren't > receiving any real recognition for other scientists citing their work. > (e.g. it doesn't contribute to the "citation score" of the paper). > > So I'm not sure which of the above sort of content postgenomic would > be interested in aggregating (if any), but would love to talk more > about this if it's something you think is worthwhile. it might > require a bit more of a technical hack to set it up, since the only > RSS feed off the site currently is the RecentChanges (e.g. every change > made to the site). > > Let me know if you'd be interested in talking more. We're available > to talk by phone or email, whatever works best for you guys. > > Thanks, > Jason ******************************************************************************** DISCLAIMER: This e-mail is confidential and should not be used by anyone who is not the original intended recipient. 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Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** From johncumbers at gmail.com Fri Oct 6 13:36:12 2006 From: johncumbers at gmail.com (John Cumbers) Date: Fri, 6 Oct 2006 13:36:12 -0400 Subject: [OWW-SC] Wikipedia rival calls in the experts Message-ID: I wish them luck, but I know which I'd prefer to edit... *"When will the wiki be set up?* Give us a few weeks. With luck and help, sometime in October. (Nope, not the end of September. Credit us with good intentions!) We'll continue to try very hard. Read more about the launch plan , which is under constant refinement." *Nature* *443*, 493(5 October 2006) | doi:10.1038/443493a; Published online 4 October 2006 Wikipedia rival calls in the experts Jim Giles Top of page Abstract Encyclopaedia aims to recognize status of academic editors. The current incarnation of Wikipedia is both phenomenally successful and, in the eyes of some critics, fundamentally flawed. The online encyclopaedia now includes more than a million entries in English alone. Although anyone can edit any article, its accuracy, at least on science topics, is surprisingly high. But Wikipedia has never given experts special standing when it comes to determining content. And that, critics say, deters the people who ought to be contributing from doing so. Just how big a drawback that is will now be tested, with the launch of an online encyclopaedia that will give privileged status to scientists and other experts. Citizendium, a pilot version of which is due to go live in the next week, will use all of Wikipedia's content but will host it at another website (http://citizendium.org) and edit it differently. Editors with appropriate academic qualifications will have the power to settle disputes about wording, for example, and stamp articles they perceive to be accurate as 'approved'. "One reason we are setting this up is to give scientists and other scholars a new organizational framework to clean up and improve on the work started by Wikipedia," says Larry Sanger, a philosopher and co-founder of Wikipedia, who is the driving force behind Citizendium. "Wikipedia is now the first stop for many people in their search for information on scientific topics. Many scientists would like to help make sure this resource remains accurate, but they have no desire to navigate the treacherous waters of Wikipedia's editorial system, which accords them no official role." Many scientists have no desire to navigate the treacherous waters of Wikipedia's editorial system. ADVERTISEMENT [image: Click here to find out more!] [image: Advertisement] Reactions from the many bloggers who track the progress of Wikipedia have been mixed. Some say Sanger will struggle to define what constitutes expertise, and that arguments about content will be replaced by arguments over who is or isn't an expert. Others think Citizendium will find it hard to attract regular contributors, as the prospect of having an edit overruled by a higher power will not appeal. But scientists who contribute regularly to Wikipedia say Citizendium has promise. "I like the idea notionally," says Vaughan Bell of the Institute of Psychiatry in London, who contributes to Wikipedia's schizophrenia page, among others. William Connolley of the British Antarctic Survey in Cambridge, UK, who updates Wikipedia climate entries, adds that some scientists have become frustrated with Wikipedia because of the difficulty in agreeing edits, although both he and Bell agree that conflict can sometimes result in better articles. -- 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/20061006/c3706bcb/attachment.htm From jasonk at MIT.EDU Mon Oct 9 09:16:39 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Mon, 9 Oct 2006 09:16:39 -0400 Subject: [OWW-SC] SC meeting on Thursday (10/9) Message-ID: <7c085c480610090616y45d6b94cqa4519acbba6bee9b@mail.gmail.com> Hi folks, Reminder that we will have a SC meeting on this Thursday at Noon EST - please shoot me an email if you plan to call in. You can add