From rvidal at openwetware.org Mon Jun 2 13:08:07 2008 From: rvidal at openwetware.org (Ricardo Vidal) Date: Mon, 2 Jun 2008 13:08:07 -0400 Subject: [OWW-Discuss] Elsevier Grand Challenge Message-ID: <213fc43b0806021008v6776dbebq31311244ecb9b5cc@mail.gmail.com> This looks interesting. Thought it'd be of interest to others. http://www.elseviergrandchallenge.com/ Ricardo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080602/27f45676/attachment.htm From russell2 at qiezi.net Mon Jun 2 14:10:47 2008 From: russell2 at qiezi.net (Russell Hanson) Date: Mon, 02 Jun 2008 14:10:47 -0400 Subject: [OWW-Discuss] Elsevier Grand Challenge In-Reply-To: <213fc43b0806021008v6776dbebq31311244ecb9b5cc@mail.gmail.com> References: <213fc43b0806021008v6776dbebq31311244ecb9b5cc@mail.gmail.com> Message-ID: <484437A7.8070907@qiezi.net> Wow. Elsevier gets free consulting services for peanuts. And a free membership to sciencedirect! Amazing. Greets from the Disruptive Technologies Lab at Elsevier, Amsterdam... Russell Ricardo Vidal wrote: > This looks interesting. Thought it'd be of interest to others. > http://www.elseviergrandchallenge.com/ > > > Ricardo > ------------------------------------------------------------------------ > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > From hoatlinm at ohsu.edu Mon Jun 2 16:25:01 2008 From: hoatlinm at ohsu.edu (Maureen Hoatlin) Date: Mon, 02 Jun 2008 13:25:01 -0700 Subject: [OWW-Discuss] San Diego Science Festival Message-ID: This looks like an amazing event for joining people in all types of science. Although it is in San Diego, there is a facebook-like social network and lots of interesting content is starting to appear. I don't see much on synthetic biology, so I thought that OWW should be aware of this in case they want to make some contributions. I am evangelizing for this after I read the call to action: http://www.sdsciencefestival.com/htmls/about/calltoaction.htm -Maureen From nkuldell at MIT.EDU Mon Jun 2 16:40:49 2008 From: nkuldell at MIT.EDU (Natalie Kuldell) Date: Mon, 02 Jun 2008 16:40:49 -0400 Subject: [OWW-Discuss] San Diego Science Festival In-Reply-To: References: Message-ID: <48445AD1.8090201@mit.edu> Hi all- I'm coordinating the Boston-area hub for an outreach and education effort that will be linked to this festival. Anyone in the Boston-area interested in networking and partnering with great institutions around town (incl. WGBH, Boston's Museum of Science, and lots of others) to cross-promoter activities and move science from the fringe to center stage, email me (nkuldell at mit.edu). We had a great kick-off meeting in early May. We'll be holding our second mixer event on July 29th at the WGBH studios in Somerville to preview the summer NovaNOW series. We have a third mixer and showcase planned for Sept 26th at the MIT Museum as part of their anniversary celebration. If you're not in the Boston-area, there may be a hub in your area. Check out: http://www.copusproject.org/ My experiences with this group have been inspiring. There are so many incredible folks involved, doing exciting educational and engaging work. Hope you'll consider joining the fun! Natalie Maureen Hoatlin wrote: > This looks like an amazing event for joining people in all types of science. > Although it is in San Diego, there is a facebook-like social network and > lots of interesting content is starting to appear. I don't see much on > synthetic biology, so I thought that OWW should be aware of this in case > they want to make some contributions. > > I am evangelizing for this after I read the call to action: > > http://www.sdsciencefestival.com/htmls/about/calltoaction.htm > > -Maureen > > > > > > > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss From bill.altmail at gmail.com Mon Jun 2 17:24:16 2008 From: bill.altmail at gmail.com (Bill Flanagan) Date: Mon, 2 Jun 2008 17:24:16 -0400 Subject: [OWW-Discuss] OWW going down this evening at 9:00 EST for upgrade. Please allow 2 hrs Message-ID: <26428aaa0806021424v44681ed6l1bfecf43df0f40c4@mail.gmail.com> The system will be available for read access for most of this time but will not be available for update. You may notice flakiness re: internet addresses as the DNS moves from the current server to the new one. I anticipate making the DNS change within 15 minutes of the transfer. (around 9:15 PM EST) I'll post the status on the openwetware twitter feed. Comments: 1. All user accounts on the current server should be migrated asap. Austin and Ilya are the only people who need to be concerned. 2. If either Austin or Ilya are not available, contact me. I already have moved a backup of all /home directories to the new server. 3. Almost all of the packages formerly loaded and compiled manually have been loaded via the RHEL5 YUM facility. 4. The database has moved from MySQL 4 to MySQL 5. 5. The MySQL files are still located in the /data directory as they are on the current server. 6. The stock PHP server is used rather than a custom compile. 7. All strategic historical log files have been migrated to the new server. This includes -openetware access/error logs for the last 2-3 years (none have been deleted) -yeastpheromonemodel access/error logs (none have been deleted) -syntheticbiology access/error (none have been deleted) -maillogs for openwetware.org 8. All data and image files have been replicated to the new server. They will be re-synced before the final cut-over. This includes - OWW and private wiki image files - all source, extensions, etc. 9. All historical logfiles have been purged from the existing server. A final export will be done after the cut-over. 10. There may be a few extensions relying upon Tex support that will not immediately be functional. This will be addressed ASAP. Because of the nature of the system config, I've had a hard time testing all extensions on the new system. 11. A set of script files now are used to manage the final sync of the systems. 12. I will test all private wikis to make sure they continue to work after the move. There should be no impact. 13. I will test the wordpress-mu blog software to make sure all is well with it. There should be no impact. OWW Also moving to MediaWiki 1.12 This will be done during the same cut-over. 1. There should be no effect on existing users. 2. All extensions have been checked with 1.12. No problems are present. 3. All private wikis will be upgraded at the same time. Issues 1. The web server's network address configuration is "challenging". I know it's just a text file and it can be modified if problems ensue. The complication in our case is the tight relationship between modifications to the MediaWiki source code and the network configuration. I've tested this to the extent that I can. I'm satisfied that making the server switch will work. 2. Because of the upgrade from the current Red Hat 4 to RedHat 5 Linux server release, there are issues that may crop up that I have not tested. I'll do my best to navigate these issues. 3. If the migration to 1.12 takes too long (not anticipated), I will re-enable access to the server with the existing 1.9 release. I do not foresee having to do this. There will be no effect on users regardless of the version. I'm sorry I have to take it down this early; I've not managed to stay up late enough to do it safely over the last week. Thanks! Bill Flanagan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080602/9cdb8bbf/attachment.htm From rvidal at gmail.com Mon Jun 2 19:13:58 2008 From: rvidal at gmail.com (Ricardo Vidal) Date: Mon, 2 Jun 2008 19:13:58 -0400 Subject: [OWW-Discuss] Facebook's Open Platform Message-ID: <213fc43b0806021613l4aba7565md63f1fb16c223f5c@mail.gmail.com> As someone said last week. Facebook has made their platform available. http://developers.facebook.com/fbopen/ I'm curious to see what applications it will be given. -- Ricardo Vidal -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080602/750e1dfa/attachment.htm From lorrielejeune at gmail.com Tue Jun 3 14:25:26 2008 From: lorrielejeune at gmail.com (Lorrie LeJeune) Date: Tue, 3 Jun 2008 14:25:26 -0400 Subject: [OWW-Discuss] OpenWetWare Community Town Hall meeting: Thursday, June 10 at 12 noon. Message-ID: <6ac0a26a0806031125j42f6a60fqaefb8bef1811a3c0@mail.gmail.com> Hi Folks, To better reflect the community focus of OpenWetWare, we're relaunching our monthly steering meeting as the OWW Community Town Hall.