[Bioperl-l] [Wg-phyloinformatics] Summer of Code: project summaries

Han, Mira mirhan at indiana.edu
Tue Sep 16 01:18:47 EDT 2008


Hi,
Just writing to summarize the final product of this summer. (even though it's overdue)
The phyloXML support in BioPerl project is finished officially,
I've created three new modules,
Bio::TreeIO::phyloxml,
Bio::Tree::AnnotatableNode,
and Bio::Annotation::Relation.
The parsing is done for all elements except for <ProteinDomain>
And the validation step is still missing.
I'm planning to add those in in the future.

I was contemplating to make a Bio::Annotation::XML till the end,
But decided not to since there was already a new module Bio::Annotation::TagTree, that looked like the same thing.
Currently, the module does not use TagTree, it uses nested AnnotationCollections instead, because TagTree was a temporary stub at the time.
There are methods in phyloxml that seem out of place there,
For example, the print_annotation and print_attr functions that print the annotations in phyloXML format.
Or the read_annotation function that reads the value of the annotation for a certain object.
I feel like these functions should go with the Annotation object,
But since there were no Annotation object that is phyloXML specific,
I just put them in the TreeIO::phyloxml.
This may change too in the future.

The documentations are all finished and can be seen in
http://www.bioperl.org/wiki/Module:Bio::TreeIO::phyloxml
http://www.bioperl.org/wiki/Module:Bio::Tree::AnnotatableNode
http://www.bioperl.org/wiki/Module:Bio::Annotation::Relation

The detailed progress of the project is documented in
http://www.bioperl.org/wiki/PhyloXML_support_in_BioPerl

and there is also a demo page that describes the use in
http://www.bioperl.org/wiki/Phyloxml_Project_Demo


Finally I'd like to thank Chris Fields and Hilmar Lapp,
for the constant support during the summer.
And the people on the list for providing helpful suggestions when I came with a question.
See you around.

Mira Han




On 9/14/08 1:15 PM, "Hilmar Lapp" <hlapp at duke.edu> wrote:

Hi all,

the 2008 Google Summer of Code program is officially over now. First
off, I'd like to congratulate all of our students: you all passed your
end-of-term evaluation, and you all passed solidly. Thanks for all
your hard work, beginning with writing and refining your project
applications and finally wrapping it up with documentation and a
demonstration project.

Based on what I can see, the students have all uploaded the code you
produced over the summer to the Google Code repository, as requested
by Google, so I'm not going to bore you with repeating the
instructions for how to do this. If you are still having trouble with
this process or have other questions regarding this though, don't
hesitate to let me know and ask any question you have.

For our imminently due Annual Report to NSF, we will need to document
your projects, and I am asking you for your help in this. Essentially,
we will need to produce similar information to what we composed for
the 2007 fall NESCent newsletter: for each project we need a short
summary of the project and the benefits of the results, written for a
scientific but otherwise general audience, a headshot of you (the
student), and a visual of the results. See

http://www.nescent.org/news/newsletter_10_07.php#google

for the example from last year as to what we have in mind. Kistin
Jenkins or Jory Weintraub from NESCent's Education and Outreach group
(both copied) will be in touch with you to possibly edit the summaries
and fine-tune the other material, but if the students could please
send your draft summary text, headshot, and visual as soon as you can
to eog at nescent.org that would be great. If you are not sure what to
use for the visual, I'd encourage you to speak with your mentor;
however, feel free to ask me as well.

Thanks again for working with us, and on your projects, and I hope you
all not only had a most enjoyable summer but also will keep involved
in your project as much as possible. I will also arrange for an end-of-
term teleconference with the students shortly, and one of the things
that I'd like to talk about is how we can best facilitate you
remaining involved beyond the official end of the program.

Cheers,

        -hilmar

--
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: Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
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