tag:blogger.com,1999:blog-3643556495084083743.comments2022-12-09T08:52:54.666-08:00Skeptic WonderPsi Wavefunctionhttp://www.blogger.com/profile/10829712736757471647noreply@blogger.comBlogger816125tag:blogger.com,1999:blog-3643556495084083743.post-36407621372582889152015-04-15T09:08:11.674-07:002015-04-15T09:08:11.674-07:00Seems like a great looking tree! It's great to...Seems like a great looking tree! It's great to see the information spread like this. If you update it again, please share with us!Jordanhttp://www.microbe.com/noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-96751764169490102015-03-25T08:43:51.403-07:002015-03-25T08:43:51.403-07:00This is certainly a useful tool, any plans to expa...This is certainly a useful tool, any plans to expand it? Genetic Researcherhttp://pharmacogeneticstesting.comnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-41121090564726909392015-03-16T08:56:23.282-07:002015-03-16T08:56:23.282-07:00The reason I was asking about automation is that t...The reason I was asking about automation is that there are a lot of people out there who are interested in more reproducible, automatable ways to annotate trees and render them (e.g., see discussion at https://github.com/OpenTreeOfLife/tree-illustrator/wiki/Design-notes). These are not sophisticated enough for your purposes, but your tree could serve as a challenging use-case.Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-83224296906000973762015-03-16T08:54:35.932-07:002015-03-16T08:54:35.932-07:00I think it would be interested to see how much of ...I think it would be interested to see how much of this is covered in OpenTree's synthetic tree (opentreeoflife.org). The way to do this is in a blog that I wrote about OpenTree web services last fall: http://blog.opentreeoflife.org/2014/10/07/tree-for-all-hackathon-series-introduction/ <br /><br />For instance, you can query with a set of names: <br /><br />curl -X POST http://api.opentreeoflife.org/v2/tnrs/match_names -H "content-type:application/json" -d'{"names":["angiosperms","gymnosperms", "floridiophytes", "Naegleria"]}'<br /><br />and this will try to match against a taxonomy database. In this case, the floridiophytes are not included. Then you can take the IDs (the ottId values, specifically), and run a query against the tree: <br /><br />curl -X POST http://api.opentreeoflife.org/v2/tree_of_life/induced_subtree -H "content-type:application/json" -d '{"ott_ids":[592507, 99252, 641875]}'<br /><br />And you'll get back the sub-tree: <br /><br />('Naegleria_ott641875',('Gymnosperma_ott592507','Magnoliophyta_ott99252'))<br /><br />where Magnoliophyta is the favored synonym for angiosperms. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-81280002124639908682015-03-16T08:23:34.962-07:002015-03-16T08:23:34.962-07:00This comment has been removed by the author.Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-52492218875049482322015-03-12T17:15:05.738-07:002015-03-12T17:15:05.738-07:00Rosie: Thanks! I hope to pick things up again... o...Rosie: Thanks! I hope to pick things up again... once I get a transcriptome going! ;-)<br /><br />Arlin: Did it entirely manually... first, five years ago, via Powerpoint (may have been slightly insane), but now editing and modifying it with Illustrator. It's a synthesis, not a real tree, one a rather subjective one. But if, for whatever reason, you need a computer-readable one, just email me! I'm hesitant about making one and putting one up because, again, it's not *directly* based on real data, and I'm afraid that people may treat it as such if I post a Newick version.<br /><br />That said, it is based on literature and input from experts in this area. The problem with real data trees is that every tree lies, but between many differently-lying trees you can start to assemble the truth, somewhat ;-)Psi Wavefunctionhttps://www.blogger.com/profile/10829712736757471647noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-34529485142838059322015-03-10T08:29:58.372-07:002015-03-10T08:29:58.372-07:00How do you generate the graphics (and the tree)? ...How do you generate the graphics (and the tree)? Is that done manually? Is there a computable (computer-readable) version? Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-59500819224493305172015-03-10T08:29:50.553-07:002015-03-10T08:29:50.553-07:00This comment has been removed by the author.Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-48719065885364201602015-03-10T07:49:09.422-07:002015-03-10T07:49:09.422-07:00I just linked this article on Facebook account. it...I just linked this article on Facebook account. it's a very interesting article for everyone.<br /><a href="http://mosquitocontrol.com/commercial-spray/" rel="nofollow">Commercial Mosquito Control</a>Anonymoushttps://www.blogger.com/profile/01452176707372573199noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-58247303337238076512015-03-04T18:56:59.529-08:002015-03-04T18:56:59.529-08:00Welcome back!Welcome back!Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-67872955622154138442014-12-16T09:32:14.570-08:002014-12-16T09:32:14.570-08:00Welcome home.Welcome home.Edwardhttps://www.blogger.com/profile/04295927435118827266noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-26453000726595878242014-12-15T20:28:18.550-08:002014-12-15T20:28:18.550-08:00Welcome back! We've missed you :-)Welcome back! We've missed you :-)Christopher Taylorhttps://www.blogger.com/profile/11075565866351612441noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-55251014927287687662014-12-10T16:20:21.467-08:002014-12-10T16:20:21.467-08:00Stumbled upon your blog when I was searching up th...Stumbled upon your blog when I was searching up the habitats of onychophorans, whether they live in forest or meadows etc. I really enjoyed reading the social onychoporan post. You are honestly hilarious and have quite a way with words. I don't normally read blogs or follow people but how can one not follow your posts. :)))<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-42471802130219394182014-12-01T08:52:01.108-08:002014-12-01T08:52:01.108-08:00This is a great topic!