* Unless otherwise indicated, we intend to hold it on the second Thursday of the month at 12 noon. Our next Town Hall will take place next Thursday, June 12, at 12 noon EDT. The conference bridge is 617-452-5208. Instructions on which chat client to use will follow. One topic I'd like to cover at this month's meeting is discussion forums and better ways of communicating with other OWW members. Please post your ideas at: http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting At the May meeting, each person agreed to personally invite another OWW member to attend the meeting. So send out those invitations! Pertinent action items from the May meeting: * John to look into Social Text. * Ricardo to do some viral marketing for lab Notebook out in the blogosphere * Lorrie to come up with a blog posting schedule on OWW (to highlight new features on the site or other items of interest) * We'll be following up shortly with more information about OWW and the research cycle. Notes from the May meeting: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_May_2008 Best regards, --Lorrie *For anyone who's not familiar with the term, a town hall meeting is an informal public meeting derived from the traditional town meetings of New England in the U.S. (http://en.wikipedia.org/wiki/Town_hall_meeting). In this spirit, anyone in the OWW community is welcome to attend, raise issues of interest to the community, and voice their opinions. OpenWetWare is a growing community with many new members, and I really encourage any or all of you to call in or log into the chat. From sjkoch at unm.edu Tue Jun 3 15:45:12 2008 From: sjkoch at unm.edu (Steven J. Koch) Date: Tue, 3 Jun 2008 13:45:12 -0600 Subject: [OWW-Discuss] Wiki still not editable? Message-ID: <001801c8c5b2$569fc160$03df4420$@edu> Hey all, I don't see anything on the twitter feed and haven't received any new discuss messages. It appears to us in our lab that both public and private wikis are still not editable? Is this the case, or do we need to do something in terms of refreshing our browsers? The message on the wiki doesn't give any new details and the twitter feed doesn't show anything. --Steve -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080603/ae03c788/attachment.htm From rvidal at gmail.com Tue Jun 3 15:50:26 2008 From: rvidal at gmail.com (Ricardo Vidal) Date: Tue, 3 Jun 2008 15:50:26 -0400 Subject: [OWW-Discuss] Wiki still not editable? In-Reply-To: <001801c8c5b2$569fc160$03df4420$@edu> References: <001801c8c5b2$569fc160$03df4420$@edu> Message-ID: <213fc43b0806031250g4adf51abne70a3bf5b7301cb4@mail.gmail.com> Hi Steven, I've just updated the twitter feed. DNS is propagating. The old server still has the message at the top and edits are locked. The new server is up and running properly (as far as I've noticed). So, as soon as you see that message at the top disappear, it should mean you are on the new server and DNS has fully propagated. Sorry for the slow twitter updates. Cheers, Ricardo On Tue, Jun 3, 2008 at 3:45 PM, Steven J. Koch wrote: > Hey all, > > I don't see anything on the twitter feed and haven't received any new > discuss messages. It appears to us in our lab that both public and private > wikis are still not editable? Is this the case, or do we need to do > something in terms of refreshing our browsers? The message on the wiki > doesn't give any new details and the twitter feed doesn't show anything. > > --Steve > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > > -- Ricardo Vidal rvidal at gmail.com | http://my.biotechlife.net http://www.openwetware.org - Share your Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080603/6362ca17/attachment.htm From jasonk at MIT.EDU Wed Jun 4 00:36:48 2008 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 4 Jun 2008 00:36:48 -0400 Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn In-Reply-To: References: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com> Message-ID: <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> OK, LinkedIn group now exists. It seems like a pretty new feature for them, and I can't figure out how to link to the group page. If you search OpenWetWare or go to my profile in linkedIn you should be able to click the logo and sign up. thanks, jason On Mon, May 26, 2008 at 7:26 PM, Maureen Hoatlin wrote: > Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a > OWW group on facebook! I use the mobile version my iPhone so much (which > doesn't list groups) that I forgot. Pathetic. > -Maureen > > > > Maureen E. Hoatlin, PhD. > Biochemistry and Molecular Biology & Molecular and Medical Genetics > Hematologic Malignancies Program, Oregon Cancer Institute > Program in Molecular & Cellular Biosciences > Oregon Health & Science University > 3181 S.W. Sam Jackson Pk. Rd. > Medical Research Building, Rm 518 > Mailcode L224 > Portland, OR 97239 > Office: 503-494-1123 > Mobile: 503-805-6816 > Lab: 503-494-5427 > FAX: 503-494--8393 > Departmental phone: 503-494-7781 > Email: hoatlinm at OHSU.edu > Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab > LinkedIn Profile: http://www.linkedin.com/in/hoatlin > > > > > > > On 5/26/08 1:39 PM, "Jason Kelly" wrote: > >> There is a facebook group -- Maureen you're in it ;) not sure if this >> link will work but it's here: >> http://www.facebook.com/group.php?gid=2235655118 >> >> if you search for openwetware in facebook, it should come up -- it has >> 62 members at the moment. >> >> I agree with Steve about LinkedIn, we may as well get a group set up >> so I submitted one of those too -- will send out a link when LinkedIN >> approves it (takes a couple days, apparently). >> >> I think we can think about what kind of "social networking" would be >> useful to people on OWW. OpenSocial is just a technical protocol from >> Google allowing for 'distributed' social networking -- the real >> question is what would we want out of home-grown network? if we >> figured that out, then we could decide the best technology for >> implementing it. >> >> thanks, >> jason >> >> >> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin wrote: >>> I looked for a facebook OWW but didn't find one. The OWW group decal on >>> LinkedIn would serve mainly to link all those using this network and to >>> increase OWW visibility. More of an enhancement rather than network >>> duplication I think. >>> Also, in addition to Steve's points, it may be useful for labs who are >>> trying to establish collaborations with industry. >>> -M >>> >>> >>> On 5/26/08 11:09 AM, "John Cumbers" wrote: >>> >>> Hi Maureen, >>> I thought that there was a facebook group, but I can't see it, anyone else >>> remember? >>> I think I'd be in favor of starting a new social network rather than trying >>> to create duplicate networks elsewhere, Ricardo, what 's the deal with >>> Open Social? >>> >>> also, (btw Maureen, try this list discuss at openwetware.org instead in the >>> future, as we're fazing out the sc list) >>> cheers, >>> John >>> >>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin wrote: >>> >>> Hi All, >>> >>> I suggest that OWW get a group designation on LinkedIn (professional >>> networking) and Facebook (social networking). It might help get more >>> exposure if the OWW badge were displayed on our pages. What do you think? >>> >>> -Maureen >>> >>> >>> >>> _______________________________________________ >>> 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 jasonk at MIT.EDU Wed Jun 4 00:36:48 2008 From: jasonk at MIT.EDU (Jason Kelly) Date: Wed, 4 Jun 2008 00:36:48 -0400 Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn In-Reply-To: References: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com> Message-ID: <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> OK, LinkedIn group now exists. It seems like a pretty new feature for them, and I can't figure out how to link to the group page. If you search OpenWetWare or go to my profile in linkedIn you should be able to click the logo and sign