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Python Battery Mathematical Modelling (PyBaMM) Python电池数学建模（PyBaMM）
Journal of Open Research Software Pub Date : 2020-02-06 DOI: 10.1149/osf.io/5npy8
V. Sulzer, S. Marquis, R. Timms, Martin Robinson, S. J. Chapman
{"title":"Python Battery Mathematical Modelling (PyBaMM)","authors":"V. Sulzer, S. Marquis, R. Timms, Martin Robinson, S. J. Chapman","doi":"10.1149/osf.io/5npy8","DOIUrl":"https://doi.org/10.1149/osf.io/5npy8","url":null,"abstract":"As the UK battery modelling community grows, there is a clear need for software that uses modern software engineering techniques to facilitate cross-institutional collaboration and democratise research progress. The Python package PyBaMM aims to provide a flexible platform for implementation and comparison of new models and numerical methods. This is achieved by implementing models as expression trees and processing them in a modular fashion through a pipeline. Comprehensive testing provides robustness to changes and hence eases the implementation of model extensions. PyBaMM is open source and available on GitHub at https://github.com/pybamm-team/PyBaMM.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42427013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 107
Moirai Version 3: A Data Processing System to Generate Recent Historical Land Inputs for Global Modeling Applications at Various Scales Moirai版本3:一个数据处理系统，用于在各种尺度上为全球建模应用程序生成最近的历史土地输入
Journal of Open Research Software Pub Date : 2020-01-15 DOI: 10.5334/jors.266
A. Vittorio, C. Vernon, Shijie Shu
{"title":"Moirai Version 3: A Data Processing System to Generate Recent Historical Land Inputs for Global Modeling Applications at Various Scales","authors":"A. Vittorio, C. Vernon, Shijie Shu","doi":"10.5334/jors.266","DOIUrl":"https://doi.org/10.5334/jors.266","url":null,"abstract":"","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48771726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Using SAS Macros for Multiple Mediation Analysis in R. 在R中使用SAS宏进行多重中介分析。
Journal of Open Research Software Pub Date : 2020-01-01 Epub Date: 2020-10-07 DOI: 10.5334/jors.277
Paige Fisher, Wentao Cao, Qingzhao Yu
{"title":"Using SAS Macros for Multiple Mediation Analysis in R.","authors":"Paige Fisher, Wentao Cao, Qingzhao Yu","doi":"10.5334/jors.277","DOIUrl":"10.5334/jors.277","url":null,"abstract":"<p><p>Mediation analysis refers to the process of making inferences on effects of third variables that intervene in the relationship between an exposure and response variable. The relationships among variables can be modelled by generalized linear models (GLM). However, GLM are not sufficient to describe relationships among variables when there are nonlinear relationships and potential interaction effects. A general mediation analysis method was developed using not only GLMs, but also multiple additive regression trees and smoothing splines by Yu and Li (2017). The method is implemented in the R package, <i>mma</i>. In this paper, we developed SAS macros so that functions in the mma package can be called and the mediation analysis performed in the SAS environment.</p>","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39282539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Figure One Web Tool for Visualization of Experimental Designs. 用于实验设计可视化的图一网络工具。
Journal of Open Research Software Pub Date : 2020-01-01 Epub Date: 2020-03-30 DOI: 10.5334/jors.243
Foo Cheung
{"title":"A Figure One Web Tool for Visualization of Experimental Designs.","authors":"Foo Cheung","doi":"10.5334/jors.243","DOIUrl":"https://doi.org/10.5334/jors.243","url":null,"abstract":"<p><p>This manuscript introduces a user-friendly, point and click open source and platform-independent software tool that aids the graphical representation of experimental studies. A graphical summary can give a high-level view of a study and represent in one illustration the important features of the data. Examples include sample collections, the time of each data collection, perturbations, and analysis performed. Graphical summaries can be useful in clarifying and documenting the complex relationships within an experiment by breaking down the component parts and expressing them visually. Commonly used cases for this tool include generating summary figures for presentation and publications. This tool was used either alone or in conjunction with other tools to generate schematic diagrams for talks and publications on several different on-going research projects.</p>","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"8 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38146529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
