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Publisher: Ubiquity Press Limited   (Total: 45 journals)   [Sort by number of followers]

Showing 1 - 45 of 45 Journals sorted alphabetically
Ancient Asia     Open Access   (Followers: 10)
Archaeology Intl.     Open Access   (Followers: 20)
Architectural Histories     Open Access   (Followers: 11)
Belgian J. of Radiology     Open Access   (Followers: 1, SJR: 0.167, CiteScore: 0)
Bulletin of the History of Archaeology     Open Access   (Followers: 15)
Citizen Science : Theory and Practice     Open Access   (Followers: 1)
Comics Grid : J. of Comics Scholarship     Open Access   (Followers: 9)
Cultural Science J.     Open Access  
Data Science J.     Open Access   (Followers: 14, SJR: 0.23, CiteScore: 1)
Future Cities and Environment     Open Access   (Followers: 4)
Glocality     Open Access  
Glossa : A J. of General Linguistics     Open Access   (Followers: 3)
Health Psychology Bulletin     Open Access  
Insights : the UKSG journal     Open Access   (Followers: 103, SJR: 0.473, CiteScore: 0)
Intl. J. of Integrated Care     Open Access   (Followers: 10, SJR: 0.662, CiteScore: 2)
Intl. Review of Social Psychology / Revue Intl.e de Psychologie Sociale     Open Access   (SJR: 0.421, CiteScore: 1)
J. of Circadian Rhythms     Open Access   (Followers: 1, SJR: 0.524, CiteScore: 1)
J. of Cognition     Open Access  
J. of Computer Applications in Archaeology     Open Access  
J. of Conservation and Museum Studies     Open Access   (Followers: 18)
J. of European Psychology Students     Open Access   (Followers: 1)
J. of Interactive Media in Education     Open Access   (Followers: 5)
J. of Molecular Signaling     Open Access   (SJR: 0.677, CiteScore: 2)
J. of Open Archaeology Data     Open Access   (Followers: 9)
J. of Open Hardware     Open Access  
J. of Open Humanities Data     Open Access   (Followers: 2)
J. of Open Psychology Data     Open Access   (Followers: 3)
J. of Open Research Software     Open Access   (Followers: 3)
J. of Portuguese Linguistics     Open Access  
KULA : knowldge creation, dissemination, and preservation studies     Open Access  
Laboratory Phonology : J. of the Association for Laboratory Phonology     Open Access   (Followers: 6)
Le foucaldien     Open Access  
MaHKUscript. J. of Fine Art Research     Open Access  
Metaphysics     Open Access  
Open Health Data     Open Access   (Followers: 4)
Open J. of Bioresources     Open Access   (Followers: 1)
Open Quaternary     Open Access   (Followers: 1)
Papers from the Institute of Archaeology     Open Access   (Followers: 15)
Physical Activity and Health     Open Access  
Present Pasts     Open Access   (Followers: 2)
Psychologica Belgica     Open Access   (SJR: 0.426, CiteScore: 1)
Secularism and Nonreligion     Open Access  
Stability : Intl. J. of Security and Development     Open Access   (Followers: 7, SJR: 0.438, CiteScore: 1)
Utrecht J. of Intl. and European Law     Open Access   (Followers: 14)
Worldwide Waste : J. of Interdisciplinary Studies     Open Access  
Journal Cover
Journal of Open Research Software
Number of Followers: 3  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2049-9647
Published by Ubiquity Press Limited Homepage  [45 journals]
  • Fidimag – A Finite Difference Atomistic and Micromagnetic Simulation

    • Abstract: Fidimag is an open-source scientific code for the study of magnetic materials at the nano- or micro-scale using either atomistic or finite difference micromagnetic simulations, which are based on solving the Landau-Lifshitz-Gilbert equation. In addition, it implements simple procedures for calculating energy barriers in the magnetisation through variants of the nudged elastic band method. This computer software has been developed with the aim of creating a simple code structure that can be readily installed, tested, and extended. An agile development approach was adopted, with a strong emphasis on automated builds and tests, and reproducibility of results. The main code and interface to specify simulations are written in Python, which allows simple and readable simulation and analysis configuration scripts. Computationally costly calculations are written in C and exposed to the Python interface as Cython extensions. Docker containers are shipped for a convenient setup experience. The code is freely available on GitHub and includes documentation and examples in the form of Jupyter notebooks. Funding Statement: We acknowledge financial support from EPSRC’s Centre for Doctoral Training in Next Generation Computational Modelling, (EP/L015382/1), EPSRC’s Doctoral Training Centre in Complex System Simulation (EP/G03690X/1), CONICYT Chilean scholarship programme Becas Chile (72140061), Horizon 2020 European Research Infrastructure project OpenDreamKit (676541), National Natural Science Foundation of China (11604169), and the Gordon and Betty Moore Foundation through Grant GBMF #4856, by the Alfred P. Sloan Foundation and by the Helmsley Trust. Published on 2018-09-06 13:16:49
  • vaCATE: A Platform for Automating Data Output from Compartmental Analysis
           by Tracer Efflux

