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Some things to fix in a future version:
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- trim a bit of time
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- add more about ipython and my own python work, reduce that of others
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- add a final python pros/cons, esp.
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It will make things more balanced.
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Python in Scientific Computing
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Python & Scientific Computing
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An Introduction
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\begin_layout Author
Fernando\InsetSpace ~
Pérez
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<Fernando.Perez@colorado.edu>
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John Hunter
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<jdh2358@gmail.com>
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Applied Mathematics, U.
of Colorado at Boulder
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Tradelink
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CU\InsetSpace ~
Boulder/Tradelink
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NCAR, Boulder
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Dec 7, 2007
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NCAR, 12/7/07
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[pausesections]
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Scientific Computing
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SciComp
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Traditional approaches
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Status quo
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FORTRAN, C and C++
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Tools optimized for CPUs, not humans.
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Low-level:
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Primitive data types (no good strings, sets, hash tables,
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).
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Manual memory management: bugs, bugs, bugs.
Hard ones.
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Slow edit/compile/test cycle.
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Clumsy access to visualization, quick profiling, text processing,
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No interactive facilities - scientific work is inherently exploratory.
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However!
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They deliver excellent performance.
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Millions of LOC in proven scientific codes.
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We need to
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, not replace them!
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Higher level tools in the last decade
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Mathematica and Maple: a unique niche we won't address today.
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IDL and Matlab: extremely popular, for good reasons.
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Great interactivity, visualization, and extensive libraries.
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Unpleasant languages for large-scale programs and non-numerical tasks.
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Expensive/proprietary: lock-in.
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Often considered `prototyping' tools: this leads to a lot of code rewriting.
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A common approach (I've been there): mix and match multiple tools:
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FORTRAN, C, C++ programs ...
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driven by Bash/awk/sed/Perl scripts ...
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which feed them input and take their outputs ...
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and pass them to Gnuplot, Grace, OpenDX, etc.
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Many different syntaxes:
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huge context switching overhead!
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Python?
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Python
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Python in this context
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Free
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Interactive
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Extremely readable syntax (
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).
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Simple
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: non-professional programmers can become (and remain) proficient with a
very small effort (c.f.
C++).
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Clean object oriented model, but
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not mandatory
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.
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Rich built-in types: lists, sets, dictionaries (hash tables), strings, ...
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Very comprehensive standard library (
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Standard libraries for IDL/Matlab-like arrays (NumPy)
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Easy to wrap existing C, C++ and FORTRAN codes.
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Interlude: Python in the real world
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Examples
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EEG analysis for epilepsy
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EEG
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Data analysis for epilepsy surgery
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Isolating the origin of drug-resistant epileptic seizures which require
surgery.
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John Hunter, Department of Pediatric Neurology, University of Chicago.
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Electrode location in 3D, combined with MRI data
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Correlation analysis of seizure data
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Final location of epileptic foci for surgery
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Multiwavelets for PDEs
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PDEs
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Adaptive, multiwavelet algorithms for integral operators
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Gregory Beylkin, Vani Cheruvu, Fernando Perez.
Applied Math, U.
of Colorado at Boulder.
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Fast application of integral kernels.
(Partial Differential Equations)
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Implementation went from 1 to 3 dimensions directly (
\emph on
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Very complex algorithm that goes beyond pure numerics.
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Very good performance, thanks to NumPy, F2PY and weave.
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JPL: Mars mission data visualization
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JPL - Mars
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JPL: Mars mission trajectory design and nav data
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Ted Drain and Lynn Craig, Jet Propulsion Laboratory (NASA/Caltech)
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From: Name Elided <nameelided@jpl.nasa.gov>
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Date: Oct 2, 2007 7:15 PM
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Subject: Fwd: matplotlib bug numbers
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To: John Hunter <jdh2358@gmail.com>
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One of my lead developers mentioned that they had sent a bug to you about
the annotations feature of MatPlotLib.
Would you be able to let me know what the timeline is to resolve that bug?
The reason is that the feature is needed for the Phoenix project and their
arrival at Mars will be in March sometime, but they are doing their testing
in the coming few months.
