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. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI).

Using citizen science to bridge taxonomic discovery with education and outreach.

PREMISE OF THE STUDY: Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss. Efforts to fully leverage collections are impeded by a lack of trained taxonomists and a lack of interest and engagement by the public. We provide a model of a crowd-sourced data collection project that produces quality taxonomic data sets and empowers citizen scientists through real contributions to science. Entitled MicroPlants, the project is a collaboration between taxonomists, citizen science experts, and teachers and students from universities and K-12. METHODS: We developed an online tool that allows citizen scientists to measure photographs of specimens of a hyper-diverse group of liverworts from a biodiversity hotspot. RESULTS: Using the MicroPlants online tool, citizen scientists are generating high-quality data, with preliminary analysis indicating non-expert data can be comparable to expert data. DISCUSSION: More than 11,000 users from both the website and kiosk versions have contributed to the data set, which is demonstrably aiding taxonomists working toward establishing conservation priorities within this group. MicroPlants provides opportunities for public participation in authentic science research. The project's educational component helps move youth toward engaging in scientific thinking and has been adopted by several universities into curriculum for both biology and non-biology majors.

Snapshot Serengeti, high-frequency annotated camera trap images of 40 mammalian species in an African savanna.

Camera traps can be used to address large-scale questions in community ecology by providing systematic data on an array of wide-ranging species. We deployed 225 camera traps across 1,125 km(2) in Serengeti National Park, Tanzania, to evaluate spatial and temporal inter-species dynamics. The cameras have operated continuously since 2010 and had accumulated 99,241 camera-trap days and produced 1.2 million sets of pictures by 2013. Members of the general public classified the images via the citizen-science website www.snapshotserengeti.org. Multiple users viewed each image and recorded the species, number of individuals, associated behaviours, and presence of young. Over 28,000 registered users contributed 10.8 million classifications. We applied a simple algorithm to aggregate these individual classifications into a final 'consensus' dataset, yielding a final classification for each image and a measure of agreement among individual answers. The consensus classifications and raw imagery provide an unparalleled opportunity to investigate multi-species dynamics in an intact ecosystem and a valuable resource for machine-learning and computer-vision research.

The notes from nature tool for unlocking biodiversity records from museum records through citizen science.

Legacy data from natural history collections contain invaluable and irreplaceable information about biodiversity in the recent past, providing a baseline for detecting change and forecasting the future of biodiversity on a human-dominated planet. However, these data are often not available in formats that facilitate use and synthesis. New approaches are needed to enhance the rates of digitization and data quality improvement. Notes from Nature provides one such novel approach by asking citizen scientists to help with transcription tasks. The initial web-based prototype of Notes from Nature is soon widely available and was developed collaboratively by biodiversity scientists, natural history collections staff, and experts in citizen science project development, programming and visualization. This project brings together digital images representing different types of biodiversity records including ledgers , herbarium sheets and pinned insects from multiple projects and natural history collections. Experts in developing web-based citizen science applications then designed and built a platform for transcribing textual data and metadata from these images. The end product is a fully open source web transcription tool built using the latest web technologies. The platform keeps volunteers engaged by initially explaining the scientific importance of the work via a short orientation, and then providing transcription "missions" of well defined scope, along with dynamic feedback, interactivity and rewards. Transcribed records, along with record-level and process metadata, are provided back to the institutions.  While the tool is being developed with new users in mind, it can serve a broad range of needs from novice to trained museum specialist. Notes from Nature has the potential to speed the rate of biodiversity data being made available to a broad community of users.

Small-scale-structure of the interstellar medium probed through diffuse band observations.

The carriers of the diffuse interstellar band spectrum represent an important baryonic component of the interstellar medium (ISM) and it is expected that their identification will contribute significantly to the understanding of the chemistry and physics of interstellar clouds. It is widely held that the carriers are linked to the presence of dust grains on account of the good correlation of their strengths with interstellar reddening, so they offer an important potential route to improving our understanding of the composition and chemistry of grains and grain surfaces. In addition to the challenge of making the spectral assignments, an important current question concerns the spatial distribution and physical state of interstellar material, with recent observational atomic and molecular line absorption studies suggesting that diffuse clouds are more 'clumpy' than previously thought. We describe here high signal-to-noise optical observations made at the Anglo-Australian Telescope using UCLES that were undertaken to investigate the spatial distribution of diffuse band carriers. We describe the first detection of 'small-scale-structure' in the diffuse band carrier distribution in the ISM, and comment on the possibilities that these data hold for contributing to the solution of the diffuse band problem and our understanding of the nature of small-scale-structure in the diffuse ISM.