    • Abstract: Compartmental analysis by tracer efflux (CATE) is fundamental to examinations of membrane transport, allowing study of solute movement among subcellular compartments with high temporal, spatial, and chemical resolution. CATE can provide a wealth of information about fluxes and pool sizes in complex systems, but is a mathematically intensive procedure, and there is a need for software designed to fully, easily, and dynamically analyse results from CATE experiments. Here we present vaCATE (Visualized Automation of Compartmental Analysis by Tracer Efflux), a software package that meets these criteria. A robust suite of test cases using CATE datasets from experiments with intact rice (Oryza sativa L.) root systems reveals the high fidelity of vaCATE and the ease with which parameters can be extracted, using a three-compartment model and a curve-stripping procedure to distinguish them on the basis of variable exchange rates. vaCATE was developed using Python 2.7 and can be used in most situations where compartmental analysis is required. Funding Statement: This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Ontario Graduate Scholarship Fund (OGS). Published on 2018-08-17 17:01:36
  • CERF – A Geospatial Model for Assessing Future Energy Production
           Technology Expansion Feasibility

    • Abstract: The Capacity Expansion Regional Feasibility (CERF) model is an open-source geospatial model, written in Python and C++, that is designed to determine the on-the-ground feasibility of achieving a projected energy technology expansion plan. Integrated human-Earth systems models and grid expansion models typically do not have sufficient spatial, temporal, or process-level resolution to account for technology-specific siting considerations—for example, the value or costs of connecting a new power plant to the electric grid at a particular location or whether there is sufficient cooling water to support the installation of thermal power plants in a certain region. CERF was developed to specifically examine where power plant locations can be feasibly sited when considering high spatial resolution siting suitability data as well as the net locational costs (i.e., considering both net operating value and interconnection costs), at a spatial resolution of 1 km2. The outputs from CERF can provide insight into factors that influence energy system resilience under a variety of future scenarios can be used to refine model-based projections and be useful for capacity expansion planning exercises. CERF is open-source and publicly available via GitHub. Funding Statement: The original development of the CERF model was conducted under the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory, a multi-program national laboratory operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. Further development and ongoing demonstration of CERF is supported by the U.S. Department of Energy, Office of Science, as part of research in Multi-Sector Dynamics, Earth and Environmental System Modeling Program. Published on 2018-08-06 10:13:50
  • BEAT 3.0 – a Tool for Integrated Biodiversity Assessments

    • Abstract: BEAT 3.0 is a multi-metric indicator-based tool for integrated assessments of marine biodiversity status implemented in R. It follows the structure and requirements of the EU Marine Strategy Framework Directive and allows for use of monotonic, unimodal, conditional, trend-based and qualitative indicators. The tool handles tabular data files (.txt format), in which the assessment structure and indicator results are specified. Integration of indicators is primarily based on weighted averaging, where both spatial assessment scale and ecosystem level are considered. Parallel to the biodiversity status assessment, a confidence assessment is also included. BEAT 3.0 uses HELCOM Assessment units and HELCOM core indicators as default but can be customized for use in any geographical region and any set of indicators. Funding Statement: BEAT 3.0 was developed in the HELCOM coordinated EU co-financed project ‘Baltic Sea project to boost regional coherence of marine strategies through improved data flow, assessments, and knowledge base for development of measures (BalticBOOST)’ EU grant number 11.0661/2015/712632/SUB/ENVC.2. Published on 2018-08-02 12:16:14
  • Billie. A Prototypical Framework for Building Information Model

