Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models

The approaches taken to describe and develop spatial discretisations of the domains required for geophysical simulation models are commonly ad hoc, model or application specific and under-documented. This is particularly acute for simulation models that are flexible in their use of multi-scale, anisotropic, fully unstructured meshes where a relatively large number of heterogeneous parameters are required to constrain their full description. As a consequence, it can be difficult to reproduce simulations, ensure a provenance in model data handling and initialisation, and a challenge to conduct model intercomparisons rigorously. This paper takes a novel approach to spatial discretisation, considering it much like a numerical simulation model problem of its own. It introduces a generalised, extensible, self-documenting approach to carefully describe, and necessarily fully, the constraints over the heterogeneous parameter space that determine how a domain is spatially discretised. This additionally provides a method to accurately record these constraints, using high-level natural language based abstractions, that enables full accounts of provenance, sharing and distribution. Together with this description, a generalised consistent approach to unstructured mesh generation for geophysical models is developed, that is automated, robust and repeatable, quick-to-draft, rigorously verified and consistent to the source data throughout. This interprets the description above to execute a self-consistent spatial discretisation process, which is automatically validated to expected discrete characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under revie

R2O, an extensible and semantically based database-to-ontology mapping language

We present R2O, an extensible and declarative language to describe mappings between relational DB schemas and ontologies implemented in RDF(S) or OWL. R2O provides an extensible set of primitives with welldefined semantics. This language has been conceived expressive enough to cope with complex mapping cases arisen from situations of low similarity between the ontology and the DB models

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

An extensible architecture for run-time monitoring of conversational web services

Trust in Web services will be greatly enhanced if these are subject to run-time verification, even if they were previously tested, since their context of execution is subject to continuous change; and services may also be upgraded without notifying their consumers in advance. Conversational Web services introduce added complexity when it comes to run-time verification, since they follow a conversation protocol and they have a state bound to the session of each consumer accessing them. Furthermore, conversational Web services have different policies on how they maintain their state. Access to states can be private or shared; and states may be transient or persistent. These differences must be taken into account when building a scalable architecture for run-time verification through monitoring. This paper, building on a previously proposed theoretical framework for run-time verification of conversational Web services, presents the design, implementation and validation of a novel run-time monitoring architecture for conversational services, which aims to provide a holistic monitoring framework enabling the integration of different verification tools. The architecture is validated by running a sequence of test scenarios, based on a realistic example. The experimental results revealed that the monitoring activities have a tolerable overhead on the operation of a Web service