up. thanks, jason On Mon, May 26, 2008 at 7:26 PM, Maureen Hoatlin wrote: > Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a > OWW group on facebook! I use the mobile version my iPhone so much (which > doesn't list groups) that I forgot. Pathetic. > -Maureen > > > > Maureen E. Hoatlin, PhD. > Biochemistry and Molecular Biology & Molecular and Medical Genetics > Hematologic Malignancies Program, Oregon Cancer Institute > Program in Molecular & Cellular Biosciences > Oregon Health & Science University > 3181 S.W. Sam Jackson Pk. Rd. > Medical Research Building, Rm 518 > Mailcode L224 > Portland, OR 97239 > Office: 503-494-1123 > Mobile: 503-805-6816 > Lab: 503-494-5427 > FAX: 503-494--8393 > Departmental phone: 503-494-7781 > Email: hoatlinm at OHSU.edu > Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab > LinkedIn Profile: http://www.linkedin.com/in/hoatlin > > > > > > > On 5/26/08 1:39 PM, "Jason Kelly" wrote: > >> There is a facebook group -- Maureen you're in it ;) not sure if this >> link will work but it's here: >> http://www.facebook.com/group.php?gid=2235655118 >> >> if you search for openwetware in facebook, it should come up -- it has >> 62 members at the moment. >> >> I agree with Steve about LinkedIn, we may as well get a group set up >> so I submitted one of those too -- will send out a link when LinkedIN >> approves it (takes a couple days, apparently). >> >> I think we can think about what kind of "social networking" would be >> useful to people on OWW. OpenSocial is just a technical protocol from >> Google allowing for 'distributed' social networking -- the real >> question is what would we want out of home-grown network? if we >> figured that out, then we could decide the best technology for >> implementing it. >> >> thanks, >> jason >> >> >> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin wrote: >>> I looked for a facebook OWW but didn't find one. The OWW group decal on >>> LinkedIn would serve mainly to link all those using this network and to >>> increase OWW visibility. More of an enhancement rather than network >>> duplication I think. >>> Also, in addition to Steve's points, it may be useful for labs who are >>> trying to establish collaborations with industry. >>> -M >>> >>> >>> On 5/26/08 11:09 AM, "John Cumbers" wrote: >>> >>> Hi Maureen, >>> I thought that there was a facebook group, but I can't see it, anyone else >>> remember? >>> I think I'd be in favor of starting a new social network rather than trying >>> to create duplicate networks elsewhere, Ricardo, what 's the deal with >>> Open Social? >>> >>> also, (btw Maureen, try this list discuss at openwetware.org instead in the >>> future, as we're fazing out the sc list) >>> cheers, >>> John >>> >>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin wrote: >>> >>> Hi All, >>> >>> I suggest that OWW get a group designation on LinkedIn (professional >>> networking) and Facebook (social networking). It might help get more >>> exposure if the OWW badge were displayed on our pages. What do you think? >>> >>> -Maureen >>> >>> >>> >>> _______________________________________________ >>> 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 rvidal at openwetware.org Wed Jun 4 00:42:38 2008 From: rvidal at openwetware.org (Ricardo Vidal) Date: Wed, 4 Jun 2008 00:42:38 -0400 Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn In-Reply-To: <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> References: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com> <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> Message-ID: <213fc43b0806032142r7bbbadb8h24301ac8cfc8050d@mail.gmail.com> Could this be the link: http://www.linkedin.com/groupInvitation?groupID=110865&sharedKey=77852667C0A2&goback=%2Esrp_1_1212540752334_in R On Wed, Jun 4, 2008 at 12:36 AM, Jason Kelly wrote: > OK, LinkedIn group now exists. It seems like a pretty new feature for > them, and I can't figure out how to link to the group page. If you > search OpenWetWare or go to my profile in linkedIn you should be able > to click the logo and sign up. > > thanks, > jason > > On Mon, May 26, 2008 at 7:26 PM, Maureen Hoatlin > wrote: > > Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a > > OWW group on facebook! I use the mobile version my iPhone so much (which > > doesn't list groups) that I forgot. Pathetic. > > -Maureen > > > > > > > > Maureen E. Hoatlin, PhD. > > Biochemistry and Molecular Biology & Molecular and Medical Genetics > > Hematologic Malignancies Program, Oregon Cancer Institute > > Program in Molecular & Cellular Biosciences > > Oregon Health & Science University > > 3181 S.W. Sam Jackson Pk. Rd. > > Medical Research Building, Rm 518 > > Mailcode L224 > > Portland, OR 97239 > > Office: 503-494-1123 > > Mobile: 503-805-6816 > > Lab: 503-494-5427 > > FAX: 503-494--8393 > > Departmental phone: 503-494-7781 > > Email: hoatlinm at OHSU.edu > > Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab > > LinkedIn Profile: http://www.linkedin.com/in/hoatlin > > > > > > > > > > > > > > On 5/26/08 1:39 PM, "Jason Kelly" wrote: > > > >> There is a facebook group -- Maureen you're in it ;) not sure if this > >> link will work but it's here: > >> http://www.facebook.com/group.php?gid=2235655118 > >> > >> if you search for openwetware in facebook, it should come up -- it has > >> 62 members at the moment. > >> > >> I agree with Steve about LinkedIn, we may as well get a group set up > >> so I submitted one of those too -- will send out a link when LinkedIN > >> approves it (takes a couple days, apparently). > >> > >> I think we can think about what kind of "social networking" would be > >> useful to people on OWW. OpenSocial is just a technical protocol from > >> Google allowing for 'distributed' social networking -- the real > >> question is what would we want out of home-grown network? if we > >> figured that out, then we could decide the best technology for > >> implementing it. > >> > >> thanks, > >> jason > >> > >> > >> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin > wrote: > >>> I looked for a facebook OWW but didn't find one. The OWW group decal on > >>> LinkedIn would serve mainly to link all those using this network and to > >>> increase OWW visibility. More of an enhancement rather than network > >>> duplication I think. > >>> Also, in addition to Steve's points, it may be useful for labs who are > >>> trying to establish collaborations with industry. > >>> -M > >>> > >>> > >>> On 5/26/08 11:09 AM, "John Cumbers" wrote: > >>> > >>> Hi Maureen, > >>> I thought that there was a facebook group, but I can't see it, anyone > else > >>> remember? > >>> I think I'd be in favor of starting a new social network rather than > trying > >>> to create duplicate networks elsewhere, Ricardo, what 's the deal > with > >>> Open Social? > >>> > >>> also, (btw Maureen, try this list discuss at openwetware.org instead in > the > >>> future, as we're fazing out the sc list) > >>> cheers, > >>> John > >>> > >>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin > wrote: > >>> > >>> Hi All, > >>> > >>> I suggest that OWW get a group designation on LinkedIn (professional > >>> networking) and Facebook (social networking). It might help get more > >>> exposure if the OWW badge were displayed on our pages. What do you > think? > >>> > >>> -Maureen > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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 > >>> > >>> > > > > > > > -- Ricardo Vidal rvidal at gmail.com | http://my.biotechlife.net http://www.openwetware.org - Share your Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080604/0e00caca/attachment.htm From rvidal at openwetware.org Wed Jun 4 00:42:38 2008 From: rvidal at openwetware.org (Ricardo Vidal) Date: Wed, 4 Jun 2008 00:42:38 -0400 Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn In-Reply-To: <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> References: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com> <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> Message-ID: <213fc43b0806032142r7bbbadb8h24301ac8cfc8050d@mail.gmail.com> Could this be the link: http://www.linkedin.com/groupInvitation?groupID=110865&sharedKey=77852667C0A2&goback=%2Esrp_1_1212540752334_in