Scientific Computing with Python
Austin, Texas • July 6-12, 2015
 

SciPy 2015 Talk & Poster List

The SciPy organizing committee is in awe of the work the SciPy community is doing and we greatly appreciate everyone who submitted a topic for this year's conference. If your submission wasn't able to be slated into the limited number of main conference talk sessions or poster slots, we encourage you to take advantage of the lightning talk and Birds of a Feather (BoF) sessions to share your work. See this page for the talk and poster schedule

Are you a talk or poster presenter? See this page for information for presenters.

We hope to see you at SciPy in July! 



Accepted Talks

(scroll down for accepted posters)


Analyzing Genomic Data with PyEnsembl and Varcode
[More Info]
Alex Rubinsteyn, Mount Sinai School of Medicine
Tim O'Donnell, Mount Sinai School of Medicine

ETE: A Python Programming Toolkit for the Analysis and Visualization of Trees
[More Info]
Jaime Huerta-Cepas, EMBL

Python as a First Programming Language for Biomedical Scientists
[More Info]
Jeannie Irwin, University of Pittsburgh

Python Derived Imaging Biomarkers of Dementia
[More Info]
Ross Mitchell, Professor of Radiology, Mayo Clinic College of Medicine, Mayo Clinic Arizona

The Biopython Project: Freely Available Python Tools for Computational Molecular Biology and Bioinformatics
[More Info]
Tiago Antao
Big Data in Practice: The Example of Nilearn for Mining Brain Imaging Data [More Info]
Loïc Estève, Inria

Qiita: Report of Progress Towards an Open Access Microbiome Data Analysis and Visualization Platform
[More Info]
Adam Robbins-Pianka, University of Colorado, Boulder
Yoshiki Vazquez-Baeza, University of California, San Diego

Rapid Accurate and Simple Segmentation of Objects in Medical Images
[More Info]
Ross Mitchell, Professor of Radiology, Mayo Clinic College of Medicine, Mayo Clinic Arizona

scikit-bio: A Bioinformatics Library for Data Scientists, Students, and Developers
[More Info]
Jai Ram Rideout, Northern Arizona University
Evan Bolyen, Northern Arizona University

Statistical Learning of Human Brain Structure in DIPY
[More Info]
Ariel Rokem, The University of Washington eScience Institute
Franco Pestilli, Indiana University
Bagrat Amirbekian, University of California, San Francisco
Stefan van der Walt, University of California, Berkeley
Brian Wandell, Stanford University
Eleftherios Garyfallidis, University of Sherbrooke

Visualizing Physiological Signals in Real Time
[More Info]
Sebastian Sepulveda, Universidad de Valaparaiso

Astropy in 2015
[More Info]
Erik Tollerud, Hubble Fellow, Astropy/Yale University

Automated Image Quality Monitoring with IQMon
[More Info]
Josh Walawender, Instrument Astronomer, Subaru Telescope

PyNeb: Nebular Analysis Tools for Astrophysics
[More Info]
Richard Shaw, National Optical Astronomy Observatory

Python Tools for Space Mission Data Analyses
[More Info]
Michael Aye, LASP

The James Webb Space Telescope Data Calibration Pipeline
[More Info]
Howard Bushouse, Space Telescope Science Institute

Who Needs Standard Stars Anyway? Telluric Model Fitting with TelFit
[More Info]
Kevin Gullikson, University of Texas

Widgets and Astropy: Accomplishing Productive Research with Undergraduates
[More Info]
Matthew Craig, Minnesota State University Moorhead
Conference Talks

Deep Learning Versus Segmentation and ML to Classify Biological Images
[More Info]
Cedric St-Jean, Recursion Pharmaceuticals

Deep Learning for Quantity-Structure Activity Relationships
[More Info]
Rich Lewis, University of Cambridge
 
Data Science

Deep Learning for Quantity-Structure Activity Relationships
[More Info]
Rich Lewis, University of Cambridge

Deep Learning: Tips from the Road
[More Info]
Kyle Kastner, Graduate Student, Université de Montréal

pgmpy: Probabilistic Graphical Models using Python
[More Info]
Ankur Ankan
Abinash Panda

PyStruct - Structured Prediction in Python
[More Info]
Andreas Mueller, New York University Center for Data Science