This annotation feature is used on reports that present the analysis of
the trajectory to the navigation team and it shows up on our schedule.
It would really help me to know approximately when it could be resolved.
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B-plane plots are used to show the trajectory of a spacecraft with respect
to the target body (specifically perpendicular to the incoming asymptote
of the spacecraft trajectory) and we plot them with the y-axis inverted.
The plot is used heavily in flight operations so it is important to our
customers.
\end_layout
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In addition, we have what is called a thundering heard plot where many different
trajectory solutions (determined from different measurement sources) are
plotted together.
The annotations are import there so we can see which plot corresponds to
each source of data.
I hope it helps to know how your code will be used in spacecraft navigation.
\end_layout
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Thanks for all your efforts.
\end_layout
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JPL: Mars mission data visualization
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Expected communication power levels between an orbiting spacecraft and a
lander as it goes through the atmosphere:
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JPL: Mars mission data visualization (2)
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Summary of the current navigation team activities and modelling (data used,
event times etc):
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PMV: structural bioinformatics
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PMV
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PMV: the Python Molecule Viewer
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Michel F.
Sanner, Molecular Biology Department, The Scripps Research Institute.
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MayaVi: customizable data visualization
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MayaVi
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MayaVi: sophisticated data visualization
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Free, easy to use scientific data visualizer.
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Heavy lifting of OpenGL-based rendering: VTK (a C++ library).
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A very good example of how to properly use Python:
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MayaVi is a standalone GUI program...
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but also a Python library callable by any other Python program.
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Python: very easy to modify, even by adding at runtime user-defined modules
which populate the GUI automatically.
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C++: excellent rendering performance, fully hardware-accelerated OpenGL.
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The punchline:
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fully programmable visualization, with builtin access to all kinds of numerical
(and other) libraries from within the viz tool.
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FluidLab: a MayaVi based CFD visualization tool
\end_layout
\begin_layout Standard
K.
Julien, P.
Schmitt (now NCAR), B.
Barrow, F.
Pérez (App.
Math, CU).
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Volumetric rendering with FluidLab
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SAGE: System for Algebra and Geometry Experimentation
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SAGE
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SAGE: open source mathematics
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Winner of the 2007 Trophés du Libre, scientific software category
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IPython
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IPython
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Extensible interactive environment with parallel computing support
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A better Python shell
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: object introspection, system access, 'magic' command system for adding
functionality when working interactively,
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\backslash
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\color blue
An embeddable interpreter
\color none
: useful for debugging and for mixing batch-processing with interactive
work.
\end_layout
\begin_layout Enumerate
\color blue
A flexible component
\color none
: you can use it as the base environment for other systems with Python as
the underlying language.
It is very configurable in this direction.
\end_layout
\begin_layout Enumerate
\color blue
A system for interactive control of distributed/parallel computing systems.
\color none
\end_layout
\begin_layout Enumerate
\color blue
An interactive component
\color none
we can plug into GUIs, browser-based shells, etc.
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IPython: IDL-like interactive use
\end_layout
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IPython: interactive control of VTK visualizations
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IPython's future
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A 2-process kernel on the network
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Work with Brian Granger (Tech-X, Boulder) and Benjamin Ragan-Kelley (U.
C.
Berkeley physics).
\end_layout
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Distributed/parallel computing
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Think of Python as 'the CPU'
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But these souped-up kernels let you talk to it conveniently.
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PyNGL
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PyNGL - Python interface to NCAR's NCL
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import
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numpy
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, Ngl, Nio
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dirc = Ngl.pynglpath("data")
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cfile = Nio.open_file(dirc + "/cdf/seam.nc")
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\begin_layout Standard
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lon =
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numpy
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.ravel(cfile.variables["lon2d"][:,:])
\end_layout
\begin_layout Standard
\family typewriter
lat =
\family default
\color none
\family typewriter
\color blue
numpy
\color none
.ravel(cfile.variables["lat2d"][:,:])
\end_layout
\begin_layout Standard
\family typewriter
ps =
\family default
\color none
\family typewriter
\color blue
numpy
\color none
.ravel(cfile.variables["ps"][0,:,:])/100.