R On Wed, Jun 4, 2008 at 12:36 AM, Jason Kelly wrote: > OK, LinkedIn group now exists. It seems like a pretty new feature for > them, and I can't figure out how to link to the group page. If you > search OpenWetWare or go to my profile in linkedIn you should be able > to click the logo and sign up. > > thanks, > jason > > On Mon, May 26, 2008 at 7:26 PM, Maureen Hoatlin > wrote: > > Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, there *is* a > > OWW group on facebook! I use the mobile version my iPhone so much (which > > doesn't list groups) that I forgot. Pathetic. > > -Maureen > > > > > > > > Maureen E. Hoatlin, PhD. > > Biochemistry and Molecular Biology & Molecular and Medical Genetics > > Hematologic Malignancies Program, Oregon Cancer Institute > > Program in Molecular & Cellular Biosciences > > Oregon Health & Science University > > 3181 S.W. Sam Jackson Pk. Rd. > > Medical Research Building, Rm 518 > > Mailcode L224 > > Portland, OR 97239 > > Office: 503-494-1123 > > Mobile: 503-805-6816 > > Lab: 503-494-5427 > > FAX: 503-494--8393 > > Departmental phone: 503-494-7781 > > Email: hoatlinm at OHSU.edu > > Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab > > LinkedIn Profile: http://www.linkedin.com/in/hoatlin > > > > > > > > > > > > > > On 5/26/08 1:39 PM, "Jason Kelly" wrote: > > > >> There is a facebook group -- Maureen you're in it ;) not sure if this > >> link will work but it's here: > >> http://www.facebook.com/group.php?gid=2235655118 > >> > >> if you search for openwetware in facebook, it should come up -- it has > >> 62 members at the moment. > >> > >> I agree with Steve about LinkedIn, we may as well get a group set up > >> so I submitted one of those too -- will send out a link when LinkedIN > >> approves it (takes a couple days, apparently). > >> > >> I think we can think about what kind of "social networking" would be > >> useful to people on OWW. OpenSocial is just a technical protocol from > >> Google allowing for 'distributed' social networking -- the real > >> question is what would we want out of home-grown network? if we > >> figured that out, then we could decide the best technology for > >> implementing it. > >> > >> thanks, > >> jason > >> > >> > >> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin > wrote: > >>> I looked for a facebook OWW but didn't find one. The OWW group decal on > >>> LinkedIn would serve mainly to link all those using this network and to > >>> increase OWW visibility. More of an enhancement rather than network > >>> duplication I think. > >>> Also, in addition to Steve's points, it may be useful for labs who are > >>> trying to establish collaborations with industry. > >>> -M > >>> > >>> > >>> On 5/26/08 11:09 AM, "John Cumbers" wrote: > >>> > >>> Hi Maureen, > >>> I thought that there was a facebook group, but I can't see it, anyone > else > >>> remember? > >>> I think I'd be in favor of starting a new social network rather than > trying > >>> to create duplicate networks elsewhere, Ricardo, what 's the deal > with > >>> Open Social? > >>> > >>> also, (btw Maureen, try this list discuss at openwetware.org instead in > the > >>> future, as we're fazing out the sc list) > >>> cheers, > >>> John > >>> > >>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin > wrote: > >>> > >>> Hi All, > >>> > >>> I suggest that OWW get a group designation on LinkedIn (professional > >>> networking) and Facebook (social networking). It might help get more > >>> exposure if the OWW badge were displayed on our pages. What do you > think? > >>> > >>> -Maureen > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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 > >>> > >>> > > > > > > > -- Ricardo Vidal rvidal at gmail.com | http://my.biotechlife.net http://www.openwetware.org - Share your Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080604/0e00caca/attachment-0001.htm From ilyas at MIT.EDU Wed Jun 4 01:28:39 2008 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Wed, 04 Jun 2008 01:28:39 -0400 Subject: [OWW-Discuss] Six Degrees of Wikipedia Message-ID: <48462807.5000903@mit.edu> "The shortest path between two Wikipedia articles is defined as the minimum number of clicks required to move from one article to another. This can be used to discover connections between topics that are completely unrelated. ... Six Degrees of Wikipedia is an online tool that will help you find the shortest route between any two pages on Wikipedia using links." http://www.labnol.org/internet/tools/determine-the-shortest-path-between-two-wikipedia-articles/3487/ "Stephen Dolan, the researcher who created the software, has also used the code to determine which Wikipedia article is the ?center? of Wikipedia?that is, which article is the hub that most other articles must go through in the ?Six Degrees? game. Not including the articles that are just lists (e.g., years), the article closest to the center is ?United Kingdom,? at an average of 3.67 clicks to any other article." http://chronicle.com/wiredcampus/article/3041/six-degrees-of-wikipedia Unfortunately, there's no link to download the code to run on the dump of OWW. From johncumbers at gmail.com Thu Jun 5 01:19:39 2008 From: johncumbers at gmail.com (John Cumbers) Date: Wed, 4 Jun 2008 22:19:39 -0700 Subject: [OWW-Discuss] OpenWetWare Community Town Hall meeting: Thursday, June 12 at 12 noon. Message-ID: Whoops, Subject should have been June 12, at 12 noon EDT. I changed it... see you all next week, cheers, John On Tue, Jun 3, 2008 at 11:25 AM, Lorrie LeJeune wrote: > Hi Folks, > To better reflect the community focus of OpenWetWare, we're > relaunching our monthly steering meeting as the OWW Community Town > Hall.* Unless otherwise indicated, we intend to hold it on the second > Thursday of the month at 12 noon. Our next Town Hall will take place > next Thursday, June 12, at 12 noon EDT. The conference bridge is > 617-452-5208. Instructions on which chat client to use will follow. > > One topic I'd like to cover at this month's meeting is discussion > forums and better ways of communicating with other OWW members. Please > post your ideas at: > http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting > > At the May meeting, each person agreed to personally invite another > OWW member to attend the meeting. So send out those invitations! > > Pertinent action items from the May meeting: > * John to look into Social Text. > * Ricardo to do some viral marketing for lab Notebook out in the > blogosphere > * Lorrie to come up with a blog posting schedule on OWW (to highlight > new features on the site or other items of interest) > * We'll be following up shortly with more information about OWW and > the research cycle. > > Notes from the May meeting: > > http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_May_2008 > > Best regards, > > --Lorrie > > > > *For anyone who's not familiar with the term, a town hall meeting is > an informal public meeting derived from the traditional town meetings > of New England in the U.S. > (http://en.wikipedia.org/wiki/Town_hall_meeting). In this spirit, > anyone in the OWW community is welcome to attend, raise issues of > interest to the community, and voice their opinions. OpenWetWare is a > growing community with many new members, and I really encourage any or > all of you to call in or log into the chat. > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss > -- John Cumbers, Graduate Student Molecular Biology, Cell Biology, and Biochemistry 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 NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371 Moffett Field, CA 94035 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080604/7f75db08/attachment.htm From bill.altmail at gmail.com Thu Jun 5 09:25:11 2008 From: bill.altmail at gmail.com (Bill Flanagan) Date: Thu, 5 Jun 2008 09:25:11 -0400 Subject: [OWW-Discuss] Image problems after the upgrade Message-ID: <26428aaa0806050625u732c956naa65d7786ddf6c5b@mail.gmail.com> We had some serious issues with images not being present after upgrading to Mediawiki 1.12 on Wednesday. *1. Images were initially only visible when you were