Program

Listed below are confirmed presentations for SciPy2013. More details and schedule information coming soon.

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Keynotes
IPython: from the shell to a book with a single tool; the method behind the madness Fernando Perez, UC Berkeley Henry H. Wheeler Jr. Brain Imaging Center
The New Scientific Publishers William Schroeder, Kitware
Trends in Machine Learning and the SciPy community Olivier Grisel
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General
A comprehensive look at representing physical quantities in Python Bekolay, Trevor, University of Waterloo
A Portrait of One Scientist as a Graduate Student Ivanov, Paul, UC Berkeley
Analyzing IBM Watson experiments with IPython Notebook Bittner, Torsten, IBM
Breaking the diffraction limit with python and scipy Baddeley, David, Nanobiology Institute, Yale University
Bringing astronomical tools down to earth Droettboom, Michael, STScI; Dencheva, Nadia, STScI; Aldcroft, Tom, Harvard-Smithsonian Center for As
Data Agnosticism: Feature Engineering Without Domain Expertise Kridler, Nicholas, Accretive Health
DMTCP: Bringing Checkpoint-Restart to Python Arya, Kapil, Northeastern University; Cooperman, Gene, Northeastern University
Dynamics with SymPy Mechanics Moore, Jason, University of California at Davis
High Performance Reproducible Computing Zhang, Zhang, Intel Corporation; Rosenquist, Todd, Intel Corporation; Moffat, Kent, Intel Corporation
Import without a filesystem: scientific Python built-in with static linking and frozen modules Pat Marion, Kitware; Aron Ahmadia; Bradley M. Froehle, University of California, Berkeley
Julia and Python: a dynamic duo for scientific computing Bezanson, Jeff, MIT; Karpinski, Stefan, MIT
Matrix Expressions and BLAS/LAPACK Rocklin, Matthew, University of Chicago Computer Science
Modeling Complexity with Python Dr. Maksim Tsvetovat, independent; Alex Kouznesov, independent
Modeling the Earth with Fatiando a Terra Uieda, Leonardo, Observatorio Nacional; Oliveira Jr, Vanderlei C., Observatorio Nacional; Barbosa, V
Multidimensional Data Exploration with Glue Beaumont, Christopher, U. Hawaii; Robitaille, Thomas, MPIA; Borkin, Michelle, Harvard; Goodman, Alys
open('/dev/real_world') - Raspberry Pi Sensor and Actuator Control Minardi, Jack, Enthought Inc.
Opening Up Astronomy with Python and AstroML Vanderplas, Jake, University of Washington; Ivezic, Zeljko, University of Washington; Connolly, Andrew, University of Washington
Parallel Volume Rendering in yt: User Driven & User Developed Skillman, Samuel, University of Colorado at Boulder; Turk, Matthew, Columbia University
PyOP2: a Framework for Performance-Portable Unstructured Mesh-based Simulations and its Application to Finite-Element Computations Rathgeber, Florian, Imperial College London, UK; Markall, Graham R., Imperial College London, UK; Mi
Pythran: Enabling Static Optimization of Scientific Python Programs Serge Guelton, ENS; Pierrick Brunet, Télécom Bretagne; Alan Raynaud, Télécom Bretagne; Adrien Merlini, Télécom Bretagne; Mehdi Amini, SILKAN
Scientific Computing and the Materials Genome Initiative Reid, Andrew, National Institute of Standards and Technology
Scikit-Fuzzy: A New SciPy Toolkit for Fuzzy Logic Warner, Joshua, Mayo Clinic Department of Biomedical Engineering; Ottesen, Hal H., Adjunct Professor
SymPy Gamma and SymPy Live: Python and Mathematics Online Li, David, SymPy
Synoptic Atmospheric Transport of Wildfire Smoke Plume to Greenland Lavoue David, DL Modeling and Research, Milton, Ontario, Canada
The DyND Library Wiebe, Mark, Continuum Analytics
Why you should write buggy software with as few features as possible Granger, Brian, Cal Poly San Luis Obispo
XDress - Type, But Verify Scopatz, Anthony, The University of Chicago & NumFOCUS, Inc.