\end_layout
\begin_layout Standard
\family typewriter
rlist = Ngl.Resources()
\end_layout
\begin_layout Standard
\family typewriter
rlist.wkColorMap = "BlAqGrYeOrReVi200"
\end_layout
\begin_layout Standard
\family typewriter
wks_type = "ps"
\end_layout
\begin_layout Standard
\family typewriter
wks = Ngl.open_wks(wks_type,"seam",rlist)
\end_layout
\begin_layout Standard
\family typewriter
resources = Ngl.Resources()
\end_layout
\begin_layout Standard
\family typewriter
resources.sfXArray = lon
\end_layout
\begin_layout Standard
\family typewriter
resources.sfYArray = lat
\end_layout
\begin_layout Standard
\family typewriter
map = Ngl.contour_map(wks,ps,resources)
\end_layout
\begin_layout Standard
\family typewriter
Ngl.end()
\end_layout
\begin_layout BeginFrame
PyNGL
\end_layout
\begin_layout Standard
\align center
\begin_inset Graphics
filename fig/ncar-world-seam.3.png
lyxscale 50
width 90text%
\end_inset
\end_layout
\begin_layout Subsection*
Others
\end_layout
\begin_layout BeginFrame
A few other projects
\end_layout
\begin_layout FrameSubtitle
Python is becoming very popular in many different scientific areas
\end_layout
\begin_layout Itemize
\color blue
PyDAP:
\color none
Python implementation of the OpenDAP protocols (client
\series bold
and
\series default
server).
\end_layout
\begin_layout Itemize
\color blue
PyTables:
\color none
HDF-5 read-write support with excellent performance.
\end_layout
\begin_layout Itemize
\color blue
PyTrilinos:
\color none
Python interface to Sandia's Trilinos parallel solvers.
Coupled with IPython, they can be used interactively.
\end_layout
\begin_layout Itemize
\color blue
PyRAF:
\color none
Hubble Space Telescope interface to IRAF, a standard in astronomical image
processing.
\end_layout
\begin_layout Itemize
\color blue
VPython:
\color none
easy, real-time 3D programming (Carnegie Mellon, used for an introductory
mechanics course).
\end_layout
\begin_layout Itemize
\color blue
Galaxy:
\color none
integrated access to multiple tools in genomics research.
\color blue
Very impressive
\color none
.
\end_layout
\begin_layout Section
Development in Python
\begin_inset OptArg
status collapsed
\begin_layout Standard
Development\InsetSpace ~
Model
\end_layout
\end_inset
\end_layout
\begin_layout BeginPlainFrame
Python compared to IDL, Matlab, etc.
\end_layout
\begin_layout ExampleBlock
\begin_inset ERT
status open
\begin_layout Standard
<+->{Pros}
\end_layout
\begin_layout Standard
\end_layout
\end_inset
\end_layout
\begin_layout ExampleBlock
A general programming language:
\series bold
this is a feature
\series default
!
\end_layout
\begin_deeper
\begin_layout Itemize
Free, open source, extremely portable: from the OLPC or a cellphone (Nokia)
to a supercomputer.
\end_layout
\begin_layout Itemize
Networking, text processing, XML parsing, databases, etc
\begin_inset ERT
status open
\begin_layout Standard
\backslash
ldots
\end_layout
\end_inset
\end_layout
\begin_layout Itemize
Integrated support for testing (
\family typewriter
unittest
\family default
,
\family typewriter
doctest
\family default
)
\end_layout
\begin_layout Itemize
Automatic API documentation tools (
\family typewriter
epydoc, doxygen
\family default
).
\end_layout
\begin_layout Itemize
Supports all major GUI toolkits.
\end_layout
\begin_layout Itemize
Extremely expressive for complex algorithms.
\end_layout
\end_deeper
\begin_layout Separator
\end_layout
\begin_layout AlertBlock
\begin_inset ERT
status open
\begin_layout Standard
<+->{There are still rough edges!}
\end_layout
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Installation, deployment: harder than needed (but improving).