logged in. * This problem was solved yesterday at around 2:00 PM EST. Austin and I looked at the problem. He pointed out that images are not directly rendered statically by the web server but instead go through a php script. This is done to keep images from being distributed to users in the wiki is locked down. If this were not the case, anyone could look at any wiki image, either on public or private wikis. The code to do this changed in 1.12. We reverted back to the old 1.9 release for this file (img_auth.php) and the problem was solved. *2. Problems with PNG and TIFF files* Steve Kick identified another image problem I'm working on now. PNG and TIFF images are not working correctly. I'm not sure how widespread the problem is. In MediaWiki, there are typically 2 images: the image and the thumbnail. The thumbnail is rendered once. However, an image can have more than one thumbnail, depending upon the image tag used to display it. I'm looking at this problem now. If anyone sees other image problems, or any problems for that matter, please let me know. Once this is settled, Ricardo and I will put together a message describing some of the enhancements in the 1.12 MediaWiki release. In particular, we'll let you know how you can use some of the basic features as well as some of new extensions present. Now that we're at 1.12, we anticipate being in a position to track MediaWiki releases on a more regular basis. Stay tuned for more information.And thanks to Steve and Austin for their comments, help, and contributions. Bill -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080605/12a1b2a8/attachment.htm From kanzure at gmail.com Sat Jun 7 11:51:22 2008 From: kanzure at gmail.com (Bryan Bishop) Date: Sat, 7 Jun 2008 10:51:22 -0500 Subject: [OWW-Discuss] DIY Biotech Book Message-ID: <200806071051.23258.kanzure@gmail.com> Hey all, The biobarcamp guys and others are planning to do a do-it-yourself biotech book. The idea is to make a book that introduces and includes information on how to make and use the biotech equipment, the do-it-yourself scene, and so on. There's already significant content in the biotech toolkit ( http://biohack.sf.net/ ) *however* there's also tons of information from other communities that really needs to be integrated into something new -- a book -- so I'm sending out this email as notification of where everybody is. It looks like nobody is keeping notes on it yet, so I'm taking the initative and organizing everything here: http://heybryan.org/mediawiki/index.php/Book Feel free to edit it ruthlessly, copy it to another wiki, whatever. The content for the book itself should be up on a wiki, so feel free to link over to new pages with content dumps of related interest. There's going to be a lot of contributions, but we can sort through it in the end and discuss what we want to finally include and what not and so on. I'm also emailing this to a number of mailing lists. Mailing lists are limited for large collaborative projects like this where we don't have everyone on the same page and copying emails between too many mailing lists has this tendency to be a not-so-good of an idea. So, to provide a medium to more quickly organize people from different groups, I'm hanging out on IRC in #hplusroadmap on freenode and hope others will join me. There's a good number of contributors interested in this project there (>10 normally). There's also #biology, #bioinformatics, ##neuroscience, and a good number of other communities on freenode that we can dive into. Here's how you can access it: http://irchelp.org/ http://freenode.net/ irc://irc.freenode.net/#hplusroadmap Anybody using Firefox can use Chatzilla. Window users can use mIRC or something. And people on linux can apt-cache search IRC | grep IRC and get something that looks good. I'm also going to propose a 'cycle' of contributions to follow so that we have somewhat of a pulse that can beat out content. Wikipedia has a community pump, for example. There's a few options over at twitter, but in general, I think we'll get a pump going (aggregator) through IRC and then decide on twitter or whatever. Twitter is down all the time, so somebody else might have a better idea than I. In the mean time: http://twitter.com/biotecher http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solution-to-find-all-biotwitters-in-1-place/ http://twitter.com/attilacsordas http://twitter.com/kanzure http://twitter.com/mndoci I'm emailing this over to a lot of different communities into this sort of thing -- the neuralensemble group that focuses on the computational neuro side of biotech, the longevity groups, etc. All of these people are awesome and have good ideas to contribute, so I'm hoping some of them will click on the biotecher twitter, show up on the IRC discussions, and end up making an even more amazing resource for individuals. - Bryan ---------- Forwarded Message ---------- Subject: Re: [BioBarCamp] BioBarCamp topic/session suggestions Date: Saturday 07 June 2008 From: Bryan Bishop To: biobarcamp at googlegroups.com On Tuesday 03 June 2008, Attila Csordas wrote: > Hi All, > > This will be a lengthy email (sorry), but with good chance, it covers > a lot of topics that will be discussed at BBCAmp. The reason for that > length is that I include the Tentative Table of Contents of the so > called *BioTech Geek Guide* as I would like to organize the closing > session of the BBCamp with Deepak and Ricardo with the interactive > participation of you all. Let me explain: > > The *Biotech Geek Guide* is also an > ideait-folks-book-and-publish-it/>fed by a Twitter stream, just like the > BBCamp idea. Deepak complained about > the tech world's ignorance about health & genetics (a recurrent > theme) and then I suggested to write/edit/compile a biotech, biology > book for IT folks specially and publish it as an O'Reilly book. > O'Reilly Books have the fame of being the definitive guides, intros, > manuals in their technolgical fields. Ricardo came into the > conversation too and 10 minutes later I emailed Tim O'Reilly with the > suggestion and got almost instantly a very positive answer back > followed by a detailed Proposal Guidelines that needs to be filled > out to set up a schedule in order to get a final Yes or No answer to > the publishing of the book. So we started to work (just a little in > the lack of time) on it and I copy here what we've done basically the > *Book Outline/Tentative Table of Contents*. The concept of the book > later transformed into the *Biotech Geek Guide* which is too collect > every cool, major topic together that could be of interest for a > rookie/advanced biogeek, who is usually tech-savvy and biotech-savvy > too. I was talking with Deepak and others a few weeks ago about offering the Synthetic Biology Toolkit as a basis for the book. There's tons of content in the download and I think that it would be a good place to start. http://biohack.sf.net/ http://heybryan.org/mediawiki/ So the table contents, I would think, should focus mostly on (1) protocols, (2) equipment -- mostly improvised, (3) introduction to the online communities, including the broader world of bioinformatics, programming, open source communities, friendly people to talk to on the internet (seriously, an email address to me, Deepak, pimm, etc.), diybio.org groups, etc. The entire field is very quickly moving along, so it has to be a book that will not be dead in a few months (books aren't good for content like that). > And so we have an idea, an option to make a product (a book) out of > it, and define or delineate the knowledge-base and topic sensitivity > of current biotechnology, life sciences well tailored for IT people > but we lack an essential component that is behind every good animal > covered O'Reilly tech book: we lack the creative and critical > community and we need authors and commenters in the spirit of open > source and science. (That community also starts to form on FriendFeed Woah, I think we /do/ have that community. Check out the biohack.sf.net community. There's a good number of people on the mailing list. We just need to get them rallied up on a project. :-) > as *The Life > Scientists*room, > earlier