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DATE 2016-09-01

LEARN

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MESSAGE
DATE 2016-09-26
FROM Jon Tennant
SUBJECT Re: [Learn] Proposed Thesis
From learn-bounces-at-nylxs.com Mon Sep 26 09:09:22 2016
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References:
From: Jon Tennant
Date: Mon, 26 Sep 2016 13:15:12 +0100
Message-ID:
To: Ruben Safir
X-Mailman-Approved-At: Mon, 26 Sep 2016 09:09:21 -0400
Cc: learn-at-nylxs.com
Subject: Re: [Learn] Proposed Thesis
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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! :)

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

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Hey Ruben,

Thanks for getting in touch!=
So the original article is here:=C2=A0icles/srep20252">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 cladogram=
s 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 tim=
es but a really useful skill.

I hope that helps a =
bit! :)

Jon
=

On Mon, Sep 26, 2016 at 12:01 PM, Ruben Safi=
r <ank">ruben-at-mrbrklyn.com> wrote:
_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:=
1ex">Jon



Good morning.=C2=A0 As I was writing on facebook, we have been given a gor>
ahead to do a masters thesis on machine learning on fossils to build

cladiagraphs.=C2=A0 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:



nnosaurs/" rel=3D"noreferrer" target=3D"_blank">http://blogs.plos.org/=
paleocomm/2016/02/17/the-evolution-of-tyrannosaurs/



I expect to publish all our work at " rel=3D"noreferrer" target=3D"_blank">http://www.nylxs.com/thesis/



I'm very interested in openscience and we will likely try to restrictr>
our projects to Free Software.=C2=A0 I'm particularly interested in map=
ping

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

ht=
tp://www.mrbrklyn.com



DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002

http:=
//www.nylxs.com - Leadership Development in Free Software

"_blank">http://www2.mrbrklyn.com/resources - Unpublished Archive<=
br>
>http://www.coinhangout.com - coins!

ank">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




--
=3D"gmail_signature" data-smartmail=3D"gmail_signature">
iv>
>


PhD Student:=C2=A0Department of Earth Scie=
nce and Engineering,=C2=A0Royal School of Mines,=C2=A0Prince Consort Road,=
=C2=A0Imperial College London,=C2=A0SW7 2BP, UK
">
Communications Director at /www.scienceopen.com/" target=3D"_blank">ScienceOpen, Berlin.
dir=3D"ltr">
=
Website:=C2=A0 href=3D"http://fossilsandshit.com/" target=3D"_blank">http://fossilsandshi=
t.com/=C2=A0




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--===============1520739320==--

  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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