[Biopython-dev] BioGeography update/BioPython tree module discussion

Nick Matzke matzke at berkeley.edu
Tue Jul 14 19:08:56 UTC 2009

Thanks for the fix!!!  A big help.  I am currently organizing my 
functions into several classes and making sure they work, basically the 
classes look like they will be something like:

GbifXml -- for processing GBIF XML results (all of the functions for 
searching/extracting stuff from xmltree structures)

TreeSum -- for processing trees & getting summary statistics etc.

Ranges -- Geographic range of a species (collection of points, results 
of classification of those points into regions), GIS-like functions for 
processing them
   Points -- geographic locations of individual collected specimens

Brad Chapman wrote:
> Hi Nick;
> Thanks for the comprehensive update. It sounds like your discussion
> with Eric resolved most of the questions about the tree
> representation. It's great to see y'all converging on this.
>> It sounds like for my immediate purposes, Bio.Nexus.Trees is the 
>> solution for now, I will reorganize my code accordingly based on this. 
>> If/when Bio.Nexus.Trees accepts node labels I will remove a function 
>> stripping out node labels.  Also I have not forgotten previous comments 
>> from Brad et al. about bringing the other code up to specs. So I will 
>> update the BioGeography schedule and overall organization I hope to have 
>> at the end (with classes/methods etc., instead of just a 
>> list-o-functions, which is how my original schedule was explicitly laid 
>> out), and post an update when done.
> Agreed, and seconding Hilmar that the best thing about open source
> code is having others looking at your code. Conversely, feel free to
> dig in and fix current code where it is holding you up. To remove
> this blocking issue on Nexus and get us rolling again, I
> put together an initial fix. You can grab the patch from:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2788
> Let us know if this works for your files of interest.
> If this clears up the Nexus issue, it would be great to see the
> revised schedule incorporating the refactoring. Sounds like we 
> are moving in the right direction. Good stuff.
> Thanks,
> Brad

Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
Dept. personal page: 
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

"[W]hen people thought the earth was flat, they were wrong. When people 
thought the earth was spherical, they were wrong. But if you think that 
thinking the earth is spherical is just as wrong as thinking the earth 
is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 
14(1), 35-44. Fall 1989.

More information about the Biopython-dev mailing list