    • Abstract: Current software applications for Building Information Modelling provide only limited possibilities to create customized visual representations of designed buildings and planned constructions. With reusable and exchangeable visualization configurations, customized domain- and task-specific visual representations could be generated for given building information. This concept is demonstrated with a prototypical implementation: Billie is a proof-of-concept framework written in Java that accepts building information together with a visualization specification and produces scene graphs for the customized visualization of the given building information.To achieve configurability, Billie provides abstract classes as extension points to implement new BIM input data accessors, new configurations for generating the visualizations, and new scene graph types as visualization targets. With a domain specific language, the configurations become independent of their runtime environment and can be passed between different software applications. The software can be reused for research on new visualization methods in architecture, engineering, and construction or as a supporting visualization tool for research on other topics in the area. Published on 2018-05-18 22:33:48
  • Simple Monte Carlo Simulator for Modelling Linear Mode and Geiger Mode
           Avalanche Photodiodes in C++

    • Abstract: Linear mode and Geiger mode Avalanche Photodiodes are widely used to detect weak optical signals, with the latter able to detect a single photon at a time. Practical simulators for these devices should accurately produce relevant device characteristics and not be overly computationally intensive. The Simple Monte Carlo Simulator, written in C++, offers such a combination and can simulate avalanche photodiodes made with Silicon, Gallium Arsenide and Indium Gallium Phosphide, with the potential to include other semiconductor materials. The software is available on The University of Sheffield Research Data Catalogue and Repository at and on GitHub at Published on 2018-05-18 21:56:01
  • Myex: A MATLAB Interface for the Tobii Eyex

    • Abstract: Myex is a MATLAB interface for the Tobii EyeX eye-tracker. It allows MATLAB users to receive incoming data from the eye-tracker, by providing a data buffer that can receive data from the EyeX, and be queried by the user on demand. Myex enables Matlab users to take advantage of low-cost, portable eye-tracking technology, ideal for use in gaze-contingent psychophysical paradigms, or for users looking to develop assistive devices for individuals with impaired mobility. Funding statement: This work was supported by the NIHR Biomedical Research Centre located at (both) Moorfields Eye Hospital and the UCL Institute of Ophthalmology. Published on 2018-04-20 17:20:53
  • Demeter – A Land Use and Land Cover Change Disaggregation Model

    • Abstract: Demeter is an open source Python package that was built to disaggregate projections of future land allocations generated by an integrated assessment model (IAM). Projected land allocation from IAMs is traditionally transferred to Earth System Models (ESMs) in a variety of gridded formats and spatial resolutions as inputs for simulating biophysical and biogeochemical fluxes. Existing tools for performing this translation generally require a number of manual steps which introduces error and is inefficient. Demeter makes this process seamless and repeatable by providing gridded and land cover change (LULCC) products derived directly from an IAM—in this case, the Global Change Assessment Model (GCAM)—in a variety of formats and resolutions commonly used by ESMs. Demeter is publicly available via GitHub and has an extensible output module allowing for future ESM needs to be easily accommodated. Funding statement: This research was supported by the U.S. Department of Energy, Office of Science, as part of research in Multi-Sector Dynamics, Earth and Environmental System Modeling Program. It builds on previous work supported by the National Aeronautics and Space Administration Carbon Monitoring System and ACCESS programs under projects NNH12AU35I and NNH13AW58I, and by the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy under Contract DE-AC05- 76RL01830. Published on 2018-04-20 12:33:14
  • DiViDu – An Open Source Solution for Dual Task Experiments with
           Integrated Divided Visual Field Paradigm

    • Abstract: We here present DiViDu, a research software, which we developed for a dual task experiment with an integrated divided visual field paradigm. The dual task experiment consists of a lexical decision task with different semantic verb categories, and a complex tapping task with either the left or right hand. The software allows researchers the replication of our experiment, as well as the reconfiguration for further dual task experiments with alternative tapping tasks and stimuli (e.g., word classes, semantic classes, task languages) as well as adjusted experimental settings. Furthermore, with only slight modifications to the source code, researchers can implement various new experimental setups including a large variety of language tasks (e.g., silent and aloud reading, naming, verbal fluency) and non-verbal tasks. The software DiViDu is implemented using the .NET framework and is available under the Apache 2 License on GitHub ( Funding statement: The publication of the paper was supported by the Open Access Publication Fund of the University of Konstanz. Published on 2018-04-06 15:13:24
  • InDEx: Open Source iOS and Android Software for Self-Reporting and
           Monitoring of Alcohol Consumption

    • Abstract: InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub ( Funding statement: This study was funded by the Medical Research Council (MR/N028244/2). Published on 2018-03-23 16:17:32
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