Blaze + Odo
[More Info]
Phillip Cloud, Continuum Analytics

Building a Cloud-based Data Science Platform with Python
[More Info]
Stephen Hoover, Data Scientist, Civis Analytics

State of the Library: matplotlib
[More Info]
Thomas Caswell, Brookhaven National Laboratory
Benjamin Root

The Polyglot Beaker Notebook
[More Info]
Scott Draves, Two Sigma Open Source

Welcome to the Algo Wars: Leveraging Design Thinking for Building Scalable Enterprise Intelligent Systems using Python
[More Info]
Zubin Dowlaty, Mu Sigma
Subir Mansukhani, Mu Sigma
Bharat Upadrasta, Mu Sigma

xray: N-D Labeled Arrays and Datasets
[More Info]
Stephan Hoyer, The Climate Corporation

Perceptual Colormaps in matplotlib with an Application in Oceanography
[More Info]
Kristen Thyng, Assistant Research Scientist, Texas A&M University

Deploying Python Machine Learning Models in Production
[More Info]
Krishna Sridhar, Dato

Examining Malware with Python
[More Info]
Phil Roth, Endgame

Python in Data Science Research and Education
[More Info]
Randy Paffenroth, Worcester Polytechnic Institute

Structural Cohesion: Visualization and Heuristics for Fast Computation with NetworkX and matplotlib
[More Info]
Jordi Torrents, NetworkX

ASDF, a New Scientific Data Format
[More Info]
Perry Greenfield, Space Telescope Science Institute
Michael Droettboom, Space Telescope Science Institute
Erik Bray, Space Telescope Science Institute

Causal Bayesian NetworkX
[More Info]
Michael Pacer, Graduate Student, University of California, Berkeley

RESTful HDF
[More Info]
John Readey, HDF Group

UDL: Unified Interface for Deep Learning
[More Info]
Haitham Elmarakeby, Virginia Tech University

Wrapping C and C++ Libraries with CastXML
[More Info]
Brad King, Kitware
Bill Hoffman, Kitware
Matthew McCormick, Kitware
Michka Popoff
 
Engineering

An Open-Source Data Archive for Expert-Annotated Dermoscopic Images
[More Info]
Brian Helba, Kitware Inc

Basic Sound Processing in Python
[More Info]
Speaker: Allen Downey, Professor of Computer Science, Olin College

Optimal Control and Parameter Identification of Dynamcal Systems with Direct Collocation using SymPy
[More Info]
Jason Moore, Lead Developer, PyDy

pycalphad: Computational Thermodynamics in Python
[More Info]
Richard Otis, Pennsylvania State University

PyRK: A Python Package for Nuclear Reactor Kinetics
[More Info]
Kathryn Huff, Fellow, University of California, Berkeley

Signal Processing and Communications: Teaching and Research Using IPython Notebook
[More Info]
Mark Wickert, University of Colorado

The Need for New Tools for Materials Discovery
[More Info]
Christopher Wilmer, University of Pittsburgh
 
Finance / Social Sciences

Congress & New Media: A Data Driven Study of Congressional Public Relations
[More Info]
Brian Smith, Ball State University - Deptartment of Political Science

Exploring Open Source Community Dynamics with BigBang
[More Info]
Sebastian Benthall, Berkeley School of Information

Scientific Python using Mobile OS
[More Info]
Roberto Colistete Junior, UFES - Federal University of Espirito Santo (Brazil)

Will Millennials Ever Get Married? Survival Analysis and Marriage Data
[More Info]
Allen Downey, Olin College
 
General

A Cloud Service to Record Simulation Metadata
[More Info]
Yannick Congo, NIST/Blaise Pascal University
Jonathan Guyer, NIST

Dask - Out-of-core NumPy/Pandas through Task Scheduling
[More Info]
James Crist, Graduate Student, University of Minnesota

Dexy and Docker for Scientific Reproducibility
[More Info]
Ana Nelson, Cosmify, Dexy

DistArray: Distributed Array Computing for Python
[More Info]
Robert Grant, Scientific Software Developer, Enthought
Kurt Smith, Scientific Software Developer, Enthought

Jupyter / Ipython, State Of Multiuser And Real-Time Collaboration
[More Info]
Matthias Bussonnier, UC Berkeley BIDS / IPython / Jupyter
Kester Tong, Google

