A survey of the state of the practice for research software in the United States.

Research software is a critical component of contemporary scholarship. Yet, most research software is developed and managed in ways that are at odds with its long-term sustainability. This paper presents findings from a survey of 1,149 researchers, primarily from the United States, about sustainability challenges they face in developing and using research software.

Common-sense approaches to sharing tabular data alongside publication.

Numerous arguments strongly support the practice of open science, which offers several societal and individual benefits. For individual researchers, sharing research artifacts such as data can increase trust and transparency, improve the reproducibility of one's own work, and catalyze new collaborations. Despite a general appreciation of the benefits of data sharing, research data are often only available to the original investigators.

The role of metadata in reproducible computational research.

Reproducible computational research (RCR) is the keystone of the scientific method for analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, improving the reproducibility of scientific studies can accelerate evaluation and reuse. This potential and wide support for the FAIR principles have motivated interest in metadata standards supporting reproducibility.

High nitrous oxide fluxes from rice indicate the need to manage water for both long- and short-term climate impacts.

Global rice cultivation is estimated to account for 2.5% of current anthropogenic warming because of emissions of methane (CH), a short-lived greenhouse gas. This estimate assumes a widespread prevalence of continuous flooding of most rice fields and hence does not include emissions of nitrous oxide (NO), a long-lived greenhouse gas.

Hack weeks as a model for data science education and collaboration.

Across many scientific disciplines, methods for recording, storing, and analyzing data are rapidly increasing in complexity. Skillfully using data science tools that manage this complexity requires training in new programming languages and frameworks as well as immersion in new modes of interaction that foster data sharing, collaborative software development, and exchange across disciplines. Learning these skills from traditional university curricula can be challenging because most courses are not designed to evolve on time scales that can keep pace with rapidly shifting data science methods.

Journal of Open Source Software (JOSS): design and first-year review.

This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit.

Sustainable computational science: the ReScience initiative.

Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results; however, computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true.

How open science helps researchers succeed.

Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about how sharing their work will affect their careers.

The importance of individual developmental variation in stage-structured population models.

Population stage structure is fundamental to ecology, and models of this structure have proven useful in many different systems. Many ecological variables other than stage, such as habitat type, site occupancy and metapopulation status are also modelled using transitions among discrete states. Transitions among life stages can be characterised by the distribution of time spent in each stage, including the mean and variance of each stage duration and within-individual correlations among multiple stage durations.

The case for open preprints in biology.

Biologists should submit their preprints to open servers, a practice common in mathematics and physics, to open and accelerate the scientific process.

Git can facilitate greater reproducibility and increased transparency in science.

Background: Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders.

Individual heterogeneity in mortality mediates long-term persistence of a seasonal microparasite.

One of the primary objectives in population ecology is to understand mechanisms that allow a species to persist or to be driven to extinction. In most population models, individuals are assumed to be equivalent within any particular category such as age, sex, or morphological grouping. Individuals within such groupings, however, may exhibit considerable variation in traits that can significantly affect population trajectories.

Dynamics of a subterranean trophic cascade in space and time.

Trophic cascades, whereby predators indirectly benefit plant biomass by reducing herbivore pressure, form the mechanistic basis for classical biological control of pest insects. Entomopathogenic nematodes (EPN) are lethal to a variety of insect hosts with soil-dwelling stages, making them promising biocontrol agents. EPN biological control programs, however, typically fail because nematodes do not establish, persist and/or recycle over multiple host generations in the field.

Metapopulation dynamics override local limits on long-term parasite persistence.

A simple null model, particularly germane to small and vulnerable organisms such as parasites, is that local conditions set a stage upon which larger-scale dynamics play out. Soil moisture strongly influences survival of entomopathogenic nematodes (EPN), which in turn drive trophic cascades by protecting vegetation from root-feeding herbivores. In this study, we examine the mechanisms responsible for patchy occurrence of an entomopathogenic nematode, Heterorhabditis marelatus, in a California coastal prairie.

Soil mediates the interaction of coexisting entomopathogenic nematodes with an insect host.

We tested for soil substrate effects on the movement and infectivity of naturally co-occurring entomopathogenic nematodes Steinernema feltiae and Heterorhabditis marelatus, alone and in combination. We manipulated the presence and bulk density of soil and added Galleria mellonella baits within capped and perforated 15mL centrifuge tubes. Sampling tubes were then deployed in situ into field and laboratory settings as experimental traps for infective juveniles.