suggestions for the agenda here: http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting Thanks, see you thursday! Jason From jasonk at MIT.EDU Thu Oct 12 03:42:34 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Thu, 12 Oct 2006 03:42:34 -0400 Subject: [OWW-SC] hmm, not sure I agree ;) Message-ID: <7c085c480610120042t310f4245m21030eabdb3dba7c@mail.gmail.com> http://www.genengnews.com/bestofweb/list.aspx "weak points: none" gotta like that review :) jason From jasonk at MIT.EDU Thu Oct 12 11:02:31 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Thu, 12 Oct 2006 11:02:31 -0400 Subject: [OWW-SC] SC meeting in 32-262 Message-ID: <7c085c480610120802r2dc16fc5h8aec3b2d187030b5@mail.gmail.com> Realized I left off the meeting location - will be in 32-262, same as usual. Lunch provided. thanks, jason From ilyas at MIT.EDU Thu Oct 12 12:30:09 2006 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Thu, 12 Oct 2006 12:30:09 -0400 Subject: [OWW-SC] test installation @ rackspace Message-ID: <452E6D91.709@mit.edu> Please have a look, and let me know if you notice any bugs: http://97902-www1.openwetware.org/ Please note that wikitex is not working yet. Ilya From ilyas at MIT.EDU Fri Oct 13 15:42:42 2006 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Fri, 13 Oct 2006 15:42:42 -0400 Subject: [OWW-SC] today's snafu Message-ID: <452FEC32.8070300@mit.edu> As Sri already mentioned, we have moved OWW DNS settings to Rackspace yesterday. These changes should not take more than one hour to become active - enough time before the changes to the authoritative DNS server records for the domain are completed by the registrar which takes about 24 hours. However, it appears that Rackspace took much longer to update their DNS records. This has caused some of the users to be redirected to our test OWW installation at Rackspace which is almost fully functional (therefore hard to distinguish from the production installation) but has old data. My experience with Rackspace has been favorable so far, so I didn't expect this simple change to be a problem. Still, I wish I have monitored the switchover more closely and taken appropriate action when it was necessary. I have informed Rackspace about this problem and they are investigating. Ilya From jasonk at MIT.EDU Sat Oct 14 17:51:43 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Sat, 14 Oct 2006 17:51:43 -0400 Subject: [OWW-SC] Note on the PLoS blog about surridge talk... Message-ID: <7c085c480610141451o5f0d9d71k4c69490c56069719@mail.gmail.com> http://www.plos.org/cms/node/113 From skosuri at MIT.EDU Mon Oct 16 13:13:57 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Mon, 16 Oct 2006 13:13:57 -0400 Subject: [OWW-SC] Open Access 2.0 -- 2pm 10/20 -- 32-141 Message-ID: <2b0cb7a10610161013h7a36af0awa75819248dc98415@mail.gmail.com> Hey all, For those local to Boston, could you please distribute this announcement on relevant email lists. Thanks, Sri Open Access 2.0 Chris Surridge, Managing Editor, PLoS ONE Open to the Public 2pm, Friday October 20, 2006 MIT Stata Center, 32-141 Part of OpenWetWare's Seminar Series on Open Science http://openwetware.org/wiki/Seminar_Series Talk Overview Dr. Surridge is helping start PLoS ONE , an effort to democratize scientific contribution, access, review, and merit. This exciting new journal publishes scientifically sound research regardless of subjective criteria such as "likely impact" or "reader interest". Following publication, readers comment, annotate, and rate each paper, adding value to the work as time goes on. Dr. Surridge will talk of the progress to date, and the challenges that lie ahead. Biography *Adapted from the PLoS Website: * Christopher Surridge graduated with a degree in Biophysics from Leeds University in 1988 and went on to study the dynamics of microtubule assembly at Imperial College London. After a couple of years of post-doc research he moved into scientific publishing as Assistant Editor on Nature Structural Biology in December 1993. In 1995 he moved onto the editorial team at Nature where he handled an eclectic mix of subject areas mainly focusing on biophysics, mathematical and systems biology, and plant science. He also spent some time editing Nature's Brief Communication section which has never fully recovered. By mid-2005 the allure of reshaping scientific publishing to satisfy the needs of a new century became irresistible and he moved to PLoS's Cambridge office working on a new project called PLoS ONE to be launched in 2006. ---- This seminar series is sponsored by OpenWetWare (http://openwetware.org), a wiki serving the biological science and engineering community. For more information, or online videos of past lectures, go to the Seminar Serieswebsite. Those interested in meeting with Dr. Surridge, please contact Sri Kosuri (skosuri at mit.edu ). -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061016/effbd5bd/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: posterdraft.pdf Type: application/pdf Size: 719581 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-sc/attachments/20061016/effbd5bd/attachment.pdf From skosuri at MIT.EDU Tue Oct 17 14:30:45 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Tue, 17 Oct 2006 14:30:45 -0400 Subject: [OWW-SC] Discussion & Dinner with Chris Surridge Message-ID: <2b0cb7a10610171130h24803865r6931e657bbcdd6c0@mail.gmail.com> Hello all, We will be meeting with Chris Surridge on Friday at 4pm, after the talk, to discuss PLoS ONE, OpenWetWare and the future of academic publishing. This should make for an exciting discussion. Afterwards, those interested can also attend dinner afterwards. Please email me if you are interested in the dinner. All are invited to the discussion. Thanks, Sri Kosuri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061017/937cb7a7/attachment.htm From skosuri at MIT.EDU Thu Oct 19 12:05:39 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Thu, 19 Oct 2006 12:05:39 -0400 Subject: [OWW-SC] Reminder -- Chris Surridge Meeting 4pm 32-397 Message-ID: <2b0cb7a10610190905j4d2c17f7i9527239daf8d3f91@mail.gmail.com> Hi All, I wanted to remind you of our meeting with Chris Surridge at 4pm in 32-397. We will probably talk until 6pm before we go to dinner. I'm sure we will have enough to talk about. If you can attend, please let me know. Also, please contact me by today if you are interested in Dinner with Chris Surridge. There will be a couple of outsiders attending dinner as well: Hemai Parthasarathy (Managing Editor of PLoS Biology) Corie Lok (Managing Editor of Nature Network Boston) Thanks, Sri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061019/18ee3811/attachment.htm From lucks at fas.harvard.edu Thu Oct 19 12:20:33 2006 From: lucks at fas.harvard.edu (Julius Lucks) Date: Thu, 19 Oct 2006 12:20:33 -0400 Subject: [OWW-SC] science.reddit.com Message-ID: Hi SC, Reddit has just launched a subreddit for science: science.reddit.com. I think this is a great venue for OWW to try out some reddit-like activities, and bring attention to OWW to the scientific community at large. I talked with the reddit people yesterday and they say the build-your-own subreddit is still planned, but some other technical items have to be done first. In any case, since science.reddit just launched, OWW has a unique opportunity to shape the community of this subreddit. If all goes well and we really like it, I think reddit will be open to creating a subreddit just for us, even if the build-your-own feature is not released yet. Cheers, Julius ----------------------------------------------------- http://openwetware.org/wiki/User:Lucks ----------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061019/72c09fe6/attachment.htm From johncumbers at gmail.com Thu Oct 19 22:40:56 2006 From: johncumbers at gmail.com (John Cumbers) Date: Thu, 19 Oct 2006 22:40:56 -0400 Subject: [OWW-SC] science.reddit.com In-Reply-To: References: Message-ID: er... I'm not quiet convinced that this is what I want to read, I suggest we look into implementing our own OWW version of ranking top pages instead of waiting for reddit, any suggestions on how to implement it? John On 10/19/06, Julius Lucks wrote: > Hi SC, > > Reddit has just launched a subreddit for science: science.reddit.com. I > think this is a great venue for OWW to try out some reddit-like activities, > and bring attention to OWW to the scientific community at large. I talked > with the reddit people yesterday and they say the build-your-own subreddit > is still planned, but some other technical items have to be done first. In > any case, since science.reddit just launched, OWW has a unique opportunity > to shape the community of this subreddit. If all goes well and we really > like it, I think reddit will be open to creating a subreddit just for us, > even if the build-your-own feature is not released yet. > > Cheers, > > Julius > > > ----------------------------------------------------- > http://openwetware.org/wiki/User:Lucks > ----------------------------------------------------- > > > > > _______________________________________________ > 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 From johncumbers at gmail.com Fri Oct 20 17:51:09 2006 From: johncumbers at gmail.com (John Cumbers) Date: Fri, 20 Oct 2006 17:51:09 -0400 Subject: [OWW-SC] oww.reddit.com Message-ID: Hi all, So the reddit people would be willing to set up oww.reddit.com for us, but others did now want to commit to this just yet. Given that we want to try some sort of voting and commenting system out now, could we just go with it and see how it goes? The name OWW means nothing without it linked from the wiki. alternatively maybe we could have the not-so-catchy biosciencewiki.reddit.com to start with. Either way, if we embed it into an OWW webpage then nobody is going to go to the main URL anyway. We could link to it from the