Librosa: Audio and Music Signal Analysis in Python
[More Info]
Brian McFee, New York University

Teaching with IPython/Jupyter Notebooks and JupyterHub
[More Info]
Jessica Hamrick, University of California, Berkeley
Min Ragan-Kelley, IPython
Kyle Kelley, Rackspace

HDF5 is Eating the World
[More Info]
Andrew Collette, University of Colorado, Boulder

PyEDA: Data Structures and Algorithms for Electronic Design Automation
[More Info]
Chris Drake, Engineer, Google

Scientific Computing for Undergraduates: Getting Students into the Kitchen
[More Info]
Amelia McBee Henriksen, Brigham Young University
Statistical Thinking for Data Science [More Info]
Chris Fonnesbeck, Assistant Professor, Department of Biostatistics, Vanderbilt University School of Medicine

What the FORTRAN is ** Doing in Python?
[More Info]
En Zyme, Proteasome Digest

A Framework for Analyzing GADGET Simulation Data in Pandas
[More Info]
Jacob Hummel, University of Texas, Austin

Accelerating Python with the Numba JIT Compiler
[More Info]
Stanley Seibert, Continuum Analytics

Agent-Based Modeling in Python with Mesa
[More Info]
Jackie Kazil
David Masad, George Mason University

Circumventing the Linker: Using SciPy's BLAS and LAPACK within Cython
[More Info]
Ian Henriksen, Brigham Young University

Docker for Improved Reproducibility of Scientific Python Analyses
[More Info]
Matthew McCormick, Kitware

From 1-Day Release to 1-Min Release (or How to Recover Time with Automation)
[More Info]
Damian Avila, Continuum Analytics

Keep on Releasin': Continuous Delivery for Open Source
[More Info]
Philip Elson, Met Office

klepto: Unified Persistent Storage to Memory, Database, or Disk
[More Info]
Michael McKerns, UQ Foundation

So How ARE Scientists Using Python on Supercomputers?
[More Info]
Michael Milligan, Minnesota Supercomputing Institute, University of Minnesota

Towards a Better Documentation System for Scientific Python
[More Info]
Carlos Cordoba, Continuum Analytics

Typing Arrays with DyND
[More Info]
Mark Wiebe, Thinkbox Software
 
Geographic Info Systems (GIS)

Analysis and Visualization of Imaging Experiments with IPython, sklearn and bokeh
[More Info]
Blake Borgeson, Recursion Pharmaceuticals

Connecting Circuits for Asynchronous Data Workflows
[More Info]
Carson Farmer, University of Colorado, Boulder

Eigenvector Spatial Filtering using NumPy and ArcGIS
[More Info]
Bryan Chastain, University of Texas, Dallas

Spatial Income Inequality Dynamics in PySAL
[More Info]
Wei Kang, GeoDa Center for Geospatial Analysis & Computation
Sergio Rey, GeoDa Center for Geospatial Analysis and Computation

To Be Announced
 
Geophysics

Geodynamic Simulations in HPC with Python
[More Info]
Nicola Creati, OGS
Roberto Vidmar, OGS
Paolo Sterzai, OGS

Striplog: Wrangling 1D Subsurface Data
[More Info]
Matt Hall, Agile Geoscience

Touch your Data! Color 3D Printing with Python
[More Info]
Joe Kington, Chevron

Using Python to Span the Gap between Education, Research, and Industry Applications in Geophysics
[More Info]
Lindsey Heagy, University of British Columbia: Geophysical Inversion Facility

Global Hydrology Analysis Using Python
[More Info]
Mattheus Ueckermann, Creare

Practical Integration of Processing, Inversion and Visualization of Magnetotelluric Geophysical Data
[More Info]
Gudni Rosenkjaer, University of British Columbia
 
Oceanography

A Distributed, Standards-Based Framework for Searching, Accessing, Analyzing and Visualizing Met-Ocean Data: Application to Hurricane Sandy
[More Info]
Richard Signell, USGS
Filipe Fernandes, SECOORA
Kyle Wilcox, Axiom Data Science
Andrew Yan, USGS

Characterizing the Seafloor with Python as a Toolbox
[More Info]
Johanna Hansen, Woods Hole Oceanographic Institution

