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DATE 2016-09-01

LEARN

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MESSAGE
DATE 2016-09-26
FROM Ruben Safir
SUBJECT Re: [Learn] Proposed Thesis
From learn-bounces-at-nylxs.com Mon Sep 26 10:38:19 2016
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<20160926130028.GA6913-at-www.mrbrklyn.com>

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On 09/26/2016 09:03 AM, Jon Tennant wrote:
> I think they did it using the R programming language - do you know of
> it? I don't think scanning fossils in like you describe is possible, yet!
>

Yes, I'm familiar with R and have been for a few years. I haven't used
it, but it has been a free software stable for a long time. They seem
to be scanning at least some fossils for 3d printers. Once you have a
catscan you have data. I'm thinking that might be possible.

https://3dprint.com/127709/t-rex-ultimaker-naturalis/
https://sketchfab.com/models/f4303dc6b9df423b809be241f2b73e04

http://www.dailysabah.com/science/2015/06/21/inside-the-head-of-a-dinosaur-t-rex-gets-a-brain-scan-1434842177

http://digimorph.org/specimens/Pawpawsaurus_campbelli/

http://streekbladzoetermeer.nl/nieuws/valentin-print-3d-skelet-van-dinosaurus-trix-1.6394410


> Jon

> On Mon, Sep 26, 2016 at 2:00 PM, Ruben Safir > > wrote:
>
> On Mon, Sep 26, 2016 at 01:15:12PM +0100, Jon Tennant wrote:
> > Hey Ruben,
> >
> > Thanks for getting in touch! So the original article is here:
> > http://www.nature.com/articles/srep20252
>
> >
> > I don't know exactly how they drew this, but there's an R package called
> > geoscale that does this temporal calibration of cladograms quite nicely. In
> > terms of building the actual tree, you can use software like TNT and then
> > read the outputs into R, which is pretty difficult at times but a really
> > useful skill.
> >
> > I hope that helps a bit! :)
> >
>
> the data is entered by hand? Is it possible to scan a fosil into a file
> and get a summary of attributes that can be used for evaluating the
> relationship between species?
>
>
> > Jon
> >
> > On Mon, Sep 26, 2016 at 12:01 PM, Ruben Safir > > wrote:
> >
> > > Jon
> > >
> > > Good morning. As I was writing on facebook, we have been given a go
> > > ahead to do a masters thesis on machine learning on fossils to build
> > > cladiagraphs. I have some rudimentary understanding of the
> topic, but
> > > not much in terms of detail or understanding how paleontologist
> build
> > > such diagrams mapping proposed evolutionary relationships today.
> > >
> > > I've been pointed to the basic text Inferring Phylogenies by Joe
> > > Felsenstein which I ordered.
> > >
> > > I'm interested in the methodology you use, especially with the T-Rex
> > > article you did here:
> > >
> > >
> http://blogs.plos.org/paleocomm/2016/02/17/the-evolution-of-tyrannosaurs/
>
> > >
> > > I expect to publish all our work at http://www.nylxs.com/thesis/
> > >
> > > I'm very interested in openscience and we will likely try to
> restrict
> > > our projects to Free Software. I'm particularly interested in
> mapping
> > > algorithms being developed and applied to these problems, and
> > > integrating the increasing use of scanned 3d images for systematic
> > > analysis, such as what was done for the Trix TRex in Leiden.
> > >
> > > Ruben Safir
> > >
> > > --
> > > So many immigrant groups have swept through our town
> > > that Brooklyn, like Atlantis, reaches mythological
> > > proportions in the mind of the world - RI Safir 1998
> > > http://www.mrbrklyn.com
> > >
> > > DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
> > > http://www.nylxs.com - Leadership Development in Free Software
> > > http://www2.mrbrklyn.com/resources
> - Unpublished Archive
> > > http://www.coinhangout.com - coins!
> > > http://www.brooklyn-living.com
> > >
> > > Being so tracked is for FARM ANIMALS and and extermination camps,
> > > but incompatible with living as a free human being. -RI Safir 2013
> > >
> >
> >
> >
> > --
> >
> >
> > *PhD Student: *Department of Earth Science and Engineering, Royal
> School of
> > Mines, Prince Consort Road, Imperial College London, SW7 2BP, UK
> >
> > Communications Director at ScienceOpen ,
> > Berlin.
> >
> > *ORCID:* http://orcid.org/0000-0001-7794-0218
>
> > *Twitter:* -at-protohedgehog > >
> > *Website:* http://fossilsandshit.com/
> > *Blog:* http://blogs.egu.eu/palaeoblog/
>
> >
> > > >Author of Excavate! Dinosaurs
> >
> > >
> >
> > *Email:* jon.tennant.2-at-gmail.com
> > *Mob: *(+44) 7921252367
>
> --
> So many immigrant groups have swept through our town
> that Brooklyn, like Atlantis, reaches mythological
> proportions in the mind of the world - RI Safir 1998
> http://www.mrbrklyn.com
>
> DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
> http://www.nylxs.com - Leadership Development in Free Software
> http://www2.mrbrklyn.com/resources
> - Unpublished Archive
> http://www.coinhangout.com - coins!
> http://www.brooklyn-living.com
>
> Being so tracked is for FARM ANIMALS and and extermination camps,
> but incompatible with living as a free human being. -RI Safir 2013
>
>
>
>
> --
>
>
> *PhD Student: *Department of Earth Science and Engineering, Royal School
> of Mines, Prince Consort Road, Imperial College London, SW7 2BP, UK
>
> Communications Director at ScienceOpen ,
> Berlin.
>
> *ORCID:* http://orcid.org/0000-0001-7794-0218
> *Twitter:* -at-protohedgehog
> *Website:* http://fossilsandshit.com/
> *Blog:* http://blogs.egu.eu/palaeoblog/
>
> Author of Excavate! Dinosaurs
>
>
> *Email:* jon.tennant.2-at-gmail.com
> *Mob: *(+44) 7921252367
>
>
>