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Machine Learning
A Gentle Introduction To Machine Learning Kastner, Kyle, Southwest Research Institute
Hyperopt: A Python library for optimizing the hyperparameters of machine learning algorithms Bergstra, James, University of Waterloo; Yamins, Dan, Massachusetts Institute of Technology; Cox, David D., Harvard University
Implicit Sentiment Mining with SnowWhite Tsvetovat, Maksim, 2042 Labs; Alex Kouznetsov,
Infer.py: Probabilistic Programming and Bayesian Inference from Python Zinkov, Rob
mystic: a framework for predictive science Michael McKerns @ California Institute of Technology, Houman Owhadi @ California Institute of Techno
Processing biggish data on commodity hardware: simple Python patterns Author: Gael Varoquaux Institution: INRIA, Parietal team
Python Tools for Coding and Feature Learning Johnson, Leif, University of Texas at Austin
Roadmap to a Sentience Stack Eric Neuman
Skdata: Data seets and algorithm evaluation protocols in Python Bergstra, James, University of Waterloo: Pinto, Nicolas, Massachusetts Institute of Technology; Cox, David D., Harvard University
Using Python for Structured Prediction Zinkov, Rob
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Reproducible Science
An efficient workflow for reproducible science Bekolay, Trevor, University of Waterloo
Complex Experiment Configuration, Control, Automation, and Analysis using Robot Operating System (ROS) Stowers, John, TU Wien; Straw, Andrew, Research Institute of Molecular Pathology
Emacs + org-mode + python in reproducible research Kitchin, John Carnegie Mellon University
Exploring Collaborative HPC Visualization Workflows using VisIt and Python Krishnan, Harinarayan, Lawrence Berkeley National Labs; Harrison, Cyrus, Lawrence Livermore National
GraphTerm: A notebook-like graphical terminal interface for collaboration and inline data visualization Ramalingam Saravanan, Texas A&M University
IPython-powered Slideshow Reveal-ed Avila, Damian, OQUANTA;
lmonade: a platform for development and distribution of scientific software Erocal, Burcin, TU Kaiserslautern
lpEdit: An editor to facilitate reproducible analysis via literate programming Richards, Adam, Duke University, CNRS France; Kosinski Andrzej, Duke University; Bonneaud, Camille,
matplotlib: past, present and future Michael Droettboom
OS deduplication with SIDUS (single-instance distributing universal system) Quemener, Emmanuel, Centre Blaise Pascal (Lyon, France); Corvellec, Marianne, McGill University (Mon
Reproducible Documents with PythonTeX Poore, Geoffrey, Union University
The advantages of a scientific IDE Cordoba, Carlos, The Spyder Project
The Open Science Framework: Improving, by Opening, Science Spies, Jeffrey, Center for Open Science; Nosek, Brian, Center for Open Science
Using IPython Notebook with IPython Cluster for Reproducibility and Portability of Atomistic Simulations Trautt, Zachary, Materials Measurement Science Division, National Institute of Standards and Technol
Using Sumatra to Manage Numerical Simulations Davison, Andrew, CNRS (principal developer); Wheeler, Daniel, NIST (speaker)
vIPer, a new tool to work with IPython notebooks Avila, Damian, OQUANTA;
Writing Reproducible Papers with Dexy Nelson, Ana
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Astronomy and Astrophysics
Accessing the Virtual Observatory from Python Plante, Raymond, NCSA/UofIL; Fitzpatrick, Mike, NOAO; Graham, Matthew, Caltech; Tody, Doug, NRAO
Astropy, growing a community-based software system for astronomy Droettboom, Michael, STScI; Robitaille, Thomas, Max Planck Institute; Tollerud, Erik, Yale Universit
Combining C++ and Python in the LSST Software Stack Bosch, Jim, Princeton University
Ginga: an open-source astronomical image viewer and toolkit Jeschke, Eric, Subaru Telescope, National Astronomical Observatory of Japan
Python and the SKA Simon Ratcliffe SKA South Africa, Ludwig Schwardt SKA South Africa
