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DATE 2016-09-01

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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 10:34:10 2016
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<20160926130028.GA6913-at-www.mrbrklyn.com>
From: Jon Tennant
Date: Mon, 26 Sep 2016 14:03:49 +0100
Message-ID:
To: Ruben Safir
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Subject: Re: [Learn] Proposed Thesis
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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!

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
> > > Palaeontology/dp/178240144X>
> >
> > *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

--001a114049625ddc99053d68c223
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

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!

Jon
>
On Mon, Sep 26, 2016 at 2:00 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">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:

> " target=3D"_blank">http://www.nature.com/articles/srep20252

>

> I don't know exactly how they drew this, but there's an R pack=
age called

> geoscale that does this temporal calibration of cladograms quite nicel=
y. In

> terms of building the actual tree, you can use software like TNT and t=
hen

> read the outputs into R, which is pretty difficult at times but a real=
ly

> useful skill.

>

> I hope that helps a bit! :)

>



the data is entered by hand?=C2=A0 Is it possible to scan a fosil in=
to 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 <ben-at-mrbrklyn.com">ruben-at-mrbrklyn.com> wrote:

>

> > Jon

> >

> > Good morning.=C2=A0 As I was writing on facebook, we have been gi=
ven a go

> > ahead to do a masters thesis on machine learning on fossils to bu=
ild

> > cladiagraphs.=C2=A0 I have some rudimentary understanding of the =
topic, but

> > not much in terms of detail or understanding how paleontologist b=
uild

> > such diagrams mapping proposed evolutionary relationships today.<=
br>
> >

> > 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 th=
e T-Rex

> > article you did here:

> >

> > on-of-tyrannosaurs/" 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 om/thesis/" rel=3D"noreferrer" target=3D"_blank">http://www.nylxs.com/thesi=
s/

> >

> > I'm very interested in openscience and we will likely try to =
restrict

> > our projects to Free Software.=C2=A0 I'm particularly interes=
ted in mapping

> > algorithms being developed and applied to these problems, and

> > integrating the increasing use of scanned 3d images for systemati=
c

> > 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

> > _blank">http://www.mrbrklyn.com

> >

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

> > ank">http://www.nylxs.com - Leadership Development in Free Software

> > target=3D"_blank">http://www2.mrbrklyn.com/resources - Unpublishe=
d Archive

> > =3D"_blank">http://www.coinhangout.com - coins!

> > get=3D"_blank">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 201=
3

> >

>

>

>

> --

>

>

> *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 <ww.scienceopen.com/" rel=3D"noreferrer" target=3D"_blank">https://www.scien=
ceopen.com/>,

> Berlin.

>

> *ORCID:* errer" target=3D"_blank">http://orcid.org/0000-0001-7794-0218

> *Twitter:* -at-protohedgehog <ehog" rel=3D"noreferrer" target=3D"_blank">https://twitter.com/Protohe=
dgehog>

> *Website:* arget=3D"_blank">http://fossilsandshit.com/=C2=A0 </fossilsandshit.com/" rel=3D"noreferrer" target=3D"_blank">http://fossilsan=
dshit.com/>

> *Blog:* target=3D"_blank">http://blogs.egu.eu/palaeoblog/

>

> <" target=3D"_blank">http://fossilsandshit.wordpress.com/>Author=
of Excavate! Dinosaurs

> <laeontology/dp/178240144X" rel=3D"noreferrer" target=3D"_blank">http://www.=
amazon.co.uk/Excavate-Dinosaurs-Paper-Toy-Palaeontology/dp/178240=
144X>

>

> *Email:* jon.tennant.2-at-gmai=
l.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

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"ltr">
dir=3D"ltr">


PhD Student:=C2=A0Department of=
Earth Science and Engineering,=C2=A0Royal School of Mines,=C2=A0Prince Con=
sort Road,=C2=A0Imperial College London,=C2=A0SW7 2BP, UK
dir=3D"ltr">

<=
div dir=3D"ltr">Blog:yle=3D"font-size:12.8000001907349px">=C2=A0gu.eu/palaeoblog/" style=3D"font-size:12.8000001907349px" target=3D"_blank"=
>http://blogs.egu.eu/palaeoblog/

<=
a href=3D"http://fossilsandshit.wordpress.com/" style=3D"font-size:12.80000=
01907349px" target=3D"_blank">Author of .uk/Excavate-Dinosaurs-Paper-Toy-Palaeontology/dp/178240144X" target=3D"_bl=
ank">Excavate! Dinosaurs

Email: nant.2-at-gmail.com" target=3D"_blank">jon.tennant.2-at-gmail.com
Mob: =
(+44)=C2=A07921252367

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0div>




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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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