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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From: Ruben Safir
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Subject: Re: [Learn] Proposed Thesis
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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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