SunPy - Python for Solar Physicists Mumford, Stuart, University of Sheffield / SunPy
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Bioinformatics
All-by-all learning of protein complexes from mass spectrometry data Blake Borgeson, Center for Systems and Synthetic Biology, University of Texas at Austin; Cuihong Wa
Best-practice variant calling pipeline for fully automated high throughput sequencing analysis Chapman, Brad; Kirchner, Rory; Hofmann, Oliver; Hide, Winston
Detection and characterization of interactions of genetic risk factors in disease Francis-Lyon, Patricia, University of San Francisco; Belvadi, Shashank, University of San Francisco; Wang, Lin, University of San Francisco
Discussion
Discussion
Discussion
EMAN2 and EMEN2: Flexible Python-based platforms for electron microscopy Rees, Ian, Baylor College of Medicine; Ludtke, Steven, Baylor College of Medicine
Exploring disease genetics from thousands of individual genomes with Gemini Quinlan, Aaron, University of Virginia; Paila, Uma, University of Virginia; Chapman, Brad, Harvard School of Public Health; Kirchner, Rory,
Massive Online Collaborative Research and Modeling using Synapse and Python Omberg, Larsson, Sage Bionetworks
metaseq: a Python framework for integrating high-throughput sequencing analyses Dale, Ryan, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of
MIST: Micro-Simulation Tool to Support Disease Modeling Jacob Barhak
Stuff to do with your genomic intervals Pedersen, Brent; University of Colorado
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GIS - Geospatial Data Analysis
GIS Panel Panel participants: Sergio Ray (Arizona State U), Shaun Walbridge (ESRI), Andrew Wilson (TWDB)
LarvaMap - A python powered larval transport modeling system Wilcox, Kyle, Applied Science Associates (ASA); Crosby, Alex, Applied Science Associates (ASA)
Optimizing Geographic Processing and Analysis for Big Data Carissa, GeoDecisions; Gleason, Jason, GeoDecisions
SCI-WMS: A Python Based Web Map Service For Met-Ocean Data Accessible Over OpenDAP Or As NetCDF Crosby, Alexander
Streamed Clustering of Lightning Mapping Data in Python Using sklearn Bruning, Eric C., Texas Tech University
The Production of a Multi-Resolution Global Index for Geographic Information Systems MacManus, Kytt, Columbia University CIESIN
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Medical Imaging
A Rapidly-Adaptable Analytical Imaging & Measurement Standardization Platform for Cancer Diagnostics Research Garsha, Karl, Ventana Medical Systems Inc.; Ventura, Franklin, Ventana Medical Systems Inc.;
An Open Source System for De-identification and Use of Medical Images for Research Miller, Jeffrey, Center for Biomedical Informatics, The Children's Hospital of Philadelphia
Automating Quantitative Confocal Microscopy Analysis Fenner, Mark; Fenner, Barbara, King's College, Wilkes-Barre, PA
Estimating and Visualizing the Inertia of the Human Body with Python Moore, Jason, University of California at Davis; Dembia, Christopher, Stanford
Experiences in Python for Medical Image Analysis Warner, Joshua, Mayo Clinic Department of Biomedical Engineering
NeuroTrends: Large-scale automated analysis of the neuroimaging literature Carp, Joshua, University of Michigan
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Meteorology, Climatology, Atmospheric and Oceanic Science
Advances in delivery and access tools for coastal ocean model data Signell, Richard, US Geological Survey
Climate Observations from ACIS in pandas Noon, William: Northeast Regional Climate Center
Iris & Cartopy: Open source Python packages for Atmospheric and Oceanographic science Elson, Philip, UK Met Office;
Oil spill modeling and uncertainty forecasts with Python Hou,Xianlong, University of Texas at Austin; Hodges,Ben, University of Texas at Austin
Using Python to drive the General NOAA Operational Modeling Environment Barker, Christopher H. NOAA Emergency Response Division.