SnappySonic: An Ultrasound Acquisition Replay Simulator. SnappySonic：超声波采集回放模拟器
Journal of Open Research Software Pub Date : 2020-01-01 Epub Date: 2020-03-30 DOI: 10.5334/jors.289
Stephen Thompson, Thomas Dowrick, Goufang Xiao, João Ramalhinho, Maria Robu, Mian Ahmad, Dan Taylor, Matthew J Clarkson
{"title":"SnappySonic: An Ultrasound Acquisition Replay Simulator.","authors":"Stephen Thompson, Thomas Dowrick, Goufang Xiao, João Ramalhinho, Maria Robu, Mian Ahmad, Dan Taylor, Matthew J Clarkson","doi":"10.5334/jors.289","DOIUrl":"10.5334/jors.289","url":null,"abstract":"<p><p>SnappySonic provides an ultrasound acquisition replay simulator designed for public engagement and training. It provides a simple interface to allow users to experience ultrasound acquisition without the need for specialist hardware or acoustically compatible phantoms. The software is implemented in Python, built on top of a set of open source Python modules targeted at surgical innovation. The library has high potential for reuse, most obviously for those who want to simulate ultrasound acquisition, but it could also be used as a user interface for displaying high dimensional images or video data.</p>","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"8 1","pages":"8"},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37925186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Grid for Multidimensional and Multivariate Spatial Representation and Data Processing 一种用于多维和多变量空间表示和数据处理的网格
Journal of Open Research Software Pub Date : 2019-11-11 DOI: 10.31223/osf.io/9szfp
Tobias Stål, A. Reading
{"title":"A Grid for Multidimensional and Multivariate Spatial Representation and Data Processing","authors":"Tobias Stål, A. Reading","doi":"10.31223/osf.io/9szfp","DOIUrl":"https://doi.org/10.31223/osf.io/9szfp","url":null,"abstract":"Researchers use 2D and 3D spatial models of multivariate data of differing resolutions and formats. It can be challenging to work with multiple datasets, and it is time consuming to set up a robust, performant grid to handle such spatial models. We share ‘agrid’, a Python module which provides a framework for containing multidimensional data and functionality to work with those data. The module provides methods for defining the grid, data import, visualisation, processing capability and export. To facilitate reproducibility, the grid can point to original data sources and provides support for structured metadata. The module is written in an intelligible high level programming language, and uses well documented libraries as numpy, xarray, dask and rasterio.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42350747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Analysing Noisy Driver Physiology Real-Time Using Off-the-Shelf Sensors: Heart Rate Analysis Software from the Taking the Fast Lane Project 使用现成的传感器实时分析噪声驾驶员生理:来自快速通道项目的心率分析软件
Journal of Open Research Software Pub Date : 2019-10-29 DOI: 10.5334/jors.241
P. van Gent, Haneen Farah, N. van Nes, B. van Arem
{"title":"Analysing Noisy Driver Physiology Real-Time Using Off-the-Shelf Sensors: Heart Rate Analysis Software from the Taking the Fast Lane Project","authors":"P. van Gent, Haneen Farah, N. van Nes, B. van Arem","doi":"10.5334/jors.241","DOIUrl":"https://doi.org/10.5334/jors.241","url":null,"abstract":"This paper describes the functioning and development of HeartPy: a heart rate analysis toolkit designed for photoplethysmogram (PPG) data. Most openly available algorithms focus on electrocardiogram (ECG) data, which has very different signal properties and morphology, creating a problem with analysis. ECG-based algorithms generally don’t function well on PPG data, especially noisy PPG data collected in experimental studies. To counter this, we developed HeartPy to be a noise-resistant algorithm that handles PPG data well. It has been implemented in Python and C. Arduino IDE sketches for popular boards (Arduino, Teensy) are available to enable data collection as well. This provides both pc-based and wearable implementations of the software, which allows rapid reuse by researchers looking for a validated heart rate analysis toolkit for use in human factors studies.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45228171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 64