Exploring Open Access Weather Radar with the Python ARM Toolkit
[More Info]
Jonathan Helmus, Argonne National Laboratory
Scott Collis, Argonne National Laboratory

From Zero to Hero in Two Years, Open Collaborative Radar Software and the Secret to our Success
[More Info]
Scott Collis, Argonne National Laboratory
Nick Guy, University of Wyoming
Anderson Gama, SIMEPAR - Sistema Meteorológico do Paraná
Cesar Beneti, SIMEPAR - Sistema Meteorológico do Paraná
Stephen Nesbitt, University of Illinois
Scott Giangrande, Brookhaven National Laboratory
Maik Hiestermann, University of Potsdam
Kai Muehlbauer, University of Bonn

PySPLIT: a Package for the Generation, Analysis, and Visualization of HYSPLIT Air Parcel Trajectories
[More Info]
Mellissa Cross

Python in Tidal Energy: Three Tools Used in a Collaboration on Array Optimization
[More Info]
Kristen Thyng, Assistant Research Scientist, Texas A&M University
 
Visualization

A Better Default Colormap for Matplotlib
[More Info]
Stéfan van der Walt, University of California, Berkeley
Nathaniel Smith, University of California, Berkeley

HoloViews: Building Complex Visualizations Easily for Reproducible Science
[More Info]
Jean-Luc R. Stevens, University of Edinburgh
Philipp Rudiger, University of Edinburgh
James A. Bednar, University of Edinburgh

Scientific Data Analysis and Visualization with VTK and ParaView
[More Info]
Cory Quammen, Kitware

Story Time with Bokeh
[More Info]
Bryan Van de Ven, Continuum Analytics

TrendVis: An Elegant Interface for Dense, Sparkline-Like, Quantitative Visualizations of Multiple Series Using Matplotlib
[More Info]
Mellissa Cross

VisPy: Harnessing The GPU For Fast, High-Level Visualization
[More Info]
Luke Campagnola, University of North Carolina, Chapel Hill
Posters

A Bioinformatic Pipeline to Search for Genetic Variants of Wood Frog Environmental Response Genes
[More Info]
Jordan Brooker, Research Technician, Vassar College

A Web-based Visualization Platform for Microbiome Metaproteomics
[More Info]
Sandip Chatterjee, The Scripps Research Institute

Comparing and Evaluating Clustering Methods for Protein Simulations
[More Info]
Jan H. Meinke, Forschungszentrum Juelich

Computational Astrophysical Hydrodynamics for Students
[More Info]
Michael Zingale, Stony Brook University

Detecting Carcinogenic Somatic Mutations Using Scikit-learn
[More Info]
Chak-Pong Chung

Developing Robust and Maintainable PyQt GUI Applications for Neutron Scattering at a Large DOE User Facility
[More Info]
Wenduo Zhou, Oak Ridge National Laboratory
Ke An, Oak Ridge National Laboratory
Jean-Christophe Bilheux, Oak Ridge National Laboratory
Stephen D. Miller, Oak Ridge National Laboratory
Peter F. Peterson, Oak Ridge National Laboratory

Development of Large Image Analysis Workflows in the Context of “SlideAtlas”
[More Info]
Dhanannjay "Djay" Deo, Kitware Inc
Brian Helba, Kitware Inc

Epithelial Tissue Simulation and with Initial Conditions Taken From In Vivo Images
[More Info]
Melvyn Drag, Ohio State University

ESPResSo++: A Parallel Python Module for Soft Matter Simulations
[More Info]
Horacio Vargas Guzman, Max Planck Institut for Polymer Research
Torsten Stuehn, Max Planck Institute for Polymer Research

MetOceanTrack: A Desktop GUI to Simulate The Dispersal of Invasive Species in Coastal and Continental Shelf Regions
[More Info]
Andre Lobato, Metocean Solutions LTD.

