Array programming with NumPy.

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.

Egg size and asymmetric sibling rivalry in red-winged blackbirds.

How big to make an egg is a life history decision that in birds is made coincident with a series of other similar decisions (how many eggs to have, whether to fortify them with maternally derived hormones or immune system boosters, whether to hatch the eggs synchronously or asynchronously). Though within-population variation in egg size in birds has been well studied, its adaptive significance, if any, is unclear. Here we examine within-population variation in egg size in relation to asymmetric sibling rivalry in a 17-year study of red-winged blackbirds (Agelaius phoeniceus), an altricial songbird. Egg mass showed a twofold range of variation, with roughly 80% of the variation occurring across clutches. By commencing incubation before the clutch is complete, mothers create advantaged core and disadvantaged marginal elements within their brood. Previous work on this system has shown that sibling competition is asymmetric, and that core offspring enjoy priority access to food, and as a consequence show higher growth and lower mortality than marginal offspring. Here we examine the effect of initial egg size on nestling growth and survival in relation to these competitive asymmetries. Egg mass was strongly linked to hatchling mass, and remained significantly related to the mass of both core and marginal nestlings; the effect of egg size was stronger for core offspring early in the nestling period, but the disparity between core and marginal nestlings narrowed as they approached fledging age, and slower growing marginals fell victim to brood reduction. The effect of egg mass on survival differed dramatically between core and marginal nestlings. Egg mass was significantly related to the survival of marginal but not core nestlings: below average egg mass was associated primarily with very early mortality. Asymmetric sibling competition is clearly a strong determinant of the consequences of egg size variation.

Simulation of the effects of microtubules in the cortical rotation of amphibian embryos in normal and zero gravity.

This paper reports the results of computer modeling of microtubules that end up in the cortical region of a one-cell amphibian embryo, prior to the first cell division. Microtubules are modeled as initially randomly oriented semi-flexible rods, represented by several lines of point-masses interacting with one another like masses on springs with longitudinal and transverse stiffness. They are also considered to be space-filling rods floating in a viscous fluid (cytoplasm) experiencing drag forces and buoyancy from the fluid under a variable gravity field to test gravitational effects. Their randomly distributed interactions with the surrounding spherical container (the cell membrane) have a statistical nonzero average that creates a torque causing a rotational displacement between the cytoplasm and the rigid cortex. The simulation has been done for zero and normal gravity and it validates the observation that cortical rotation occurs in microgravity as well as on Earth. The speed of rotation depends on gravity, but is still substantial in microgravity.