\end_layout
\begin_layout Itemize
No good, single-point of entry integrated help system.
\end_layout
\begin_layout Itemize
Lots of good documentation, but scattered all over.
\end_layout
\begin_layout Itemize
Funding agency support for infrastructure work is difficult to get.
\end_layout
\end_deeper
\begin_layout BeginFrame
A different model of development
\end_layout
\begin_layout FrameSubtitle
\emph on
\color red
Global optimization is the root of all evil
\end_layout
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
Never write `
\family typewriter
main()
\family default
' in C anymore:
\color none
\color red
you are optimizing globally!
\end_layout
\begin_deeper
\begin_layout Itemize
Prototype the code in Python.
\end_layout
\begin_layout Itemize
Wrap existing libraries for Python access and reuse them (Numeric, LAPACK,
VTK, ...)
\end_layout
\begin_layout Itemize
Identify remaining hot spots via
\color none
\color blue
profiling
\color none
.
\end_layout
\begin_layout Itemize
Rewrite
\color none
\color blue
only
\color none
the code for those hot spots in C/C++/FORTRAN.
\end_layout
\end_deeper
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
The resulting code will be production-ready:
\color none
\color blue
no throw-away codes
\color none
.
\end_layout
\begin_deeper
\begin_layout Itemize
Make your code available as a library for
\color none
\color blue
interactive use
\color none
.
\end_layout
\begin_layout Itemize
Integrate plotting, visualization, logging, ..., into your objects.
\end_layout
\end_deeper
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
\color blue
Apply this to existing codes
\color none
\end_layout
\begin_deeper
\begin_layout Itemize
Break them into a library core and control layers.
\end_layout
\begin_layout Itemize
Wrap the libraries and expose them to Python.
\end_layout
\begin_layout Itemize
Write all new control as quick, light Python scripts.
\end_layout
\end_deeper
\begin_layout Section*
Wrapup
\end_layout
\begin_layout BeginFrame
Summary
\end_layout
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
\color blue
Python
\end_layout
\begin_deeper
\begin_layout Itemize
An excellent language for scientific computing development.
\end_layout
\begin_layout Itemize
Scales from interactive exploration to full-blown production codes.
\end_layout
\begin_layout Itemize
Accessible to scientists who are not professional programmers.
\end_layout
\end_deeper
\begin_layout Standard
\begin_inset ERT
status collapsed
\begin_layout Standard
\backslash
vskip0pt plus.5fill
\end_layout
\end_inset
\end_layout
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
\color red
Outlook
\end_layout
\begin_deeper
\begin_layout Itemize
NumPy, SciPy, matplotlib, IPython, MayaVi, Sage, etc
\begin_inset ERT
status collapsed
\begin_layout Standard
\backslash
ldots
\end_layout
\end_inset
:
\series bold
all
\series default
are moving forward and improving.
\end_layout
\begin_layout Itemize
Major DOE, NSF, NiH projects are adopting it as a core technology.
\end_layout
\begin_layout Itemize
Yearly conference at Caltech (August) growing.
\end_layout
\begin_layout Itemize
These projects are all Open Source: if you find a flaw, a bug, or a missing
feature,
\color none
\emph on
\color blue
jump on board!
\end_layout
\begin_layout Itemize
There are still many rough edges to which various projects can contribute.
\end_layout
\end_deeper
\begin_layout BeginPlainFrame
Thank you! Questions?
\end_layout
\begin_layout FrameSubtitle
Credit: http://xkcd.com/353
\end_layout
\begin_layout Standard
\align center
\begin_inset ERT
status open
\begin_layout Standard
\backslash
vspace{-5mm}
\end_layout
\end_inset
\begin_inset Graphics
filename fig/xkcd_python.png
lyxscale 50
height 85pheight%
BoundingBox -4bp -4bp 518bp 588bp
\end_inset
\end_layout
\begin_layout BeginPlainFrame
\end_layout
\begin_layout Standard
\align center
\series bold
\size largest
\color blue
We're done here!