Patient Signals - Building and Deploying Predictive Apps in Healthcare
[More Info]
Corey Chivers, University of Pennsylvania Health System

Perceptual Colormaps in matplotlib with an Application in Oceanography
[More Info]
Kristen Thyng, Assistant Research Scientist, Texas A&M University

Performance of PyCUDA (Python in GPU High Performance Computing)
[More Info]
Roberto Colistete Junior, UFES - Federal University of Espirito Santo (Brazil)

Python Tool to Load, Process, and Plot Conductive Temperature Depth (CTD) data
[More Info]
Filipe Fernandes, SECOORA

Reassortment Primes Influenza for Ecotype Switches
[More Info]
Eric Ma, Massachusetts Institute of Technology

Relation: The Missing Container
[More Info]
James Larkin, Noblis
Scott James, Noblis

Risk Analysis of Privacy Invasion in Social Network using Python with SciPy
[More Info]
Jun-Bum Park, UST(Korea University of Science and Technology) & ETRI(Electronics and Telecommunications Research Institute)

rsfmodel - A Frictional Modeling Tool for Fault and Laboratory Data Analysis
[More Info]
John Leeman, Ph.D. Candidate, Penn State University
Ryan May, UCAR/Unidata

The Use of Python in the Large-Scale Analysis and Identification of Potential Antimicrobial Peptides
[More Info]
Shaylyn Scott, George Mason University

TLS Benchmarking with IPython
[More Info]
Christopher Niemira, AOL

Toolset and Workflow for Verification, Validation and Uncertainty Quantification in Large-scale Engineering Applications
[More Info]
Damon McDougall, UT Austin

Topological Data Analysis using Python
[More Info]
Dan Dickinson

Using Python and Jupyter Notebooks for a Biomedical Imaging Phenotyping Service
[More Info]
Brian Chapman, University of Utah
John Roberts, University of Utah
Stuart Schulthies, University of Utah

Using Python to Manage 800,000 WAAS Data Points per Second
[More Info]
Benjamin Potter, Federal Aviation Administration

Using Self Organizing Maps to Visualize and Cluster High Dimensional Data
[More Info]
Richard Xie, Endgame

Working with Matplotlib via PyQt/Qt Designer
[More Info]
Jean Bilheux, Oak Ridge National Laboratory
Steve Miller, Oak Ridge National Laboratory
Wenduo Zhou, Oak Ridge National Laboratory

An MR Spectroscopy Database Query and Visualization Engine as a Clinical Diagnostic Tool
[More Info]
Justin Foong, The Hospital for Sick Children

Coupling Geophysical Terminology and Package Development
[More Info]
Rowan Cockett, The University of British Columbia

Creating a Real-Time Recommendation Engine using Modified K-Means Clustering and Remote Sensing Signature Matching Algorithms
[More Info]
David Lippa, Principal Software Engineer, RealMassive
Jason Vertrees, Chief Technology Officer, RealMassive

Efficiently Exploring the Universe of Porous Media: Generating, Simulating, and Mutating Hypothetical Pseudo-materials
[More Info]
Alec Kaija

Fast Visualization and User Interfaces with PyQtGraph
[More Info]
Luke Campagnola, UNC Chapel Hill

How Would You Like Your "Tab" to Be?
[More Info]
Hyungtae Kim, University of California, Irvine

Jupyter Notebook + SciPy = Rapid Fire Data Science
[More Info]
Jonathan Whitmore, Silicon Valley Data Science

MDSynthesis: a Python Package Enabling Data-driven Molecular Dynamics Research
[More Info]
Speaker: David Dotson, Arizona State University

OOF 3D: Modular Software Design in the Face of Major Feature Changes
[More Info]
Andrew Reid, NIST

Psi4: Open-Source Quantum Chemistry
[More Info]
Lori Burns, Georgia Tech Chemistry

PyCO2...because we need to know.
[More Info]
Juliana Leonel, Universidade Federal da Bahia
Filipe Fernandes

Python Interfaces in Mantid
[More Info]
Steve Miller, Oak Ridge National Laboratory

PyUgrid: Handling NetCDF for Unstructured Grids
[More Info]
Chris Calloway, UNC RENCI

Scientific GUI Application Development Using Qt Designer and PyQt
[More Info]
Steve Miller, Oak Ridge National Laboratory
Jean Bilheux, Oak Ridge National Laboratory
Wenduo Zhou, Oak Ridge National Laboratory

SciPy and Real-time Big Data for Site Optimization
[More Info]
Winnie Cheng, Chief Data Scientist, Bankrate

Testing for serial correlation and non-stationarity of long time series after ARIMA modeling with SciPy and Statsmodels
[More Info]
Margaret Mahan