Proceedings of SciPy 2019

MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. With the development of highly optimized MD software packages on high performance computing (HPC) resources, the size of simulation trajectories is growing up to many terabytes in size.

Plotly's Dash is a library that empowers data scientists to create interactive web applications declaratively in Python. Dash Bio is a bioinformatics-oriented suite of components that are compatible with Dash.

Nearly every machine learning model requires hyperparameters, parameters that the user must specify before training begins and influence model performance. Finding the optimal set of hyperparameters is often a time- and resource-consuming process.

PyDDA is a new community framework aimed at wind retrievals that depends only upon utilities in the SciPy ecosystem such as scipy, numpy, and dask. It can support retrievals of winds using information from weather radar networks constrained by high resolution forecast models over grids that cover thousands of kilometers at kilometer-scale resolution.

Parkinson’s disease (PD) affects over 6.2 million people around the world. Despite its prevalence, there is still no cure, and diagnostic methods are extremely subjective, relying on observation of physical motor symptoms and response to treatment protocols.

As Machine Learning (ML) becomes more widely known and popular, so too does the desire for new users from other backgrounds to apply ML techniques to their own domains. A difficult prerequisite that often confounds new users is the feature creation and engineering process.

A Bayesian approach to solving inverse problems provides insight regarding model limitations as well as the underlying model and observation uncertainty. In this paper we introduce pymcmcstat, which provides a wide variety of tools for estimating unknown parameter distributions.

A grocery list is an integral part of the shopping experience of many consumers. Several mobile retail studies of grocery apps indicate that potential customers place the highest priority on features that help them to create and manage personalized shopping lists.

This paper describes the development of a 3D audio simulator for use in cognitive hearing science studies and also for general 3D audio experimentation. The framework that the simulator is built upon is pyaudio\_helper, which is a module of the package scikit-dsp-comm.

We present a case study of optimizing a Python-based cosmology data processing pipeline designed to run in parallel on thousands of cores using supercomputers at the National Energy Research Scientific Computing Center (NERSC).

The solutions of a system of polynomials in several variables are often needed, e.g.: in the design of mechanical systems, and in phase-space analyses of nonlinear biological dynamics. Reliable, accurate, and comprehensive numerical solutions are available through PHCpack, a FOSS package for solving polynomial systems with homotopy continuation.

When designing microprocessors, engineers must verify whether the proposed design, defined in hardware description language, does what is intended. During this verification process, engineers run simulation tests and can fix bugs if the tests have failed.

Codebraid executes code blocks and inline code in Pandoc Markdown documents as part of the document build process. Code can be executed with a built-in system or Jupyter kernels. Either way, a single document can involve multiple programming languages, as well as multiple independent sessions or processes per language.

The pandas library has become the de facto library for data wrangling in the Python programming language. However, inconsistencies in the pandas application programming interface (API), while idiomatic due to historical use, prevent use of expressive, fluent programming idioms that enable self-documenting pandas code.

Parkinson's disease (PD) is a highly prevalent neurodegenerative condition originating in subcortical areas of the brain and resulting in progressively worsening motor, cognitive, and psychiatric (e.g.

The purpose of this project is to provide a real time geolocation solution by generating code for the complex ambiguity function (CAF) in a hardware description language (HDL) and the implementation on FPGA hardware.

The freud Python library analyzes particle data output from molecular dynamics simulations. The library's design and its variety of high-performance methods make it a powerful tool for many modern applications.

We outline a synthesis of strategies created in collaboration with 35+ colleges and universities on how to advance undergraduate data science education on a national scale. The four core pillars of this strategy include the integration of data science education across all domains, establishing adoptable and scalable cyberinfrastructure, applying data science to non-traditional domains, and incorporating ethical content into data science curricula.

Automatic modulation classification is a challenging problem with multiple applications including cognitive radio and signals intelligence. Most of the existing efforts to solve this problem are only applicable when the signal to noise ratio (SNR) is high and/or long observations of the signal are available.

Automatic modulation classification is a challenging problem with multiple applications including cognitive radio and signals intelligence. Most of the existing efforts to solve this problem are only applicable when the signal to noise ratio (SNR) is high and/or long observations of the signal are available.