Proceedings of SciPy 2021

The Biological Magnetic Resonance Data Bank (BioMagResBank or BMRB https://bmrb.io), founded in 1988, is the international, open archive for data generated by Nuclear Magnetic Resonance (NMR) spectroscopy of biological systems.

Social media is very popularly used every day with daily content viewing and/or posting that in turn influences people around this world in a variety of ways. Social media platforms, such as YouTube, have a lot of activity that goes on every day in terms of video posting, watching and commenting.

Why did a decision maker select a certain decision? What behaviour does a certain objective incentivise? How can we improve this behaviour and ensure that a decision-maker chooses decisions with safer or fairer consequences? This paper introduces the Python package PyCID, built upon pgmpy, that implements (causal) influence diagrams, a widely used graphical modelling framework for decision-making problems.

CLAIMED is a component library for artificial intelligence, machine learning, \textquotedbl{}extract, transform, load\textquotedbl{} processes and data science. The goal is to enable low-code/no-code rapid prototyping by providing ready-made components for various business domains, supporting various computer languages, working on various data flow editors and running on diverse execution engines.

Most areas of Python data science have standardized on using Pandas DataFrames for representing and manipulating structured data in memory. Natural Language Processing (NLP), not so much. We believe that Pandas has the potential to serve as a universal data structure for NLP data.

Molecular dynamics (MD) computer simulations help elucidate details of the molecular processes in complex biological systems, from protein dynamics to drug discovery. One major issue is that these MD simulation files are now commonly terabytes in size, which means analyzing the data from these files becomes a painstakingly expensive task.

The Dark Energy Spectroscopic Instrument (DESI) will create the most detailed 3D map of the Universe to date by measuring redshifts in light spectra of over 30 million galaxies. The extraction of 1D spectra from 2D spectrograph traces in the instrument output is one of the main computational bottlenecks of DESI data processing pipeline, which is predominantly implemented in Python.

The signac data management framework (https://signac.io) helps researchers execute reproducible computational studies, scales workflows from laptops to supercomputers, and emphasizes portability and fast prototyping.

Protein crystallography produces most of the protein structures used in structure-based drug design. The process of protein structure determination is computationally intensive and error-prone because many software packages are involved.

Any application involving sensitive measurements of the physical world starts with accurate, precise, and low-noise signal chain. Modern, highly integrated data acquisition devices can often be directly connected to sensor outputs, performing analog signal conditioning, digitization, and digital filtering on a single silicon device, greatly simplifying system electronics.

PDFrw was used to prepopulate Covid-19 vaccination forms to improve the efficiency and integrity of the vaccination process in terms of federal and state privacy requirements. We will describe the vaccination process from the initial appointment, through the vaccination delivery, to the creation of subsequent required documentation.

Live-cell imaging is a highly used technique to study cell migration and dynamics over time. Although many computational tools have been developed during the past years to automatically detect and track cells, they are optimized to detect cell nuclei with similar shapes and/or cells not clustering together.

In this paper a Time of Flight (ToF) camera specific data processing pipeline is presented, followed by real life applications using artificial intelligence. These applications include use cases such as gesture recognition, movement direction estimation or physical exercises monitoring.

A modern CPU delivers performance through parallelism. A program that exploits the performance available from a CPU must run in parallel on multiple cores. This is usually best done through multithreading.

Machine learning (ML) relies on stochastic algorithms, all of which rely on gradient approximations with \textquotedbl{}batch size\textquotedbl{} examples. Growing the batch size as the optimization proceeds is a simple and usable method to reduce the training time, provided that the number of workers grows with the batch size.

In 2021, more than 30\% of users at the National Energy Research Scientific Computing Center (NERSC) used Python on the Cori supercomputer. To determine this we have developed and open-sourced a simple, minimally invasive monitoring framework that leverages standard Python features to capture Python imports and other job data via a package called \textquotedbl{}Customs\textquotedbl{}.

Characterizing dynamic sub-cellular morphologies in response to perturbation remains a challenging and important problem. Many organelles are anisotropic and difficult to segment, and few methods exist for quantifying the shape, size, and quantity of these organelles.

This article introduces PyRSB, a Python interface to the LIBRSB library. LIBRSB is a portable performance library offering so called Sparse BLAS (Sparse Basic Linear Algebra Subprograms) operations for modern multicore CPUs.

Mitigating bias in AI-enabled systems is a topic of great concern within the research community. While efforts are underway to increase model interpretability and de-bias datasets, little attention has been given to identifying biases that are introduced by developers as part of the software engineering process.

This contribution shows how the symbolic computing Python library SymPy can be used to improve flow force modeling due to a Couette-type flow, i.e. a flow of viscous fluid in the region between two bodies, where one body is in tangential motion relative to the other.