Just watch out for the cont...This is a great topic!<br />Just watch out for the controversy<br />http://retractionwatch.com/2014/12/01/nature-issues-expression-of-concern-for-paper-by-author-who-threatened-to-sue-retraction-watch/Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-23814431587866580322014-04-26T17:34:12.044-07:002014-04-26T17:34:12.044-07:00<3
I have critter ADD, but am a Practicing Pla...<3<br /><br />I have critter ADD, but am a Practicing Plant Taxonomist and warper^H^H^H^H^H^H teacher of young minds. Bwahahahahaha. I'd love to use your phylogeny in class if I might. I adore higher level phylogeny, and yours really is top notch (IMO).<br /><br />and your sense of humor rocks.Susanhttps://www.blogger.com/profile/06931140462465806953noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-55710094909938689242013-07-17T11:35:58.686-07:002013-07-17T11:35:58.686-07:00There is recent publication in PNAS regarding meta...There is recent publication in PNAS regarding metaboly that you could be interested in.<br /><br />Reverse engineering the euglenoid movement<br />http://www.pnas.org/content/109/44/17874Anonymoushttps://www.blogger.com/profile/09171206184862617001noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-45499297846116314652013-07-15T13:13:22.258-07:002013-07-15T13:13:22.258-07:00Loved the pics and comments on early Hoosier ocean...Loved the pics and comments on early Hoosier ocean life. I took lots of mortality plates from those rdcuts down on the 37 when I was at IU. Maybe you could do us all a favor and go explore the bizarre wacko blown-up fossil brachiopods, crinoid heads etc that populate one particular level (Salem formation?) in the area. Find them in Yellowstone(?) creek near you at IUB. All along that creek. Many are hollow and infilled w/ quartz & goethite xls. When I was there 10 years ago and prior, there was speculation as to how this particular formed or expanded so wildly, but I didn't get the impression there was definitive or consensus.<br />new follower,<br />tjAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-26581382263474038242013-05-23T18:57:21.459-07:002013-05-23T18:57:21.459-07:00I don't comment on blogs. In fact, this is my ...I don't comment on blogs. In fact, this is my first (comment, that is. ever. seriously.) but had to say that you are a terrific and engaging writer so I hope you keep it going. Scientists (myself included) aren't usually known for their lit skills. Nice job.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-78597569923983806682013-03-23T14:49:03.710-07:002013-03-23T14:49:03.710-07:00Too bad you are not keeping your blog up to date!Too bad you are not keeping your blog up to date!Anonymoushttps://www.blogger.com/profile/03073736782991629338noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-70310444441993112932013-03-03T15:49:27.087-08:002013-03-03T15:49:27.087-08:00I am currently studying this material as an underg...I am currently studying this material as an undergrad and surfing the net for some clarity led me to this awesome outlook.<br />thankQ for taking the time to write this because I get confused with the protist taxonomy (it doesn't make sense sometimes!)<br />So now I know to suck it up and remember what I need to know for the exam, and still know that I can trust myself that there must be a better way to organize this tree of organisms. Will I be the one doing it? Who knows, I wish you well and admire your critical outlook.<br />Cheers!radicahttps://www.blogger.com/profile/16606905980065748796noreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-75592512940393172112013-01-25T12:02:42.298-08:002013-01-25T12:02:42.298-08:00replica plate it!replica plate it!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-73139982156160881182012-11-27T15:48:31.219-08:002012-11-27T15:48:31.219-08:00The fossils are actually from Porter et al., 2003 ...The fossils are actually from Porter et al., 2003 in Journal of Paleontology v77. Loving your blog!Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-54789642511890179102012-11-18T11:15:01.363-08:002012-11-18T11:15:01.363-08:00The mysterious flagellate blob is maybe a Polytome...The mysterious flagellate blob is maybe a Polytomella... <br />but I'm not sure...<br />What do you think?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-62116826751379356542012-09-07T07:04:07.510-07:002012-09-07T07:04:07.510-07:00Dear Psi,
I'll drink a beer with Zachleder to...Dear Psi,<br /><br />I'll drink a beer with Zachleder tonight. I've also planed to talk about cell cycles and random mutagenesis with him. Thanks for this nice intro. The trouble about coenobia and colonies I solved with my students 6 months ago. The third name on Zach's publication is Milada Vitova. She is his daugther.<br /><br />Greetings from Switzerland, GuntherAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-3643556495084083743.post-62082413022177515452012-07-09T14:02:06.752-07:002012-07-09T14:02:06.752-07:00hi, this is a very good post!hi, this is a very good post!Anonymousnoreply@blogger.com