[sage-support] Re: Mathematica 7 coming

[Marshall Hampton]

I am planning on asking for a vote to include biopython as standard
after its 1.49 release, which completes a transition from it using
Numeric to numpy.  Currently the interact wiki gives a poor impression
of what is possible with sage and bioinformatics, since the examples I
put there avoid using biopython.  I plan on adding some nicer examples
before asking for a vote.

I've been impressed in the last year by the development efforts on
biopython, which have been picking up steam.

It will be interesting to see what Mathematica does with
bioinformatics.

-Marshall Hampton

On Nov 14, 6:03 pm, Jason Grout <[EMAIL PROTECTED]> wrote:
> William Stein wrote:
> >> * Vector and field visualization
>
> > New?  I wonder how?  It seems like they have had this for a long time.
>
> There are lots of cool visualations you could do with vector fields that
> they don't have yet.  For example, see the following (sorry, these are
> from a sage
>
> <h2>Fromhttp://ccom.unh.edu/vislab/index.html</h2>http://ccom.unh.edu/vislab/images/projects/Kat350Vert2.jpgand
> visualizing two different vector flows on top of each other <br/>
> <img src="http://ccom.unh.edu/vislab/images/projects/Kat350Vert2.jpg"/>
> <img src="http://ccom.unh.edu/vislab/images/projects/TwoLayers.jpg"/>
>
> <h2><a
> href="http://www.drake.edu/artsci/mathcs/pages/people/tmu.htm";>Timothy
> Urness, Drake University in Des Moines</a></h2>
> Using texture and color and other things to visualize, especially
> multi-value flow<br/>
> <img src="http://facstaff.l3.drake.edu/turness/images2/nat.gif"/>
> <img src="http://facstaff.l3.drake.edu/turness/images2/VDA.gif"/>
> <img src="http://facstaff.l3.drake.edu/turness/images2/strategies.gif"/>
> <img src="http://facstaff.l3.drake.edu/turness/images2/ms.gif"/>
>
> Incidentally, these last images are from Tim Urness, who said he'd be
> willing to donate the code to Sage, if we wanted it.  It's plain C code.
>
> >> * New computable data, including genomic data, protein data, and
> >> current and historical weather data
>
> > Cool.   I wonder what the license issues are with making such data
> > available?  Can somebody look into this?
>
> Ondrej, you just corresponded with Wolfram about using their Help files.
>   My guess is that they'll have similar policies about other data that
> they've accumulated, though it would still be good to check.
>
> We could probably adapt an interface to noaa.gov to get historical (and
> current!) weather data, if we wanted.  For example, this page contains a
> python script that does it:
>
> http://ubuntuforums.org/showthread.php?t=102532&page=5
>
> Python already has a Biopython suite (and we have an spkg); 
> Seehttp://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc14for ways to
> access a lot of bioinformatics data.
>
> Also, we could indirectly use the BioConductor packages for R, which may
> provide nice access to bioinformatics data.
>
> > I was expecting something involving the web / ajax in their new
> > features.  I'm surprised there isn't anything.
>
> I think that would be more for a release of webMathematica, not
> Mathematica itself.
>
> Jason
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