form is a simply > Biotecher > registertion-to-find-all-biotwitters-in-1-place/>at Twitter.) > > But I think that the BioBarCamp could collect together exactly the > Community that is needed for the succession of that book and the > whole biogeek culture!!! The authorship, content and schedule is > totally open at that point (publishing an O'Reilly book is not about > money, really, at least I think so), I'd (and probably Deepak, if he > is interested) serve as a kind of main editor, and the more coauthors > and voices we have, the better the book will be. Let's make it on a wiki, instead of requiring it a BioBarCamp-only book. I don't know if BioBarCamp would be a good venue at which to write the book, but for rapid outlining (sit there on a wiki and have a live brainstorming session) it might prove an awesome mechanism. > So by copying the content suggestions here, I'd like to invite you > all to this hypothetical closing session and invite you to become > future O'Reilly authors to define the biogeek culture. (Disclaimer: I > am not an employee of O'Reilly Media, and if they say no I still > think that the concept of the book is good enough to publish it > elsewhere). To _define_ the biotecher culture? I don't know about that. That one is already in progress. For example, biopunk.org, the F/OSS communities, the typical lab culture. > 1. *All about bio* (introduction to the book). In the > introduction we will discuss the the origins of biotechnology and how > the field has evolved over the past 25 years? As biotechnology has That's a pretty challenging part. Maybe we could start by looking over at wikibooks and see if there's anything already written that we might import. There's a lot of important people to mention from the field of bio and biotech and so on, so we need somebody pretty knowledgable and able to integrate all of the information together, showing the broader vision that people started out with (or acquired), and then integrating it all back together to make sense. I think this could be done if we ruthlessly recursively read Wikipedia for the broad overview aspects, but then we need to reinterpret in light of (1) actual research articles (references to open access papers, etc.), and (2) an interpretation in terms of the do-it-yourself culture. > evolved, it has had a significant impact on the world around us, from > how we approach problems to how we try and cure disease, to the I think it's important to emphasize just how awesome disease curing can be. I wasn't aware of the World Health Organization's attempt to cure polio via a world-wide campaign until a few years ago. That was a terribly massive medical front that I doubt can be emphasized enough. And what would happen if people were able to do that on their own? Hrm. > environment and even to DIY hackery. The world of biotechnology is > also increasingly moving towards a systems level approach, as begin > to look at our bodies as interconnected, complex machines, changing > the way we try and cure diseases. We will also propose that biology > is the ultimate information science and lay the grounds for later > discussions on the data challenges and the information that can be > gleaned > 1. the biological mindset > 2. biotechnology in general > 2. biology basics In this chapter we provide a brief introduction > of the building blocks of biology. Here we go a little beyond what > you might find in the mainstream media and tell you about how we > function and highlight the complexity of human biology > 1. The building blocks (DNA, RNA, protein, organelles, membranes, > extracellular matrix, tissues, organs, body). *Do we need > anything else here? Don't want to make it too technical.* So, a list of general componentry that people can investigate in trying to make their projects a reality. Not just "building blocks of life", but 'parts and tools that you can use to do cool stuff'. > 3. methods - I suspect that including a CD of protocols wouldn't be a bad idea. We could start with protocols-online and OpenWetWare. In fact, if there's going to be a CD, let's include the biohacking toolkit and the entire wiki output of major wikis like OWW, biodatabase.org, biohack, etc. And then we can probably also include the portions of Wikipedia that are relevant. This is critical. There's no way that we can talk about everything in a book that we all want to be published in a reasonable amount of time ... so a CD, plus the book as more of a creative 'index' (in discussion format) to the contents, might be a good idea. > 1. the lab The par excellence biologist of our time is an > experimental scientist working at the bench with different tools and > methods: DNA, RNA: > isolation, amplification, quantification, protein: western > blot, SDS PAGE, > antibodies immunocytochemistry organelle: isolation of > mitochondria, lysosomes (centrifuge), cell: in vitro cell culture > 2. Biology in silico http://heybryan.org/mediawiki/index.php/Computational_biology > 1. Bioinformatics http://bioinformatics.org/ > 2. Modeling and simulation http://heybryan.org/mediawiki/index.php/Computational_biology > 4. Postgenomic > 1. proteomics http://heybryan.org/mediawiki/index.php/List_of_bioinformatics_databases > 2. HapMap > 3. Protein Structure Initiative (Structural Genomics) CASP? > 5. Systems Biology Over the past few years, it has become http://sbml.org/ > apparent that the traditional reductionist approach to biology was > very limited. The human body is extremely complex, a function of > interconnected pathways and networks. In order to cure many > diseases, it becomes necessary to study the human body at a systems > level, getting a deep understanding of various pathways and networks. http://reactome.org/ > By combining large quantities of data, complex mathematical > modeling and advanced computer models, systems biologists are > developling predictive models of organisms and biological systems > which will not only help us develop better, more potent drugs, but > also develop new fuel sources, clean up the environment and > potentially hack the human body. 6. The future of biotech Re: future of biotech. George Church is supposedly making some incredibly cheap biotech equipment (polonator.org and so on); sequencing for everybody on the planet; do-it-yourself pharmacy; brain augmentation; etc. http://www.innerspacefoundation.org/ http://heybryan.org/recursion.html > 1. Next generation sequencing http://heybryan.org/mediawiki/index.php/DNA_sequencing Is pyrosequencing still next generation? There's also scanning tunneling microscopy for DNA (like ZS Genetics plans to be doing later this year). The STM setups technically don't cost much, but getting the reoslution needed to do nucleotide-by-nucleotide scanning, ehh. That gets tricky. See: http://heybryan.org/instrumentation/instru.html http://heybryan.org/graphene.html (sort of) > 2. Personal Genetics - Genomics http://polonator.org/ Also, the $0 genomics project. Community sequencing projects, brief notes on how to deploy something like that (run around with cotton swabs and baggies and refridgerators in a van), etc. Also, the prospects of viral gene therapy in relation to personal genomics; the prospects of downloading genes from the internet from "gene pools" (i.e., "hey, look at this!" blogs). > 3. stem cells-regenerative medicine (A) The chapter covers the > basic concepts: stem cell, uni-, mult-, pluripotency, embryonic, > adult, induced pluripotent, cancer stem cell, stem cell niche, tissue > regenerative potential, regenerative medicine. The biohacking toolkit includes some papers by Yamanaka re: iPS cells. I'm still looking into protocols for adult fibroblast extraction and colonies, but it's looking interesting. > 4. tissue engineering http://heybryan.org/mediawiki/index.php/Neuropod organotypical neural slices, also see the heart-in-a-jar and prospects of the brain-in-a-jar projects. Stem cell engineering too. Hrm. Ah, and most importantly, the in vitro meat stuff. http://heybryan.org/mediawiki/index.php/Meat_on_a_stick > 5. The biology of our age: the biology of aging Emphasis on how to do "anti-aging research" in your own home. http://sens.org/ http://grg.org/ has some people that we might want to contact (Coles? Aubrey?) > 6. synthetic biology* *Perhaps we can get Jason or someone to > do this. My preference is that we stick to non-famous people but > interview Drew and others extensively. http://syntheticbiology.org/ http://partsregistry.org/ http://biobricks.org/ http://biohack.sf.net/ http://diybio.org/ > 7. biotech DIY: set up your low budget lab at the backyard > The idea of doing biological experiments with current > biotechnological methods and conducting research projects at home is > very new. There are already many names in use referring to the same > concept: bioDIY, home biology, biotech DIY, garage biology. All you > people need is a short course > in biotech basics, a few thousands of dollars, some tinkering > capability, and enough spare time and space. The beautiful retro idea > of tinkering with > digital devices in a garage, conveyed by the > Makemagazine, can be extended to biotech > too, and some projects were already > published in Make backyard biology issue like the Home > Molecular Genetics including DNA isolation. By the way. There's a few projects out there (bioreactor project from the biohacking group) that are trying to make a completely biological setup for do-it-yourself biology experimentation. For example, in vitro DNA synthesis. http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer And also having cells generate the proteins (T7, etc.) necessary to do transcription, or other various reactions that will be needed. This way, the entire kit is self-replicable except for the metal or plastic chasis. > 7. Applications > 1. industrial biotech Might want to mention something about 'industrial ecology' and the biosphere as another ecology and how this could all fit together productively for various interests. > 2. Drug Discovery > 8. The Web and biotech > 1. Google and biotech Google's interindustrial power reached > the biotech sphere through its investment into 23andME and backing > George Church's Personal Genome Project amongst others. While > personal genomics is > in the focus of Google's recent interest, its connection with > the biomedical > sector is much more complicated. Google Health > 2. Virtual medical education and web 2.0 in medicine Maybe the diybio.org guys would like to run some of those virtual educational seminars eventually. I've been holding weekly lectures on IRC on freenode in #hplusroadmap for a while now, but it's really just whenever people feel like showing up and pestering me about some awesome topics. Anybody is welcomed to join and contribute. :) - Bryan ________________________________________ http://heybryan.org/ ------------------------------------------------------- ________________________________________ http://heybryan.org/ From bill.altmail at gmail.com Sat Jun 7 14:02:28 2008 From: bill.altmail at gmail.com (Bill Flanagan) Date: Sat, 7 Jun 2008 14:02:28 -0400 Subject: [OWW-Discuss] Image problems appear to be under control Message-ID: <26428aaa0806071102p2301d615u61c3e913c944b614@mail.gmail.com> I ran down the image problem, or at least AN image problem, that I mentioned in a previous message. The problem was in the MediaWiki 1.12 Mime table: it used the wrong mime type to attempt to process Microsoft BMP files. The type has been changed. The fix works. One point to consider in managing images within OWW. If you have a JPEG image and save it with a PNG filename, MediaWiki will accept the file. But, upon uploading it, MediaWiki attempts to guess the format of the image. Therefore, the file will have a ".jpg" file extension, but will now have a stored file type of "PNG". When you open the file, MediaWiki will invoke the JPEG handler for it rather than the PNG file handler. Bottom line: a filename is a label and not a manifest of the file's contents. Steve Koch also sent an example where a large PNG file (over 2 mb) was not shown as a thumbnail. I'm hunting down this problem. It seems to be a problem with the ImageMagick software on the server used to generate the thumbnail. I don't have a hard number for the limit but I'm looking into it. Steve also noted that he was unable to launch Powerpoint when he tried to open a ".ppt" file that had worked correctly prior to this. This may have been my fault. I reset the Mime types for all files to their correct values to make sure a query I ran was not to blame for it. Another user found that a wiki page that had been working before was being rendered wrong, making the page unusable. I fixed the specific problem . If anyone sees other aberrant behavior in images or pages, please let me know. Thanks. Bill Flanagan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080607/673829d3/attachment.htm From bill.altmail at gmail.com Sun Jun 8 13:09:27 2008 From: bill.altmail at gmail.com (Bill Flanagan) Date: Sun, 8 Jun 2008 13:09:27 -0400 Subject: [OWW-Discuss] Upload of Scalable Vector Graphics files is now working on OWW. Finally. Message-ID: <26428aaa0806081009wfe851ddy47d850236added13@mail.gmail.com> The results look promising. Keep in mind: this support may not work flawlessly for all files. Since SVG can support embedded scripting commands, the ImageMagick imaging package may not do a perfect job of handling the image. But, it works. I've turned on SVG images as a legal upload option now that it's working reliably. The image is processed by ImageMagic upon upload just to make a PNG thumbnail of the original. The original image is not affected: it's stored like any other image on the server. I've identified the problem related to large PNG image files and have a tentative solution to the problem. I'll discuss this once I have it working. Meanwhile, JPEG image files work most reliably. Please note: a new parameter added to the image import code tries to keep the image quality as high as possible. To do this, an ImageMagick feature, "sharpening", is now being invoked. This leads to higher quality-looking thumbnails or image reductions but it comes at the cost of a lot of server CPU overhead. The time to process a large 'sharpened' image is 10 time that of one that's simply reduced. For now, I'm leaving the sharpening parameter in place. For scientific apps, resolution is critical. Granted, you can still look at the original file which is what's stored on the server. But we may have to revisit this if the time to do uploads and corresponding CPU utilization proves to be a problem for the community. If anyone has any comments, please let me know. This is a pretty big change in the most recent revision that we all should be aware of. Thanks. Bill -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080608/cd2e8667/attachment.htm From jasonk at MIT.EDU Sun Jun 8 18:02:23 2008 From: jasonk at MIT.EDU (Jason Kelly) Date: Sun, 8 Jun 2008 18:02:23 -0400 Subject: [OWW-Discuss] Are academic journals obsolete? Message-ID: <7c085c480806081502i16ac67e1u2c12b6c8befc3c88@mail.gmail.com> just posted to front page of slashdot: http://ask.slashdot.org/askslashdot/08/06/08/2132254.shtml might be worth a comment or two from folks here. thanks, jason From ilyas at MIT.EDU Mon Jun 9 18:27:24 2008 From: ilyas at MIT.EDU (Ilya Sytchev) Date: Mon, 09 Jun 2008 18:27:24 -0400 Subject: [OWW-Discuss] OWW logo on facebook and LinkedIn In-Reply-To: <213fc43b0806032142r7bbbadb8h24301ac8cfc8050d@mail.gmail.com> References: <7c085c480805261339n61ac0105i1f09681cec2d7aa2@mail.gmail.com> <7c085c480806032136k77c54a9cm801ae7002cf57519@mail.gmail.com> <213fc43b0806032142r7bbbadb8h24301ac8cfc8050d@mail.gmail.com> Message-ID: <484DAE4C.5050105@mit.edu> I've updated the About page (http://openwetware.org/wiki/OpenWetWare:About#Mechanisms_to_find_out_more:) with Facebook and LinkedIn group information. Ilya Ricardo Vidal wrote: > Could this be the link: > http://www.linkedin.com/groupInvitation?groupID=110865&sharedKey=77852667C0A2&goback=%2Esrp_1_1212540752334_in > > > R > > On Wed, Jun 4, 2008 at 12:36 AM, Jason Kelly > wrote: > > OK, LinkedIn group now exists. It seems like a pretty new feature for > them, and I can't figure out how to link to the group page. If you > search OpenWetWare or go to my profile in linkedIn you should