From johncumbers at gmail.com Wed May 2 12:22:08 2007 From: johncumbers at gmail.com (John Cumbers) Date: Wed, 2 May 2007 12:22:08 -0400 Subject: [OWW-Discuss] The Death of the Scientific Paper Message-ID: I had not read this before.. best, John *The Death of the Scientific Paper*Seringhaus M, Gerstein M (2006). The Scientist. 20(9): 25. http://www.seringhaus.net/writing.html " Forget "publish or perish." Academic publishing must diversify or die. Just as PubMed indexes journal abstracts in a structured fashion, we propose cataloging a broad range of material, which would enable users to run PubMedlike queries over abstracts, full text, data sets, lay summaries, and presentations, all through a single porta While this highlights the importance of nontraditional communication in science, it is also regrettable: After all, journal articles are the main output for which scientists earn recognition, and producing them commands a huge share of our efforts. Meanwhile, virtually no credit is afforded to producing quality highlevel summaries or to online data deposition. Journals must produce more than just papers. Editors should demand online deposit of data as a requirement for publication, and enforce a unified nomenclature for biology. In addition to the traditional manuscript, The Scientist : The Death of the Scientific Paper Page 2 of 4 http://www.the-scientist.com/2006/9/1/25/1/ 9/4/2006 " Michael Seringhaus was previously mentioned on oww.. by Sri :Lyse Lyse Baby- An awesome remake of Ice, Ice Baby by Michael Seringhaus -- 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/20070502/b6f4e44a/attachment.htm From ilyas at MIT.EDU Thu May 3 17:30:35 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Thu, 03 May 2007 17:30:35 -0400 Subject: [OWW-Discuss] academic genealogy Message-ID: <463A547B.40906@mit.edu> Here's a short summary: "One's doctoral advisor is one's academic parent. This lets us define an academic genealogy of researchers, to describe the academic ancestors and descendents of a particular set of researchers." See the AI Genealogy Project (http://aigp.csres.utexas.edu/~aigp/?s=mission) for more details. Another option would be to make use of the Semantic Web extension. Here are some examples: http://wiki.ontoworld.org/wiki/People http://wiki.ontoworld.org/wiki/Valentina_Tamma I think it may be useful to do something like this for OWW. Ilya From johncumbers at gmail.com Fri May 4 09:13:00 2007 From: johncumbers at gmail.com (John Cumbers) Date: Fri, 4 May 2007 09:13:00 -0400 Subject: [OWW-Discuss] academic genealogy In-Reply-To: <463A547B.40906@mit.edu> References: <463A547B.40906@mit.edu> Message-ID: This is a really good idea Ilya, and would turn out to be really popular I think. would it take much to implement it? Best, john On 5/3/07, Ilya Sytchev wrote: > > Here's a short summary: > > "One's doctoral advisor is one's academic parent. This lets us define an > academic genealogy of researchers, to describe the academic ancestors > and descendents of a particular set of researchers." > > See the AI Genealogy Project > (http://aigp.csres.utexas.edu/~aigp/?s=mission) for more details. > > Another option would be to make use of the Semantic Web extension. Here > are some examples: > http://wiki.ontoworld.org/wiki/People > http://wiki.ontoworld.org/wiki/Valentina_Tamma > > I think it may be useful to do something like this for OWW. > > Ilya > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > -- 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/20070504/6b017990/attachment.htm From johncumbers at gmail.com Sun May 6 13:48:47 2007 From: johncumbers at gmail.com (John Cumbers) Date: Sun, 6 May 2007 13:48:47 -0400 Subject: [OWW-Discuss] Share your lab notes, long term archive of OWW Message-ID: I think that this is where the future funding of OWW could come from. Could we think about formalizing (or publisizing if it already happens on a regular interval) a dump of the OWW database. Furthermore, is there an organization out there that would store a physical copy of the dump, e.g on a tape backup, DVD, HD. A body independent of OWW that could authenticate the data has not been tampered with in cases of fraud. Other organizations must be thinking about this too. Probably something we don't want to do now, but this could form the basis of a long-term grant in the future. this also relates to a recent post about Wiki's not being a reliable source for patent cases. I'd say that we could turn them into a reliable source if we implemented a policy such as that above. Best, John http://www.nature.com/nature/journal/v447/n7140/full/447001b.html *Nature* *447*, 1-2 (3 May 2007) | doi:10.1038/447001b; Published online 2 May 2007 Share your lab notes The use of electronic laboratory notebooks should be supported by all concerned. Institutions therefore need to show leadership in this area, and funding agencies should provide additional infrastructure support earmarked for the development and upkeep of electronic notebook systems. Funding agencies also need to recognize that, by providing such support, some of the concerns over the loss of data can be assuaged, and the rigour and transparency of publicly funded research will be improved. -- 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/20070506/96f7419e/attachment.htm From tk at csail.mit.edu Sun May 6 17:29:04 2007 From: tk at csail.mit.edu (Tom Knight) Date: Sun, 