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#LyX 1.5.5 created this file. For more info see http://www.lyx.org/
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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
\end_layout
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- add a final python pros/cons, esp.
the cons part.
It will make things more balanced.
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- the PDE part repeats a bit the 'python benefits' which were already pounded
on.
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\begin_layout Title
Python in Scientific Computing
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Python & Scientific Computing
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\begin_layout Subtitle
An Overview
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\begin_layout Author
Fernando\InsetSpace ~
Pérez
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<Fernando.Perez@berkeley.edu>
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Neuroscience/BIC, U.C Berkeley
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UCB
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\begin_layout Date
UC Berkeley
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Oct 9, 2008
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UCB, 10/09/08
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Scientific Computing
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SciComp
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Existing tools
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Pure Fortran, C and C++
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Tools optimized for the CPU, not the developer.
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Low-level (data types and libraries).
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Difficult access to visualization, quick profiling, text processing,
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No interactive facilities.
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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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work with these tools
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, not replace them!
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Complementary high level tools
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Mathematica, Maple, Matlab, IDL: extremely popular, for good reasons.
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Interactivity, visualization, extensive libraries.
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Unpleasant for large-scale programs and non-mathematical tasks.
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Expensive, proprietary: lock-in.
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Another common approach: the `command pipeline'
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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 send the output ...
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to visualization/analysis programs.
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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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(BSD license), highly portable (Linux, OSX, Windows, lots...).
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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 use it effectively.
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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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batteries included
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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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\begin_layout Subsection
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
extremely
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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
\series bold
\color red
the feature is needed for the Phoenix project and their arrival at Mars
will be in March sometime
\series default
\color inherit
, 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.
\series bold
\color red
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.
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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.
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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:
\end_layout
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MayaVi is a standalone GUI program...
\end_layout
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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
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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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\color blue
A better Python shell
\color none
: object introspection, system access, 'magic' command system for adding
functionality when working interactively,
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ldots
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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.
\end_layout
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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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Distributed/parallel computing
\end_layout
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Work with Brian Granger (Cal State San Luis Obispo) and Min Ragan-Kelley
(U.
C.
Berkeley).
\end_layout
\begin_layout Standard
\align center
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filename fig/ipython_parallel.png
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High-level graphical control of parallel codes
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\begin_layout Standard
\align center
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Others
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Who else?
\end_layout
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Academia
\end_layout
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\color blue
PyRAF:
\color none
Astronomical data analysis (Hubble Space Telescope).
\end_layout
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\color blue
PyTrilinos:
\color none
Parallel solvers (Sandia National Lab's ).
\end_layout
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\color blue
DANSE:
\color none
Spallation Neutron Source (ORNL/Caltech).
\end_layout
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\color blue
CDAT
\color none
: Climate Data Analysis Tools (Lawrence Livermore).
\end_layout
\begin_layout Itemize
\color blue
OOF2
\color none
: Finite Element Analysis of Microstructures (NIST).
\end_layout
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Industry
\end_layout
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\color blue
InteractiveSupercomputing.com:
\color none
Python interface to their proprietary backend.
\end_layout
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\color blue
Numenta:
\color none
pattern recognition algorithms (Jeff Hawkins-Palm)
\end_layout
\begin_layout Itemize
\color blue
Google/YouTube:
\color none
Internally, new AppEngine web service platform.
\end_layout
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Lots
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more
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\color blue
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target "http://www.scipy.org/Topical_Software"
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Python at Berkeley (an incomplete list)
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Neuroscience
\end_layout
\begin_layout Itemize
NiPy: Neuroimaging in Python.
Mark D'Esposito, Jarrod Millman, Chris Burns, Tom Waite, Matthew Brett,
Mike Trumpis, Cindee Madison, with Jonathan Taylor (Stanford Stats).
\end_layout
\begin_layout Itemize
Numpy and Scipy: Jarrod Millman (release manager), nipy team.
\end_layout
\begin_layout Itemize
IPython: Min Ragan Kelley (Physics), with Brian Granger (Cal Poly)
\end_layout
\begin_layout Itemize
Redwood: Kilian Koepsell, Charles Cadieu, Paul Ivanov, Amir Khosrowshahi,
...
