Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis. NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.

/pdf/array-programming-with-numpy-31s3jl24ra.pdf

Array programming with NumPy

3D Slicer as an image computing platform for the Quantitative Imaging Network.

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

/pdf/scikit-image-image-processing-in-python-3tlzmiwc32.pdf

scikit-image: Image processing in Python

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence. le formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

/pdf/biopython-freely-available-python-tools-for-computational-n97zecdiip.pdf

Biopython: freely available Python tools for computational molecular biology and bioinformatics

https://perssongroup.lbl.gov/papers/compmatsci2013-pymatgen.pdf

Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

Predictive modeling's effectiveness is hindered by inherent uncertainties in the input parameters. Sensitivity and uncertainty analysis quantify these uncertainties and identify the relationships between input and output variations, leading to the construction of a more accurate model. This survey introduces the application, implementation, and underlying principles of sensitivity and uncertainty quantification

Being Sensitive to Uncertainty

The engineering analysis and microscopic simulations required for predicting materials' properties from atomistic descriptions require approaches for predicting macroscopic properties. Patch dynamics bridges the gap between the time and space scales at which the microscopic models operate, helping predict system-level behavior.

J.M. Hyman

Papers

Being Sensitive to Uncertainty

Patch dynamics for multiscale problems