6 May 2007 17:29:04 -0400 Subject: [OWW-Discuss] Share your lab notes, long term archive of OWW In-Reply-To: References: Message-ID: With MD5 or better hashes of the data, and well known techniques for hash-merging and publication, the technical problem of assuring dated unforgeable records was solved 10 years ago. We just need to implement well known solutions to these problems. We don't need a third party to authenticate records. The records, and the public irrevocable and untamperable disclosure (in print, e.g. in the NY Times) of a daily hash are sufficient. Internet Archive (www.archive.org) will gladly store our records. It is a drop in the bucket compared to what they are storing every day. Brewster Kahle (who runs it) is a personal friend, but that wouldn't make it more likely to happen. On May 6, 2007, at 1:48 PM, John Cumbers wrote: > I think that this is where the future funding of OWW could come from.? > Could we think about formalizing (or publisizing if it already happens > on a regular interval) a? dump of the OWW database.??? Furthermore, is > there an organization out there that would store a physical copy of > the dump, e.g on a tape backup, DVD, HD.? A body independent of OWW > that could authenticate the data has not been tampered with in cases > of fraud.? Other organizations must be thinking about this too.? > Probably something we don't want to do now, but this could form the > basis of a long-term grant in the future. > > this also relates to a recent post about Wiki's not being a reliable > source for patent cases.? I'd say that we could turn them into a > reliable source if we implemented a policy such as that above. > > Best, > ?John > > > http://www.nature.com/nature/journal/v447/n7140/full/447001b.html > > Nature 447, 1-2 (3 May 2007) | doi:10.1038/447001b; Published online > 2 May 2007 > > Share your lab notes > > The use of electronic laboratory notebooks should be supported by all > concerned. > > Institutions therefore need to show leadership in this area, and > funding agencies should provide additional infrastructure support > earmarked for the development and upkeep of electronic notebook > systems. Funding agencies also need to recognize that, by providing > such support, some of the concerns over the loss of data can be > assuaged, and the rigour and transparency of publicly funded research > will be improved. > > -- > 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_______________________________________________ > 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: 2759 bytes Desc: not available Url : http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070506/ecadd7d9/attachment.bin -------------- 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-discuss/attachments/20070506/ecadd7d9/attachment-0001.bin From johncumbers at gmail.com Sun May 6 17:50:24 2007 From: johncumbers at gmail.com (John Cumbers) Date: Sun, 6 May 2007 17:50:24 -0400 Subject: [OWW-Discuss] Share your lab notes, long term archive of OWW In-Reply-To: References: Message-ID: Great, then I hope that we can look to implementing it, and also publicizing it. For those new to wiki's, they often don't see what the big deal is, it's only when you know about the history tab and can look back over X years of changes that the power becomes apparent. I'll bring up how to implement this at the next steering committee meeting, Perhaps this could be mentioned in the review article that somebody was writing about OWW? Best, John On 5/6/07, Tom Knight wrote: > > With MD5 or better hashes of the data, and well known techniques for > hash-merging and publication, the technical problem of assuring dated > unforgeable records was solved 10 years ago. We just need to > implement well known solutions to these problems. > > We don't need a third party to authenticate records. The records, and > the public irrevocable and untamperable disclosure (in print, e.g. in > the NY Times) of a daily hash are sufficient. > > Internet Archive (www.archive.org) will gladly store our records. It > is a drop in the bucket compared to what they are storing every day. > Brewster Kahle (who runs it) is a personal friend, but that wouldn't > make it more likely to happen. > > > On May 6, 2007, at 1:48 PM, John Cumbers wrote: > > > I think that this is where the future funding of OWW could come from. > > Could we think about formalizing (or publisizing if it already happens > > on a regular interval) a dump of the OWW database. Furthermore, is > > there an organization out there that would store a physical copy of > > the dump, e.g on a tape backup, DVD, HD. A body independent of OWW > > that could authenticate the data has not been tampered with in cases > > of fraud. Other organizations must be thinking about this too. > > Probably something we don't want to do now, but this could form the > > basis of a long-term grant in the future. > > > > this also relates to a recent post about Wiki's not being a reliable > > source for patent cases. I'd say that we could turn them into a > > reliable source if we implemented a policy such as that above. > > > > Best, > > John > > > > > > http://www.nature.com/nature/journal/v447/n7140/full/447001b.html > > > > Nature 447, 1-2 (3 May 2007) | doi:10.1038/447001b; Published online > > 2 May 2007 > > > > Share your lab notes > > > > The use of electronic laboratory notebooks should be supported by all > > concerned. > > > > Institutions therefore need to show leadership in this area, and > > funding agencies should provide additional infrastructure support > > earmarked for the development and upkeep of electronic notebook > > systems. Funding agencies also need to recognize that, by providing > > such support, some of the concerns over the loss of data can be > > assuaged, and the rigour and transparency of publicly funded research > > will be improved. > > > > -- > > 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_______________________________________________ > > OpenWetWare Discussion Mailing List > > discuss at openwetware.org > > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > -- 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/20070506/24838d77/attachment.htm From ilyas at MIT.EDU Tue May 8 19:56:25 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Tue, 08 May 2007 19:56:25 -0400 Subject: [OWW-Discuss] academic genealogy In-Reply-To: References: <463A547B.40906@mit.edu> Message-ID: <46410E29.6060209@mit.edu> I've sent an email to the Math Genealogy project (the original project) but haven't heard anything back. I think our best bet would be to implement this idea ourselves using the Semantic MediaWiki extension or some social networking software like Elgg or PeopleAggregator - need to think about it a bit more. Ilya John Cumbers wrote: > This is a really good idea Ilya, and would turn out to be really popular > I think. would it take much to implement it? > Best, > john > > On 5/3/07, *Ilya Sytchev * > wrote: > > Here's a short summary: > > "One's doctoral advisor is one's academic parent. This lets us define an > academic genealogy of researchers, to describe the academic ancestors > and descendents of a particular set of researchers." > > See the AI Genealogy Project > (http://aigp.csres.utexas.edu/~aigp/?s=mission) for more details. > > Another option would be to make use of the Semantic Web > extension. Here > are some examples: > http://wiki.ontoworld.org/wiki/People > http://wiki.ontoworld.org/wiki/Valentina_Tamma > > > I think it may be useful to do something like this for OWW. > > Ilya > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > > > > -- > 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 From skosuri at MIT.EDU Wed May 9 10:35:24 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Wed, 9 May 2007 10:35:24 -0400 Subject: [OWW-Discuss] compendium of species... Message-ID: <2b0cb7a10705090735n6d6fe51ch3759027c91b2e5d3@mail.gmail.com> Scientists Work on Encyclopedia of Life http://www.physorg.com/news97867782.html From ilyas at MIT.EDU Thu May 10 00:59:30 2007 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Thu, 10 May 2007 00:59:30 -0400 Subject: [OWW-Discuss] Scientists Work on Encyclopedia of Life Message-ID: <4642A6B2.80503@mit.edu> "The pages can be adjusted so that they provide useful information for both a schoolchild and a research biologist alike, with an emphasis on encouraging "citizen-scientists" to add their sightings. While amateurs can contribute in clearly marked side pages, the key detail and science parts of the encyclopedia will be compiled and reviewed by experts." http://news.wired.com/dynamic/stories/E/ENCYCLOPEDIA_OF_LIFE?SITE=WIRE&SECTION=HOME&TEMPLATE=DEFAULT http://www.eol.org/ From bcanton at MIT.EDU Mon May 21 18:41:36 2007 From: bcanton at MIT.EDU (Barry Canton) Date: Mon, 21 May 2007 18:41:36 -0400 Subject: [OWW-Discuss] A collaborative letter to the editor Message-ID: <52c0d2160705211541v233e8504t6db302ff1f75a4fa@mail.gmail.com> Here's an interesting example of a "Web2.0" collaboration responding to an "old media" article: http://thelede.blogs.nytimes.com/2007/05/21/to-the-editor-please-see-wiki/ Although the specific example is based on copyright, one can imagine the same thing happening in science. Barry -- Barry Canton Endy Lab Biological Engineering Division Massachusetts Institute of Technology Tel.:(617) 899 6062 Email1: bcanton at mit.edu Email2: bcanton at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20070521/e2c03c33/attachment.htm From skosuri at MIT.EDU Tue May 22 00:07:15 2007 From: skosuri at MIT.EDU (Sri Kosuri) Date: Tue, 22 May 2007 00:07:15 -0400 Subject: [OWW-Discuss] Article on Mozilla Foundation Message-ID: <2b0cb7a10705212107t32aa254bw57ca7cfb0ccb6674@mail.gmail.com> Considering our ongoing discussions on the volunteer community, fundraising, and long-term sustainability.. I thought the following article in the NYTimes on the Mozilla foundation was interesting: May 21, 2007 Link by Link Firefox and the Anxiety of Growing Pains By NOAM COHEN IF the open-source software movement were an upstart political campaign, Chris Messina would be one of its community organizers ? the young volunteer who decamps to New Hampshire, knocking on doors, putting up signs. In 2004, Mr. Messina, a 26-year-old Web entrepreneur from San Francisco, found his dream candidate in Firefox, the open-source Internet browser that is a rival to Microsoft's Internet Explorer. Unlike the other candidate he volunteered for that year, Howard Dean, Firefox is still racking up victories. And unlike Mr. Dean, the people behind Firefox have a dilemma: what happens ? and what is owed to volunteer contributors ? when an open-source project starts to become successful? Some 1,000 to 2,000 people have contributed code to Firefox, according to the Mozilla