OPTIMADE, an API for exchanging materials data

The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification.

Materials Cloud, a platform for open computational science

Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts (1) archival and dissemination services for raw and curated data, together with their provenance graph, (2) modelling services and virtual machines, (3) tools for data analytics, and pre-/post-processing, and (4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow retracing and reproducing any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain.

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and data to manage. Next-generation exascale supercomputers will harden these challenges, such that automated and scalable solutions become crucial. In recent years, we have been developing AiiDA (aiida.net), a robust open-source high-throughput infrastructure addressing the challenges arising from the needs of automated workflow management and data provenance recording. Here, we introduce developments and capabilities required to reach sustained performance, with AiiDA supporting throughputs of tens of thousands processes/hour, while automatically preserving and storing the full data provenance in a relational database making it queryable and traversable, thus enabling high-performance data analytics. AiiDA's workflow language provides advanced automation, error handling features and a flexible plugin model to allow interfacing with external simulation software. The associated plugin registry enables seamless sharing of extensions, empowering a vibrant user community dedicated to making simulations more robust, user-friendly and reproducible.

Antimicrobial resistance of staphylococci and streptococci isolated from dogs

A study was conducted for the examination of bacterial species isolated in dogs from Animal Clinics of Nanjing Agricultural University, China. Forty nasal swabs were taken from dogs having respiratory signs. Staphylococcus pseudintermedius was the most frequently isolated pathogen (37.50 %) followed by Staphylococcus aureus (18.75%), Streptococcus pluranimalium (10.93%), Streptococcus canis (9.37%), Staphylococcus schleiferi (9.37%), Staphylococcus intermedius (6.25%), Staphylococcus cohnii (4.71%) and Staphylococcus hominis (3.12%). S. pseudintermedius and S. pluranimalium were subjected to commonly used antibiotics for determination of resistant drugs. Antimicrobial resistance in S. pseudintermedius was common in gentamicin (70.83%) and tetracycline (50%) while in S. pluranimalium was common in enrofloxacin (71.42%) and gentamicin (57.14%).