\end_layout
\begin_layout Standard
\series bold
\color blue
Astronomy
\end_layout
\begin_layout Itemize
Josh Bloom's group: Dan Starr, Christopher Klein, Damian Eads (UCSC)
\end_layout
\begin_layout Standard
\series bold
\color blue
Molecular Biology/Biochem
\end_layout
\begin_layout Itemize
Julius Lucks
\end_layout
\begin_layout Standard
\series bold
\color blue
LBL
\end_layout
\begin_layout Itemize
Lots of interest from NERSC, some of you here are from LBL.
\end_layout
\begin_layout Standard
\align center
\series bold
\size larger
\color blue
YOU!
\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 is a general programming language
\end_layout
\begin_layout ExampleBlock
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->{
\end_layout
\begin_layout Standard
\end_layout
\end_inset
\series bold
It's not a bug, it's a feature
\series default
!
\begin_inset ERT
status open
\begin_layout Standard
}
\end_layout
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Get others to develop the non-scientific tools you may need.
\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 automated testing.
\end_layout
\begin_layout Itemize
Excellent documentation tools
\end_layout
\begin_layout Itemize
Supports all major GUI toolkits.
\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 - but we're working on these}
\end_layout
\end_inset
\end_layout
\begin_deeper
\begin_layout Itemize
Installation, deployment: harder than needed.
\end_layout
\begin_layout Itemize
No good, single-point of entry environment (but see Sage)
\end_layout
\begin_layout Itemize
Documentation too scattered.
\end_layout
\begin_layout Itemize
Your favorite/critical tool may well not exist
\series bold
yet
\series default
.
\end_layout
\begin_layout Itemize
Funding agency support for infrastructure work is difficult to get.
\end_layout
\end_deeper
\begin_layout BeginFrame
Using your codes from today with Python
\end_layout
\begin_layout Itemize
Code too monolithic but with good core pieces?
\end_layout
\begin_deeper
\begin_layout Itemize
Break into a
\color blue
library core
\color inherit
and control layers.
\end_layout
\begin_layout Itemize
\color blue
Wrap
\color inherit
the libraries and expose them to Python.
\end_layout
\begin_layout Itemize
Use Python for control or use
\color blue
interactively
\color inherit
.
\end_layout
\end_deeper
\begin_layout Pause
\end_layout
\begin_layout Itemize
For existing libraries in C/C++/Fortran
\end_layout
\begin_deeper
\begin_layout Itemize
Provide Python
\color blue
bindings
\color inherit
for them.
\end_layout
\begin_layout Itemize
It will make it much easier for others to test/use them.
\end_layout
\begin_layout Itemize
The network economy benefits all.
In this case,
\color blue
\begin_inset Formula $O(n^{2})$
\end_inset
is good!
\end_layout
\end_deeper
\begin_layout BeginFrame
Writing a new code?
\end_layout
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
Avoid whole programs in C/Fortran:
\color none
\color red
you are optimizing globally!
\end_layout
\begin_deeper
\begin_layout Itemize
Prototype the problem in Python (get the algorithm right first)
\end_layout
\begin_deeper
\begin_layout Itemize
using fast libraries.
\end_layout
\end_deeper
\begin_layout Itemize
\color blue
Profile
\color none
the hotspots.
\end_layout
\begin_layout Itemize
Optimize
\color none
\color blue
only those
\color inherit
, if needed.
\end_layout
\end_deeper
\begin_layout Itemize
\begin_inset ERT
status collapsed
\begin_layout Standard
<+->
\end_layout
\end_inset
The result may be production-ready:
\color none
\color blue
less throw-away prototypes.
\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 Section*
Wrapup
\end_layout
\begin_layout BeginFrame
Wrapup
\end_layout
\begin_layout Standard
\series bold
\color blue
Python
\end_layout
\begin_layout Itemize
Rapidly growing in scientific computing.
\end_layout
\begin_layout Itemize
Collaborative effort:
\color blue
by scientists, for scientists.
\end_layout
\begin_layout Itemize
An open stack supports truly
\color blue
reproducible computational research
\color inherit
.
\end_layout
\begin_layout Pause
\end_layout
\begin_layout Standard
\series bold
\color blue
What's in it for you?
\end_layout
\begin_layout Itemize
Hopefully a very useful tool.
\end_layout
\begin_layout Itemize
Provide Python bindings to your own research codes.
\end_layout
\begin_deeper
\begin_layout Itemize
...
and we all benefit from the resulting network effect.
\end_layout
\end_deeper
\begin_layout Pause
\end_layout
\begin_layout Standard
\align center
\series bold
\size large
Join in,
\color blue
there's plenty to do!
\end_layout
\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
Let's start working!
\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