Foundation, which distributes the Firefox browser. An estimated 10,000 people act as testers for the program, and an estimated 80,000 help spread the word. ? In 2004, with the release of version 1.0, Firefox became the dream of techies like Mr. Messina. Much in the way he helped coordinate supporters for Mr. Dean online, he got behind Spread Firefox, a campaign to rally the open-source base behind the browser. That effort culminated in a fund-raising drive to advertise Firefox in The New York Times. The ad, a double-page spread designed by Mr. Messina, ran on Dec. 16, 2004. "It was 10,000 people, putting in like 5 bucks to ? I don't know what the highest was," he said. "It was in the spirit of the Howard Dean campaign." The Firefox campaign has been very successful, according to Mitchell Baker, the chairwoman of the nonprofit Mozilla Foundation that directs the project. "The best we can figure, 75 to 100 million people are using Firefox," she said. "Those people did not get it in a box. That is 75 million decisions, somewhere around the world to put this piece of software on someone's machine." According to outside estimates, Firefox has about 15 percent of the market, Internet Explorer has more than 78 percent, and Apple's Safari a little less than 5 percent. Mozilla has 90 employees and revenue of more than $100 million in the last couple of years. Mozilla plans to make enough money to keep growing. But a windfall came in the form of a royalty contract with Google, which, like the other search companies, is always competing for better placement on browsers. Under the agreement, the Google search page is the default home page when a user first installs Firefox, and is the default in the search bar. In the last two years, the deal has brought in more than $100 million. (Google has a similar placement with Apple's Safari.) So far, no one has figured out how to balance keeping an open-source or collaborative project fully financed while remaining independent and noncommercial. Wikipedia, for example, holds occasional fund-raisers, while its leaders debate if it should take steps toward some sort of sponsorship or advertising. Thanks to the Google agreement, the Mozilla Foundation went from revenue of nearly $6 million in 2004 to more than $52 million the next year. The foundation plans to increase its work force, and to add some engineering capability. In 2005, the foundation created a subsidiary, the for-profit Mozilla Corporation, also led by Ms. Baker, mainly to deal with the tax and other issues related to the Google contract. (The foundation's 2006 tax return has not yet been made public, but Ms. Baker said the Google revenue will remain about the same.) She described the decision to align with Google as an organic one that predates the official release of Firefox. "We had Google in a beta version for a long time, so we approached them first," she said. Mitch Kapor, who is on the Mozilla board, said that accepting a deal with Google was a no-brainer. "Always on my mind, in all my involvement is, how is it going to be sustainable?" he said. "I am a big believer that begging is not the right business model. When it began to become clear there was a business opportunity, in monetizing search in the browser, I saw this as a great opportunity." ? But with opportunities came changes. By creating a corporation to run the Firefox project, Mozilla was committing to be less transparent. In part, that is because Google insists on the secrecy of "its arrangement and agreements," Mr. Kapor said. (Google declined to comment for this article.) Because transparency is one of the principles of the so-called Mozilla manifesto released in February, Mr. Kapor said, there was "some tension around getting the deal done and disclosure." Another complication for Mozilla, some critics say, is that it could be perceived as acting as an extension of Google. For example, they note that one of Google's growth areas, Web-based software applications, would have a better chance of success with a browser not controlled by its biggest rival, Microsoft. The exact nature of Mozilla's relationship with Google has been good fodder for bloggers. When Mr. Messina recently posted a 50-minute video of his thoughts about Firefox development, the comments included a back and forth between Asa Dotzler of the Mozilla Corporation, and a commentator on the blog named Corey. When Corey wrote that "it seems like half" of the top contributors to Mozilla "work directly for Google," Mr. Dotzler responded harshly, dismissing the claim outright: "No one who has looked at the actual development of Firefox recently could say with a straight face that Google employees are top contributors to Mozilla." Finally, there is the problem of what Mozilla should do with the money, at least the portion that isn't being reinvested in the Firefox. Throwing money around among volunteers can backfire, Ms. Baker said, though the foundation has been quietly assisting contributors who are hampered by poor equipment. Instead, Mozilla's solution is to put money into what Mr. Kapor calls "community purposes." To that end, the foundation is looking for a new executive director who would focus on worthy projects, although no decisions on what constitutes a worthy project has been made. "We go out and ask," Ms. Baker said, "and even the community is not actually clear where large amounts of money should go."