main page to give it initial publicity, and if it works, eventually show the top n articles on the main page. I think this would be a good way to experiment with it, but if you have concerns please voice them now. We could try and synchronise the logins eventually and we could arrange it so that the comments and postings are licensed under creative comments. Please let me know cheers, John -- 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/20061020/28d1aa8c/attachment.htm From lucks at fas.harvard.edu Fri Oct 20 17:56:09 2006 From: lucks at fas.harvard.edu (Julius Lucks) Date: Fri, 20 Oct 2006 17:56:09 -0400 Subject: [OWW-SC] oww.reddit.com In-Reply-To: References: Message-ID: Note that no loggins are required to see the results - only to comment and vote. I also don't see a problem for oww.reddit.com - I think reddit can filter out pages posted from other locations so this one will have only OWW content. Cheers, Julius ----------------------------------------------------- http://openwetware.org/wiki/User:Lucks ----------------------------------------------------- On Oct 20, 2006, at 5:51 PM, John Cumbers wrote: > Hi all, > So the reddit people would be willing to set up oww.reddit.com for > us, but others did now want to commit to this just yet. Given > that we want to try some sort of voting and commenting system out > now, could we just go with it and see how it goes? The name OWW > means nothing without it linked from the wiki. > > alternatively maybe we could have the not-so-catchy > biosciencewiki.reddit.com to start with. Either way, if we embed > it into an OWW webpage then nobody is going to go to the main URL > anyway. We could link to it from the main page to give it initial > publicity, and if it works, eventually show the top n articles on > the main page. I think this would be a good way to experiment with > it, but if you have concerns please voice them now. > > We could try and synchronise the logins eventually and we could > arrange it so that the comments and postings are licensed under > creative comments. > > Please let me know > cheers, > John > > > -- > 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 > _______________________________________________ > 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/20061020/7042e81a/attachment.htm From ilyas at MIT.EDU Sun Oct 22 21:26:43 2006 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Sun, 22 Oct 2006 21:26:43 -0400 Subject: [OWW-SC] new server Message-ID: <453C1A53.3080109@mit.edu> Today (Oct 22) OpenWetWare has been moved to the new server hosted at Rackspace (special thanks for technical help to Austin Che). Please send email to admin at openwetware.org if you notice anything out of the ordinary with the site. Ilya From jasonk at MIT.EDU Tue Oct 24 00:20:44 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Tue, 24 Oct 2006 00:20:44 -0400 Subject: [OWW-SC] oww.reddit.com In-Reply-To: References:

Message-ID: <7c085c480610232120n1b54c1adg4d7032c94c6dd724@mail.gmail.com> I think it's worth setting it up so that people can actually try it and see how well it would work out. I think john's description of an OWW page with the embedded oww.reddit.com sounds fine -- then we can have a highlight about it on the front page so folks notice it and see how it plays out. anyone have any issues with this / other thoughts? probably worth giving it a try before the next SC meeting if its technically feasible. thanks, jason On 10/20/06, Julius Lucks wrote: > Note that no loggins are required to see the results - only to comment and > vote. I also don't see a problem for oww.reddit.com - I think reddit can > filter out pages posted from other locations so this one will have only OWW > content. > > Cheers, > > Julius > > > ----------------------------------------------------- > http://openwetware.org/wiki/User:Lucks > ----------------------------------------------------- > > > > > On Oct 20, 2006, at 5:51 PM, John Cumbers wrote: > > Hi all, > So the reddit people would be willing to set up oww.reddit.com for us, but > others did now want to commit to this just yet. Given that we want to try > some sort of voting and commenting system out now, could we just go with it > and see how it goes? The name OWW means nothing without it linked from the > wiki. > > alternatively maybe we could have the not-so-catchy > biosciencewiki.reddit.com to start with. Either way, if we embed it into an > OWW webpage then nobody is going to go to the main URL anyway. We could > link to it from the main page to give it initial publicity, and if it works, > eventually show the top n articles on the main page. I think this would be > a good way to experiment with it, but if you have concerns please voice them > now. > > We could try and synchronise the logins eventually and we could arrange it > so that the comments and postings are licensed under creative comments. > > Please let me know > cheers, > John > > > -- > 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 > _______________________________________________ > 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 endy at MIT.EDU Wed Oct 25 15:48:57 2006 From: endy at MIT.EDU (Drew Endy) Date: Wed, 25 Oct 2006 15:48:57 -0400 Subject: [OWW-SC] Surridge? Message-ID: <5D9EFBFA-4F7B-4732-BA35-9699325ACB6B@mit.edu> How was Chris Surridge's talk? (v. sorry to have missed it) -Drew From skosuri at MIT.EDU Wed Oct 25 16:12:22 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Wed, 25 Oct 2006 16:12:22 -0400 Subject: [OWW-SC] check the ums Message-ID: <2b0cb7a10610251312r2d9a07bam7395048b90b5eaa@mail.gmail.com> periodically, please check the UMS it's not sending out emails... so we have to do them manually.. sri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061025/bd67133d/attachment.htm From austin at csail.mit.edu Thu Oct 26 14:03:07 2006 From: austin at csail.mit.edu (Austin Che) Date: Thu, 26 Oct 2006 14:03:07 -0400 Subject: [OWW-SC] multiple image upload Message-ID: <87ejsvc5us.fsf@nitsua.mit.edu> I happened to notice that the mediawiki repository had an extension called MultiUpload. We had long ago talked about multiple image upload. This might not be exactly what we'd want but it seems to be a harmless extension so I've installed it for testing. Take a look here: http://openwetware.org/wiki/Special:MultipleUpload There's a limit of 5 files at a time. -- Austin Che (617)253-5899 From rshetty at MIT.EDU Fri Oct 27 12:02:48 2006 From: rshetty at MIT.EDU (Reshma Shetty) Date: Fri, 27 Oct 2006 12:02:48 -0400 Subject: [OWW-SC] copyright and OpenWetWare Message-ID: <6e9f40380610270902h50f54566yf313d0b8f58aadd7@mail.gmail.com> I thought that this article (if true) has interesting implications for potential copyright violations on OpenWetWare. http://www.slate.com/id/2152264/ The basic gist of the article is that hosting content that violates copyright is not a big problem as long as you take down the content expeditiously once notified. This particularly applies to sites that host user-generated content. Note that http://openwetware.org/wiki/OpenWetWare:Copyrights provides a mechanism for people to notify us about content on the site that violates copyright. Our situation is slightly more complicated since all material on OWW is licensed under both CC-SA and GFDL. Personally, I think we should discuss the issue of whether to permit people to choose alternate licenses for uploaded files. Mediawiki has the functionality to permit you to do this. I am undecided however. -Reshma From skosuri at MIT.EDU Fri Oct 27 12:38:56 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Fri, 27 Oct 2006 12:38:56 -0400 Subject: [OWW-SC] copyright and OpenWetWare In-Reply-To: <6e9f40380610270902h50f54566yf313d0b8f58aadd7@mail.gmail.com> References: <6e9f40380610270902h50f54566yf313d0b8f58aadd7@mail.gmail.com> Message-ID: <2b0cb7a10610270938w24e71880r5ab058f1c8ccda19@mail.gmail.com> I haven't read the article, but I am quite sure that the Digital Millenium Copyright act specifically allows user generated content to have a note like we do under the Online Copyright Infringement Liability Limitation Act. Our license is a different issue, b/c that only pertains to if we put up already openly licensed material, our license may not be compatible. This is the equivalent of a copyright violation, and they holder would have to notify us. If we wanted to be perfectly legal however, our note is not sufficient. We have to fall under the requirements for "safe harbor". There are a few things that we haven't done. For example, I believe we have to (and probably l should) become a registered agent (this costs a nominal fee). This is so if people take a claim against us to the Copyright Agency, they have an address to contact. A good description is actually at wikipedia here: http://en.wikipedia.org/wiki/Online_Copyright_Infringement_Liability_Limitation_Act#Requirements_to_obtain_the_safe_harbor Since we aren't a real organization, either someone will have to put their name on it... or we ask MIT to do it. Anyways, something to bring up at the next Steering Committee meeting. Sri On 10/27/06, Reshma Shetty wrote: > > I thought that this article (if true) has interesting implications for > potential copyright violations on OpenWetWare. > > http://www.slate.com/id/2152264/ > > The basic gist of the article is that hosting content that violates > copyright is not a big problem as long as you take down the content > expeditiously once notified. This particularly applies to sites that > host user-generated content. > > Note that http://openwetware.org/wiki/OpenWetWare:Copyrights provides > a mechanism for people to notify us about content on the site that > violates copyright. > > Our situation is slightly more complicated since all material on OWW > is licensed under both CC-SA and GFDL. > > Personally, I think we should