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Posters
3D Perception: Point cloud data processing and visualization Marion, Pat, Kitware;
A Python way to an undergraduate CFD course Jaime Kardontchik
Basic Interactive Unix for Data Processing Hale, Walker, Baylor College of Medicine
Basin-hopping and beyond: Global optimization and energy landscape exploration in molecular systems Jacob Stevenson and Victor Rühle
Code as text: Open source in academia Rey, Sergio, Arizona State University
Data Wrangling with the SheafSystem™ Butler, David M., Limit Point Systems, Inc.
Dedalus: A Python-Based Spectral PDE Solver Keaton J. Burns, University of California Berkeley; Jeffrey S. Oishi, American Museum of Natural History; Geoffrey M. Vasil, University of California Berkeley; Daniel Lecoanet, University of California Berkeley; Eliot Quataert, University of California Berkeley
Experimental Mathematics with Python: Calculating Lyapunov exponents of non-elastic billiard models Alonso Espinosa & David P. Sanders* (presenter) Institution: Department of Physics, Faculty of Sciences, Universidad Nacional Autónoma de México (UNAM)
G-mode Clustering Method applied to Asteroid Taxonomy Hasselmann, P. H., Carvano, J. M., Lazzaro, D.
Hearing Assessment: Lessons learned developing a modular solution for audiometric testing Chambers, Robert D., Creare Inc.; Finger, William H., Creare Inc.; Norris, Jesse A., Creare Inc.; Cl
HTSQL - A Navigational Query Language For Relational Databases Charles Tirrell and Clark Evans
IRLB, a fast partial SVD Baglama, Jim, University of Rhode Island; Kane, Michael, Yale
Managing Ensembles of Multi-Processor Jobs with Tex-MECS and PyLauncher Tobis, Michael, Planet 3.0; Eijkhout, Victor, Texas Advanced Computing Center
Mica: data-mining the Chandra archive for satellite operations Jean M. Connelly, Smithsonian Astrophysical Observatory (SAO); Thomas L. Aldcroft, SAO
Modeling elastic wave propagation using PyOpenCL Ursula Iturraran-Viveros and Miguel Molero
Navigating the Scientific Python Communities - the missing guide Ivanov, Paul, UC Berkeley
Peatland data analysis and simulation with Python Reeve, Andrew (University of Maine); Westervelt, Claire (University of Maine)
Powering Recommendations with Distributed Computing using Python and MapReduce Caraciolo, Marcel; Atapassar
PyDocX: Parsing Word documents in order to increase greater collaboration in collaborative writing Portnow, Samuel, University of Virginia; Ward, Jason, PolicyStat LLC; Spies, Jeff, R, Center for Open Science
Scholarly: An open, freely accessible dataset of the academic citation network Rybacki, Harry, UNCG; Carp, Joshua, University of Michigan; Spies, Jeffery, Center for Open Science
Self-documenting runtime: becoming omniscient with Contexture Alexander Kouznetsov
Technical and social challenges in creating the Python ARM Radar Toolkit (Py-ART) Helmus, Jonathan, Argonne National Laboratory; Collis, Scott, Argonne National Laboratory
The UQ Foundation: Supporting the Right Scientific Tools for Reproducibility Drew Marsden1, Michael McKerns2, Houman Owhadi2, Clint Scovel2, Tim Sullivan3
The Use of Python in the Prompt Assessment of Global Earthquake Response (PAGER) System Hearne, Michael, US Geological Survey
Ureka: a distribution of Python & IRAF software for astronomy Turner, James, Gemini Observatory; Slocum, Christine, Space Telescope Science Institute; Sienkiewicz
Using Git to improve reproducibility & transparency Gemayel, Toni, Banyan
Using Python to Study Rotational Velocity Distributions of Hot Stars Bragança, Gustavo, Observatório Nacional; Daflon, Simone, Observatório Nacional
UV-CDAT Re-sharable Analyses and Diagnostics (U-ReAD): a framework to create and share UV-CDAT plugins Doutriaux, Charles, LLNL