Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

The Sequence Read Archive (SRA) is a large public repository that stores raw next-generation sequencing data from thousands of diverse scientific investigations. Despite its promise, reuse and re-analysis of SRA data has been challenged by the heterogeneity and poor quality of the metadata that describe its biological samples. Recently, the MetaSRA project standardized these metadata by annotating each sample with terms from biomedical ontologies. In this work, we present a pair of Jupyter notebook-based tools that utilize the MetaSRA for building structured datasets from the SRA in order to facilitate secondary analyses of the SRA’s human RNA-seq data. The first tool, called the Case-Control Finder, finds suitable case and control samples for a given disease or condition where the cases and controls are matched by tissue or cell type. The second tool, called the Series Finder, finds ordered sets of samples for the purpose of addressing biological questions pertaining to changes over a numerical property such as time. These tools were the result of a three-day-long NCBI Codeathon in March 2019 held at the University of North Carolina at Chapel Hill.

Numerical ordinality in a wild nectarivore

Ordinality is a numerical property that nectarivores may use to remember the specific order in which to visit a sequence of flowers, a foraging strategy also known as traplining. In this experiment, we tested whether wild, free-living rufous hummingbirds ( Selasphorus rufus ) could use ordinality to visit a rewarded flower. Birds were presented with a series of linear arrays of 10 artificial flowers; only one flower in each array was rewarded with sucrose solution. During training, birds learned to locate the correct flower independent of absolute spatial location. The birds' accuracy was independent of the rewarded ordinal position (1st, 2nd, 3rd or 4th), which suggests that they used an object-indexing mechanism of numerical processing, rather than a magnitude-based system. When distance cues between flowers were made irrelevant during test trials, birds could still locate the correct flower. The distribution of errors during both training and testing indicates that the birds may have used a so-called working up strategy to locate the correct ordinal position. These results provide the first demonstration of numerical ordinal abilities in a wild vertebrate and suggest that such abilities could be used during foraging in the wild.

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive

The Sequence Read Archive (SRA) is a large public repository that stores raw next-generation sequencing data from thousands of diverse scientific investigations. Despite its promise, reuse and re-analysis of SRA data has been challenged by the heterogeneity and poor quality of the metadata that describe its biological samples. Recently, the MetaSRA project standardized these metadata by annotating each sample with terms from biomedical ontologies. In this work, we present a pair of Jupyter notebook-based tools that utilize the MetaSRA for building structured datasets from the SRA in order to facilitate secondary analyses of the SRA’s human RNA-seq data. The first tool, called the Case-Control Finder, finds suitable case and control samples for a given disease or condition where the cases and controls are matched by tissue or cell type. The second tool, called the Series Finder, finds ordered sets of samples for the purpose of addressing biological questions pertaining to changes over a numerical property such as time. These tools were the result of a three-day-long NCBI Codeathon in March 2019 held at the University of North Carolina at Chapel Hill.

Integrals on a moving manifold and geometrical probability

For a manifold which is moving and changing with time, consider some numerical property which at each instant is equal to an integral over the manifold. We derive a general expression for the time rate of change of this integral. Corollaries include a precise general form of Crofton's boundary theorem, de Hoff's interface displacement equations (with some new extensions) and a theorem in fluid mechanics.

Integrals on a moving manifold and geometrical probability

For a manifold which is moving and changing with time, consider some numerical property which at each instant is equal to an integral over the manifold. We derive a general expression for the time rate of change of this integral. Corollaries include a precise general form of Crofton's boundary theorem, de Hoff's interface displacement equations (with some new extensions) and a theorem in fluid mechanics.