discuss the issue of whether to permit > people to choose alternate licenses for uploaded files. Mediawiki has > the functionality to permit you to do this. I am undecided however. > > -Reshma > _______________________________________________ > 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/20061027/0d92980f/attachment.htm From austin at csail.mit.edu Sat Oct 28 17:44:56 2006 From: austin at csail.mit.edu (Austin Che) Date: Sat, 28 Oct 2006 17:44:56 -0400 Subject: [OWW-SC] calendar on sidebar Message-ID: <87r6ws8693.fsf@nitsua.mit.edu> Someone overwrote the calendar.png icon that was part of the sidebar: http://openwetware.org/wiki/Image:Calendar.png As we've talked about just removing the calendar link, I've removed it from the sidebar for now. If anyone really likes the calendar link, they can add it back and contact Cys about overwriting images. -- Austin Che (617)253-5899 From jasonk at MIT.EDU Mon Oct 30 10:09:07 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Mon, 30 Oct 2006 10:09:07 -0500 Subject: [OWW-SC] Fwd: Postgenomic + OWW In-Reply-To: References: <7c085c480610300510v6fa4b4ak3c5628546500098e@mail.gmail.com> Message-ID: <7c085c480610300709k1cb46d0atbd3cf545b62fc635@mail.gmail.com> We'll this is a step towards getting OWW citations/contributions more into the mainstream: http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou rce=openwetware jason ---------- Forwarded message ---------- From: Adie, Euan Date: Oct 30, 2006 8:22 AM Subject: Re: Postgenomic + OWW To: Jason Kelly Hi Jason, Sorry, I meant to email you back sooner. Postgenomic is now collecting links from OWW - for examples see: http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou rce=openwetware It'd be good to have an excerpt rather than just the basic "this paper has been cited on OWW" message; I'll work on that. Thanks for the test pages - that definitely helps. Cheers, Euan On 30/10/06 13:10, "Jason Kelly" wrote: > Hi Euan, > > How are things going? Please let us know if there's anything that > makes sense for us to do on our end. I made a little test page in > case that would help, it has some sample edits that are related to > adding or modifying references. > > adding 3 references: > http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8 > 3725 > > removing 2 of them: > http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8 > 3726 > > adding one back: > http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8 > 3727 > > removing them all: > http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8 > 3728 > > modifying a pmid: > http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8 > 3731 > > Thanks, > jason > > > On 10/16/06, Adie, Euan wrote: >> Hi Jason, >> >> Yeah, the fulltext feed thing is mostly laziness on my part, to be honest - >> that way I could just add OWW as a "blog" feed and only have to write a >> small amount of code to look for the Biblio markup. My main worry was >> recognizing when references have been removed or modified... >> >> Having thought about it some more, though, a better solution might be to >> just watch the existing "changes" feed and if anything that looks like a >> reference crops up then Postgenomic can retrieve the whole page itself, >> parse out the paper links and delete / modify / add internally as >> appropriate. That wouldn't require any coding on your part. >> >> I'll have a more in-depth look at it this afternoon and let you know if I >> come across any problems. >> >> Cheers! >> >> Euan >> >> >> >>> That would be a pretty obvious thing for you to look for, so you'd >>> know when someone added a reference to a paper and you'd know the URL >>> of the page that references it. >>> >>> We thought a little about making the feed contain the whole page -- >>> the issue then will be that you will get the whole page (including the >>> Bibliography tags) sent every time there is any edit to it. (e.g. >>> correcting a typo) So i guess it would look like multiple posts that >>> are all the same? Though I suppose you could just check and not allow >>> repeated posts from the same URL? We were wondering why you guys need >>> the whole page through the feed -- is it just a technical issue in >>> that it will be easier to post that on postgenomic without having to >>> follow the link and scrape the page or something? >>> >>> OK, thanks again for working with us on this, seems like this would be >>> a great thing to get working properly. >>> >>> best, >>> jason >>> >>> On 10/4/06, Adie, Euan wrote: >>>> Hi Jason, >>>> >>>> The short answer is yes - I'm definitely interested. :) >>>> >>>> I think that at the very least it'd be cool to link papers already in the >>>> Postgenomic database to the wiki pages that cite them - we do something >>>> similar already with Faculty of 1000 reviews. As you say, this sort of >>>> thing >>>> is currently outside of the current paper-cites-paper referencing