\end_layout
\begin_layout EndFrame
\end_layout
\begin_layout Section*
\start_of_appendix
\begin_inset Note Note
status collapsed
\begin_layout Standard
All of the following is optional and typically not needed.
\end_layout
\end_inset
Appendix
\end_layout
\begin_layout Subsection*
URLs
\end_layout
\begin_layout BeginFrame
Some useful URLs
\end_layout
\begin_layout Itemize
A collection of links on Python and Scientific Computing:
\color blue
\newline
\begin_inset LatexCommand htmlurl
target "http://amath.colorado.edu/faculty/fperez/python/scicomp"
\end_inset
\end_layout
\begin_layout Itemize
SciPy:
\color none
\color blue
\begin_inset LatexCommand htmlurl
target "http://www.scipy.org"
\end_inset
\end_layout
\begin_layout Itemize
IPython, an improved interactive shell
\color blue
:
\newline
\begin_inset LatexCommand htmlurl
target "http://ipython.scipy.org"
\end_inset
\end_layout
\begin_layout Itemize
Matplotlib, 2d plotting with Matlab syntax
\color blue
:
\newline
\begin_inset LatexCommand htmlurl
target "http://matplotlib.sourceforge.net"
\end_inset
\end_layout
\begin_layout Itemize
MayaVi, 3d data visualization:
\color blue
\newline
\begin_inset LatexCommand htmlurl
target "http://mayavi.sourceforge.net"
\end_inset
\end_layout
\begin_layout Itemize
PyX, programmatic PostScript generation (with
\begin_inset ERT
status collapsed
\begin_layout Standard
\backslash
LaTeX
\end_layout
\end_inset
support)
\color blue
:
\newline
\begin_inset LatexCommand htmlurl
target "http://pyx.sourceforge.net"
\end_inset
\end_layout
\begin_layout Itemize
F2Py (FORTRAN):
\color none
\color blue
\begin_inset LatexCommand htmlurl
target "http://cens.ioc.ee/projects/f2py2e"
\end_inset
\color none
\end_layout
\begin_layout Itemize
SWIG (C/C++ for Python):
\color none
\color blue
\begin_inset LatexCommand htmlurl
target "http://swig.org"
\end_inset
\end_layout
\begin_layout BeginFrame
URLs for projects mentioned earlier
\end_layout
\begin_layout Itemize
VPython, real-time 3D:
\color none
\color blue
\begin_inset LatexCommand htmlurl
target "http://vpython.org"
\end_inset
\end_layout
\begin_layout Itemize
UCSF Chimera - interactive molecular graphics
\color blue
:
\newline
\begin_inset LatexCommand htmlurl
target "http://www.cgl.ucsf.edu/chimera"
\end_inset
\end_layout
\begin_layout Itemize
PyRAF - Hubble Space Telescope interface to IRAF
\color blue
:
\newline
\begin_inset LatexCommand htmlurl
target "http://www.stsci.edu/resources/software_hardware/pyraf"
\end_inset
\end_layout
\begin_layout Itemize
BioPython -
\color none
\color blue
\begin_inset LatexCommand htmlurl
target "http://biopython.org"
\end_inset
\end_layout
\begin_layout Itemize
VisionEgg - vision research experiments (OpenGL):
\color blue
\newline
\begin_inset LatexCommand htmlurl
target "http://www.visionegg.org"
\end_inset
\color none
\end_layout
\begin_layout Itemize
Natural Language Toolkit:
\newline
\color blue
\begin_inset LatexCommand htmlurl
target "http://nltk.sourceforge.net"
\end_inset
\end_layout
\begin_layout Itemize
Neural Integrator - visual programming for neural networks:
\newline
\color blue
\begin_inset LatexCommand htmlurl
target "http://starship.python.net/crew/seehof/NeuralPython.html"
\end_inset
\end_layout
\begin_layout Itemize
Orange - component-based data mining:
\newline
\color blue
\begin_inset LatexCommand htmlurl
target "http://www.ailab.si/orange"
\end_inset
\end_layout
\begin_layout EndFrame
\end_layout
\end_body
\end_document