be able > to click the logo and sign up. > > thanks, > jason > > On Mon, May 26, 2008 at 7:26 PM, Maureen Hoatlin > wrote: > > Thanks for setting up the LinkedIn OWW group Jason. Oh yeah, > there *is* a > > OWW group on facebook! I use the mobile version my iPhone so much > (which > > doesn't list groups) that I forgot. Pathetic. > > -Maureen > > > > > > > > Maureen E. Hoatlin, PhD. > > Biochemistry and Molecular Biology & Molecular and Medical Genetics > > Hematologic Malignancies Program, Oregon Cancer Institute > > Program in Molecular & Cellular Biosciences > > Oregon Health & Science University > > 3181 S.W. Sam Jackson Pk. Rd. > > Medical Research Building, Rm 518 > > Mailcode L224 > > Portland, OR 97239 > > Office: 503-494-1123 > > Mobile: 503-805-6816 > > Lab: 503-494-5427 > > FAX: 503-494--8393 > > Departmental phone: 503-494-7781 > > Email: hoatlinm at OHSU.edu > > Lab Web Page: http://openwetware.org/wiki/Hoatlin_Lab > > LinkedIn Profile: http://www.linkedin.com/in/hoatlin > > > > > > > > > > > > > > On 5/26/08 1:39 PM, "Jason Kelly" > wrote: > > > >> There is a facebook group -- Maureen you're in it ;) not sure > if this > >> link will work but it's here: > >> http://www.facebook.com/group.php?gid=2235655118 > >> > >> if you search for openwetware in facebook, it should come up -- > it has > >> 62 members at the moment. > >> > >> I agree with Steve about LinkedIn, we may as well get a group set up > >> so I submitted one of those too -- will send out a link when > LinkedIN > >> approves it (takes a couple days, apparently). > >> > >> I think we can think about what kind of "social networking" would be > >> useful to people on OWW. OpenSocial is just a technical > protocol from > >> Google allowing for 'distributed' social networking -- the real > >> question is what would we want out of home-grown network? if we > >> figured that out, then we could decide the best technology for > >> implementing it. > >> > >> thanks, > >> jason > >> > >> > >> On Mon, May 26, 2008 at 2:32 PM, Maureen Hoatlin > > wrote: > >>> I looked for a facebook OWW but didn't find one. The OWW group > decal on > >>> LinkedIn would serve mainly to link all those using this > network and to > >>> increase OWW visibility. More of an enhancement rather than network > >>> duplication I think. > >>> Also, in addition to Steve's points, it may be useful for labs > who are > >>> trying to establish collaborations with industry. > >>> -M > >>> > >>> > >>> On 5/26/08 11:09 AM, "John Cumbers" > wrote: > >>> > >>> Hi Maureen, > >>> I thought that there was a facebook group, but I can't see it, > anyone else > >>> remember? > >>> I think I'd be in favor of starting a new social network rather > than trying > >>> to create duplicate networks elsewhere, Ricardo, what 's the > deal with > >>> Open Social? > >>> > >>> also, (btw Maureen, try this list discuss at openwetware.org > instead in the > >>> future, as we're fazing out the sc list) > >>> cheers, > >>> John > >>> > >>> On Mon, May 26, 2008 at 11:01 AM, Maureen Hoatlin > > wrote: > >>> > >>> Hi All, > >>> > >>> I suggest that OWW get a group designation on LinkedIn > (professional > >>> networking) and Facebook (social networking). It might help get > more > >>> exposure if the OWW badge were displayed on our pages. What do > you think? > >>> > >>> -Maureen > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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 > >>> > >>> > > > > > > > > > > > -- > Ricardo Vidal > rvidal at gmail.com | http://my.biotechlife.net > http://www.openwetware.org - Share your Science > > > ------------------------------------------------------------------------ > > _______________________________________________ > OpenWetWare Discussion Mailing List > discuss at openwetware.org > http://mailman.mit.edu/mailman/listinfo/oww-discuss From johncumbers at gmail.com Wed Jun 11 16:02:03 2008 From: johncumbers at gmail.com (John Cumbers) Date: Wed, 11 Jun 2008 13:02:03 -0700 Subject: [OWW-Discuss] OpenWetWare Community Town Hall meeting: Thursday, June 12 at 12 noon. In-Reply-To: References: Message-ID: Hi all, A quick reminder about the Town Hall Meeting tomorrow, please see Lorrie's note below, cheers John Second Thursday of the month at 12 noon. Our next Town Hall will take place > tomorrow, June 12, at 12 noon EDT. The conference bridge is > 617-452-5208. Chat here:http://openwetware.org/chat/. > > Better ways of communicating with other OWW members. You can post ideas > here: > http://openwetware.org/wiki/OpenWetWare:Steering_committee_next_meeting > > At the May meeting, each person agreed to personally invite another > OWW member to attend the meeting. So send out those invitations! > > Pertinent *action items *from the May meeting: > * John to look into Social Text. > * Ricardo to do some viral marketing for lab Notebook out in the > blogosphere > * Lorrie to come up with a blog posting schedule on OWW (to highlight > new features on the site or other items of interest) > * We'll be following up shortly with more information about OWW and > the research cycle. > > Notes from the May meeting: > > http://openwetware.org/wiki/OpenWetWare:Steering_committee/Meeting_-_May_2008 > > *For anyone who's not familiar with the term, a town hall meeting is > an informal public meeting derived from the traditional town meetings > of New England in the U.S. > (http://en.wikipedia.org/wiki/Town_hall_meeting). In this spirit, > anyone in the OWW community is welcome to attend, raise issues of > interest to the community, and voice their opinions. OpenWetWare is a > growing community with many new members, and I really encourage any or > all of you to call in or log into the chat. > > John Cumbers, Graduate Student, NASA Ames Research Center Mail Stop 239-20, Bldg N239 Rm 371 Moffett Field, CA 94035, USA. +1 401 523 8190 Graduate Program in Molecular Biology, Cell Biology, and Biochemistry Brown University, Box G-W Providence, RI, 02912, USA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080611/82225bf8/attachment.htm From lorrielejeune at gmail.com Thu Jun 12 09:34:06 2008 From: lorrielejeune at gmail.com (Lorrie LeJeune) Date: Thu, 12 Jun 2008 09:34:06 -0400 Subject: [OWW-Discuss] Chat info for today's OWW Community Town Hall Message-ID: <6ac0a26a0806120634w3150afc6wa1e6a1fb9f0f8425@mail.gmail.com> Hi Folks, We're going to try a new chat client at today's OWW Community Town Hall: http://openwetware.org/wiki/OpenWetWare:Steering_committee/Town_Hall_Meeting/2008/06/12#Chat The password is openresearch if it asks for one. Hope to talk to you at noon, --Lorrie -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mailman.mit.edu/pipermail/oww-discuss/attachments/20080612/5b69033d/attachment.htm From johncumbers at gmail.com Thu Jun 12 11:35:43 2008 From: johncumbers at gmail.com (John Cumbers) Date: Thu, 12 Jun 2008 08:35:43 -0700 (PDT) Subject: [OWW-Discuss] John Cumbers invites you to join the "The Life Scientists" room on FriendFeed Message-ID: <20080612153543.9629AE436DE@friendfeed.com> Message from John Cumbers: I'd like to invite you to join the "The Life Scientists" room on FriendFeed, a place for us to share and discuss things. I hope you'll join the room. You can check it out here: http://friendfeed.com/rooms/the-life-scientists ------ To join the "The Life Scientists" room on FriendFeed, visit http://friendfeed.com/invite?code=HarSUnKxTu To see John Cumbers's FriendFeed, check out http://friendfeed.com/johncumbers If you have any questions, please contact feedback at friendfeed.com. Thanks, Your friends at FriendFeed From johncumbers at gmail.com Thu Jun 12 11:42:52 2008 From: johncumbers at gmail.com (John Cumbers Gmail) Date: Thu, 12 Jun 2008 08:42:52 -0700 Subject: [OWW-Discuss] Friendfeed.com, room 'the life scientists' socialtext.com Message-ID: <06C3C30C-ECB4-4D85-86EF-9FC0B756211D@gmail.com> Sorry folks, I'm stuck in traffic and can't join the call until later. Two links to send though, friendfeed.com try joining the lifesciences room, isn't this the type of communication channel that we're talking about? Secondly, Check out socialtext.com, would we want to try out something like this? Cheers John