DataDeps.jl: Repeatable Data Setup for Reproducible Data Science DataDeps。可复制数据科学的可重复数据设置
Journal of Open Research Software Pub Date : 2019-10-29 DOI: 10.5334/jors.244
Lyndon White, R. Togneri, Wei Liu, Bennamoun
{"title":"DataDeps.jl: Repeatable Data Setup for Reproducible Data Science","authors":"Lyndon White, R. Togneri, Wei Liu, Bennamoun","doi":"10.5334/jors.244","DOIUrl":"https://doi.org/10.5334/jors.244","url":null,"abstract":"We present DataDeps.jl: a julia package for the reproducible handling of static datasets to enhance the repeatability of scripts used in the data and computational sciences. It is used to automate the data setup part of running software which accompanies a paper to replicate a result. This step is commonly done manually, which expends time and allows for confusion. This functionality is also useful for other packages which require data to function (e.g. a trained machine learning based model). DataDeps.jl simplifies extending research software by automatically managing the dependencies and makes it easier to run another author’s code, thus enhancing the reproducibility of data science research.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43888721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
gcamland v1.0 – An R Package for Modelling Land Use and Land Cover Change gcamland v1.0 -一个模拟土地利用和土地覆盖变化的R包
Journal of Open Research Software Pub Date : 2019-10-22 DOI: 10.5334/jors.233
K. Calvin, R. Link, M. Wise
{"title":"gcamland v1.0 – An R Package for Modelling Land Use and Land Cover Change","authors":"K. Calvin, R. Link, M. Wise","doi":"10.5334/jors.233","DOIUrl":"https://doi.org/10.5334/jors.233","url":null,"abstract":"gcamland v1.0 is an open source R package that was built to allocate land across a variety of uses based on changes in agricultural yield and commodity price. The land allocation algorithm is based on the one included in the Global Change Assessment Model (GCAM). gcamland v1.0 includes the ability to run in a historical mode, enabling model validation and parameter estimation, or in a future mode, simulating changes in land use/land cover in the future. For both modes, gcamland v1.0 can run a single simulation or a large ensemble of simulations with different parameters. When ensembles are generated in the historical mode, gcamland v1.0 calculates the likelihood of a given parameter set by comparing to observational data. gcamland v1.0 is publicly available via GitHub and has can be adjusted to represent alternative scenarios or configured to different regions and land types.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70681095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
A Multilingual Copy Task: Measuring Typing and Motor Skills in Writing with Inputlog 多语言复制任务:用输入日志测量打字和写作运动技能
Journal of Open Research Software Pub Date : 2019-10-16 DOI: 10.5334/jors.234
L. Van Waes, M. Leijten, Tom Pauwaert, Eric Van Horenbeeck
{"title":"A Multilingual Copy Task: Measuring Typing and Motor Skills in Writing with Inputlog","authors":"L. Van Waes, M. Leijten, Tom Pauwaert, Eric Van Horenbeeck","doi":"10.5334/jors.234","DOIUrl":"https://doi.org/10.5334/jors.234","url":null,"abstract":"Keyboarding is an essential mode of text production. In the context of typing courses, instruments have been developed to gauge typing skills but to our knowledge there is no computerized typing test measuring both motor skills and the influence of different levels of lexicality on typing fluency. That is why, we developed a strictly controlled copy task guiding participants through seven modules in which different prompts are presented, each dealing with complementary levels of lexicality. Fine-grained keystroke logging allows for a range of analyses with Inputlog [16]. The copy task can be used in writing process studies: research shows that typing fluency has an impact in the quality of text production [1, 24]. In previous writing research studies copy tasks have been used to study the relation between writing fluency and text composition (Wallot and Grabowski, 2013). The Inputlog copy task allows researchers to investigate different levels of lexicality in more detail. At the moment the copy task has been developed in ten different languages. The software is open-access and allows researchers to adapt the tasks to their specific needs.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46611990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
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