system. >>>> >>>> Technically speaking, ideally there'd be a feed of recently modified pages >>>> that included the full text of the page (not just the edit): if you're >>>> using >>>> the MediaWiki citation plugin (?) then we could get everything else by >>>> looking for that markup... >>>> >>>> I don't know how feasible that is on your end: I don't really know an awful >>>> lot about the MediaWiki internals, unfortunately. :( >>>> >>>> Anyway, thanks for your mail, >>>> >>>> Cheers, >>>> >>>> Euan >>>> >>>> >>>> On 28/9/06 05:26, "Jason Kelly" wrote: >>>> >>>>> >>>>> (1) Commentary about a particular paper (e.g. a summary or critique) - >>>>> this most closely resembles the blog-type content that postgenomic >>>>> currently aggregates. >>>>> http://openwetware.org/wiki/Stephanopoulos:Literature_Reviewed >>>>> >>>>> (2) Reference to a paper in a protocol, material description (e.g. >>>>> media recipe), etc. >>>>> http://openwetware.org/wiki/Bacterial_Transformation#References >>>>> >>>>> (3) Reference to a paper in a research project description (e.g. >>>>> referencing it as prior work) >>>>> http://openwetware.org/wiki/Reshma_Shetty/Thesis_research >>>>> >>>>> What's interesting about the last 2 types is that they are analogous >>>>> to references in a typical peer-reviewed publication. However, since >>>>> OWW falls outside the normal referencing system, author's aren't >>>>> receiving any real recognition for other scientists citing their work. >>>>> (e.g. it doesn't contribute to the "citation score" of the paper). >>>>> >>>>> So I'm not sure which of the above sort of content postgenomic would >>>>> be interested in aggregating (if any), but would love to talk more >>>>> about this if it's something you think is worthwhile. it might >>>>> require a bit more of a technical hack to set it up, since the only >>>>> RSS feed off the site currently is the RecentChanges (e.g. every change >>>>> made to the site). >>>>> >>>>> Let me know if you'd be interested in talking more. We're available >>>>> to talk by phone or email, whatever works best for you guys. >>>>> >>>>> Thanks, >>>>> Jason >>>> >>>> >>>> *************************************************************************** >>>> ** >>>> *** >>>> DISCLAIMER: This e-mail is confidential and should not be used by anyone >>>> who >>>> is >>>> not the original intended recipient. If you have received this e-mail in >>>> error >>>> please inform the sender and delete it from your mailbox or any other >>>> storage >>>> mechanism. 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Macmillan Publishers Limited Registered in England and Wales with registered number 785998 Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS ******************************************************************************** From austin at csail.mit.edu Mon Oct 30 14:55:29 2006 From: austin at csail.mit.edu (Austin Che) Date: Mon, 30 Oct 2006 14:55:29 -0500 Subject: [OWW-SC] Fwd: Postgenomic + OWW In-Reply-To: <7c085c480610300709k1cb46d0atbd3cf545b62fc635@mail.gmail.com> (Jason Kelly's message of "Mon, 30 Oct 2006 10:09:07 -0500") References: <7c085c480610300510v6fa4b4ak3c5628546500098e@mail.gmail.com> <7c085c480610300709k1cb46d0atbd3cf545b62fc635@mail.gmail.com> Message-ID: <87u01l7f4e.fsf@nitsua.mit.edu> "Jason Kelly" scribbled quickly: > We'll this is a step towards getting OWW citations/contributions more > into the mainstream: > > http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou > rce=openwetware That's interesting they got all those pages on there so quickly. I don't see any bots from postgenomic in the server logs. Do we know how they are scraping OWW? Is it only Biblio tags? For example, would it get the references on this page: http://openwetware.org/wiki/BIO254:DarkNoise -- Austin Che (617)253-5899 From jasonk at MIT.EDU Mon Oct 30 15:53:56 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Mon, 30 Oct 2006 15:53:56 -0500 Subject: [OWW-SC] Fwd: Postgenomic + OWW In-Reply-To: <87u01l7f4e.fsf@nitsua.mit.edu> References: <7c085c480610300510v6fa4b4ak3c5628546500098e@mail.gmail.com> <7c085c480610300709k1cb46d0atbd3cf545b62fc635@mail.gmail.com> <87u01l7f4e.fsf@nitsua.mit.edu> Message-ID: <7c085c480610301253s7cd99b46na28c41590c994f87@mail.gmail.com> They should be getting it from the RecentChanges RSS feed from here on out, I guess -- though I guess that doesn't explain how they got the current list. I'll ask. jason On 10/30/06, Austin Che wrote: > "Jason Kelly" scribbled quickly: > > > We'll this is a step towards getting OWW citations/contributions more > > into the mainstream: > > > > http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou > > rce=openwetware > > That's interesting they got all those pages on there so quickly. I > don't see any bots from postgenomic in the server logs. Do we know > how they are scraping OWW? Is it only Biblio tags? For example, > would it get the references on this page: > http://openwetware.org/wiki/BIO254:DarkNoise > > -- > Austin Che (617)253-5899 > _______________________________________________ > OpenWetWare Steering Committee Mailing List > sc at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-sc > From jasonk at MIT.EDU Tue Oct 31 08:53:10 2006 From: jasonk at MIT.EDU (Jason Kelly) Date: Tue, 31 Oct 2006 08:53:10 -0500 Subject: [OWW-SC] Time Hanney at Berkman Center w/ video Message-ID: <7c085c480610310553n371bbd17r153147703f24f62c@mail.gmail.com> TImo Hanney (in charge of Nature Web publishing) apprently gave a talk about Nature's online publishing efforts recently at the Berkman center. There's a pretty good blog post about it, and there are links to a video of the talk at the bottom: http://www.hyperorg.com/blogger/mtarchive/berkman_timo_hannay_on_web_sci.html jason From skosuri at MIT.EDU Tue Oct 31 09:37:53 2006 From: skosuri at MIT.EDU (Sri Kosuri) Date: Tue, 31 Oct 2006 09:37:53 -0500 Subject: [OWW-SC] wikipedia usability tests and suggestions Message-ID: <2b0cb7a10610310637o7d6caf93y471bedceba746177@mail.gmail.com> This is a usability test on the german wikipedia site. Many of the suggestions on page creation and templating apply to our site as well. Thought I would send along the test if you were interested. Sri -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-sc/attachments/20061031/93d5c787/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: wikipedia usability.pdf Type: application/pdf Size: 1569884 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-sc/attachments/20061031/93d5c787/attachment.pdf From austin at csail.mit.edu Tue Oct 31 17:26:02 2006 From: austin at csail.mit.edu (Austin Che) Date: Tue, 31 Oct 2006 17:26:02 -0500 Subject: [OWW-SC] reddit and jotspot acquired Message-ID: <87iri03yx1.fsf@nitsua.mit.edu> Google bought JotSpot (wiki software company) and Wired bought Reddit. Interesting how we were discussing how long reddit would stay around at the recent steering committee meetings... http://slashdot.org/article.pl?sid=06/10/31/1910231&from=rss -- Austin Che (617)253-5899 From rshetty at MIT.EDU Tue Oct 31 16:25:17 2006 From: rshetty at MIT.EDU (Reshma Shetty) Date: Tue, 31 Oct 2006 16:25:17 -0500 Subject: [OWW-SC] oww.reddit.com In-Reply-To: <7c085c480610232120n1b54c1adg4d7032c94c6dd724@mail.gmail.com> References:

<7c085c480610232120n1b54c1adg4d7032c94c6dd724@mail.gmail.com> Message-ID: <6e9f40380610311325k3a921a84n6b586ef1ecf6cef@mail.gmail.com> Reddit has been purchased and apparently the founders are moving to SF. http://www.techcrunch.com/2006/10/31/breaking-news-conde-nastwired-acquires-reddit/ I am not sure what this means for oww.reddit.com. -Reshma On 10/23/06, Jason Kelly wrote: > I think it's worth setting it up so that people can actually try it > and see how well it would work out. I think john's description of an > OWW page with the embedded oww.reddit.com sounds fine -- then we can > have a highlight about it on the front page so folks notice it and see > how it plays out. > > anyone have any issues with this / other thoughts? probably worth > giving it a try before the next SC meeting if its technically > feasible. > > thanks, > jason > > > > On 10/20/06, Julius Lucks wrote: > > Note that no loggins are required to see the results - only to comment and > > vote. I also don't see a problem for oww.reddit.com - I think reddit can > > filter out pages posted from other locations so this one will have only OWW > > content. > > > > Cheers, > > > > Julius > > > > > > ----------------------------------------------------- > > http://openwetware.org/wiki/User:Lucks > > ----------------------------------------------------- > > > > > > > > > > On Oct 20, 2006, at 5:51 PM, John Cumbers wrote: > > > > Hi all, > > So the reddit people would be willing to set up oww.reddit.com for us, but > > others did now want to commit to this just yet. Given that we want to try > > some sort of voting and commenting system out now, could we just go with it > > and see how it goes? The name OWW means nothing without it linked from the > > wiki. > > > > alternatively maybe we could have the not-so-catchy > > biosciencewiki.reddit.com to start with. Either way, if we embed it into an > > OWW webpage then nobody is going to go to the main URL anyway. We could > > link to it from the main page to give it initial publicity, and if it works, > > eventually show the top n articles on the main page. I think this would be > > a good way to experiment with it, but if you have concerns please voice them > > now. > > > > We could try and synchronise the logins eventually and we could arrange it > > so that the comments and postings are licensed under creative comments. > > > > Please let me know > > cheers, > > John > > > > > > -- > > 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 > > _______________________________________________ > > 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 >