--
So many immigrant groups have swept through our town
that Brooklyn, like Atlantis, reaches mythological
proportions in the mind of the world - RI Safir 1998
http://www.mrbrklyn.com

DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002
http://www.nylxs.com - Leadership Development in Free Software
http://www2.mrbrklyn.com/resources - Unpublished Archive
http://www.coinhangout.com - coins!
http://www.brooklyn-living.com

Being so tracked is for FARM ANIMALS and and extermination camps,
but incompatible with living as a free human being. -RI Safir 2013
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  1. 2016-09-01 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: LIU CS course
  2. 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] LIU Brooklyn Student Update
  3. 2016-09-04 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Brooklyn Student Update
  4. 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lockout
  5. 2016-09-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Computer Sciences
  6. 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Lock Out
  7. 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] [Hangout-NYLXS] Fwd: LIU Lock Out
  8. 2016-09-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lock Out
  9. 2016-09-12 Amy Rothenberg <Amy.Rothenberg-at-liu.edu> Re: [Learn] LIU Lock Out
  10. 2016-09-13 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [isoc-ny] ISOC-NY joins coalition of groups supporting
  11. 2016-09-14 From: "Ruben.Safir" <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Calendar Update
  12. 2016-09-19 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Thesis option
  13. 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fossil computational oppurtunities
  14. 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fossil computational oppurtunities
  15. 2016-09-22 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Sad News
  16. 2016-09-23 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of
  17. 2016-09-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis - topic Machine learning in the determination of the
  18. 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Cladistics and Computational Math
  19. 2016-09-25 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis
  20. 2016-09-25 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Thesis - topic Machine learning in the determination of
  21. 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Cladistics and Computational Math
  22. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis
  23. 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis
  24. 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis
  25. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis
  26. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Proposed Thesis
  27. 2016-09-27 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] phylip
  28. 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] phylip
  29. 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] t-rex web server
  30. 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better
  31. 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better
  32. 2016-09-28 league-at-contrapunctus.net Re: [Learn] meet up for thesis?
  33. 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis?
  34. 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis?
  35. 2016-09-28 Maneesh Kongara <maneeshkongara-at-gmail.com> Re: [Learn] meet up for thesis?
  36. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] meet up for thesis?
  37. 2016-09-28 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of
  38. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] meet up for thesis?
  39. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Notice: Learn Mailing List for LIU
  40. 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death
  41. 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death
  42. 2016-09-29 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Announcing LIU Votes 2016!
  43. 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] phylogenetics
  44. 2016-09-29 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] phylogenetics
  45. 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] two textbooks
  46. 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data
  47. 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis data
  48. 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data
  49. 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis data

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