OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows

Biomedical ontologies are key elements for building up the Life Sciences Semantic Web. Reusing and building biomedical ontologies requires flexible and versatile tools to manipulate them efficiently, in particular for enriching their axiomatic content. The Ontology Pre Processor Language (OPPL) is an OWL-based language for automating the changes to be performed in an ontology. OPPL augments the ontologists’ toolbox by providing a more efficient, and less error-prone, mechanism for enriching a biomedical ontology than that obtained by a manual treatment. Results We present OPPL-Galaxy, a wrapper for using OPPL within Galaxy. The functionality delivered by OPPL (i.e. automated ontology manipulation) can be combined with the tools and workflows devised within the Galaxy framework, resulting in an enhancement of OPPL. Use cases are provided in order to demonstrate OPPL-Galaxy’s capability for enriching, modifying and querying biomedical ontologies. Conclusions Coupling OPPL-Galaxy with other bioinformatics tools of the Galaxy framework results in a system that is more than the sum of its parts. OPPL-Galaxy opens a new dimension of analyses and exploitation of biomedical ontologies, including automated reasoning, paving the way towards advanced biological data analyses.

Validation of a CFD wake model based on the actuator disk technique and the thrust coefficient. Preliminary results

A simplified CFD wake model based on the actuator-disk concept is used to simulate the wind turbine, represented by an actuator disk upon which a distribution of forces, defined as axial momentum sources, are applied on the incoming flow. The rotor is supposed to be uniformly loaded, with the exerted forces as a function of the incident wind speed, the thrust coefficient and the rotor diameter. The model is validated through experimental measurements downwind of a wind turbine in terms of wind speed deficit. Validation on turbulence intensity will also be made in the near future.

Stability of liquid bridges between an elliptical and a circular supporting disk

A numerical method has been developed to determine the stability limits for liquid bridges held between noncircular supporting disks and the application to a configuration with a circular and an elliptical disk subjected to axial acceleration has been made. The numerical method led to results very different from the available analytical solution which has been revisited and a better approximation has been obtained. It has been found that just retaining one more term in the asymptotic analysis the solution reproduces the real behavior of the configuration and the numerical results.

Enhanced reproducibility of SADI web service workflows with Galaxy and Docke

Background: Semantic Web technologies have been widely applied in the life sciences, for example by data providers such as OpenLifeData and through web services frameworks such as SADI. The recently reported OpenLifeData2SADI project offers access to the vast OpenLifeData data store through SADI services. Findings: This article describes how to merge data retrieved from OpenLifeData2SADI with other SADI services using the Galaxy bioinformatics analysis platform, thus making this semantic data more amenable to complex analyses. This is demonstrated using a working example, which is made distributable and reproducible through a Docker image that includes SADI tools, along with the data and workflows that constitute the demonstration. Conclusions: The combination of Galaxy and Docker offers a solution for faithfully reproducing and sharing complex data retrieval and analysis workflows based on the SADI Semantic web service design patterns.