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Rhodium: Python Library for Many-Objective Robust Decision Making and Exploratory Modeling Rhodium:用于多目标稳健决策和探索性建模的Python库
Journal of Open Research Software Pub Date : 2020-06-09 DOI: 10.5334/jors.293
A. Hadjimichael, D. Gold, D. Hadka, P. Reed
{"title":"Rhodium: Python Library for Many-Objective Robust Decision Making and Exploratory Modeling","authors":"A. Hadjimichael, D. Gold, D. Hadka, P. Reed","doi":"10.5334/jors.293","DOIUrl":"https://doi.org/10.5334/jors.293","url":null,"abstract":"","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45466711","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: 14
Spectram: A MATLAB® and GNU Octave Toolbox for Transition Model Guided Deconvolution of Dynamic Spectroscopic Data Spectram:用于动态光谱数据的过渡模型引导反卷积的MATLAB®和GNU倍频工具箱
Journal of Open Research Software Pub Date : 2020-06-09 DOI: 10.5334/jors.323
M. Rabe
{"title":"Spectram: A MATLAB® and GNU Octave Toolbox for Transition Model Guided Deconvolution of Dynamic Spectroscopic Data","authors":"M. Rabe","doi":"10.5334/jors.323","DOIUrl":"https://doi.org/10.5334/jors.323","url":null,"abstract":"Spectroscopic data, depending on an experimentally controllable variable, contains a wealth of information for researchers. However, complex spectra with overlapping peaks and multiple transitions complicate its straightforward interpretation and often the full contained information cannot be extracted. Here, the Spectram toolbox for MATLAB® and GNU Octave is described which was developed to analyse such data by a method based on singular value decomposition (SVD) and transition model coupled recombination. The method employs user-defined transition models, which depend on the control variable and are often known, or empirical descriptions of the transitions, which often can be guessed, to deconvolute such data. The outcome are the spectral components associated to the transitions and the model parameters. Both can be directly interpreted in terms of their physical meaning. Spectram can be applied to any desired spectroscopic technique and gives full freedom in the choice of the applied models, making it highly reusable.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47415382","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: 1
EIT-MESHER – Segmented FEM Mesh Generation and Refinement EIT-MESHER -分段有限元网格生成和细化
Journal of Open Research Software Pub Date : 2020-05-22 DOI: 10.20944/preprints202005.0351.v1
T. Dowrick, J. Avery, Mayo Faulkner, D. Holder, K. Aristovich
{"title":"EIT-MESHER – Segmented FEM Mesh Generation and Refinement","authors":"T. Dowrick, J. Avery, Mayo Faulkner, D. Holder, K. Aristovich","doi":"10.20944/preprints202005.0351.v1","DOIUrl":"https://doi.org/10.20944/preprints202005.0351.v1","url":null,"abstract":"EIT-MESHER (https://github.com/EIT-team/Mesher) is C++ software, based on the CGAL library, which generates high quality Finite Element Model tetrahedral meshes from binary masks of 3D volume segmentations. Originally developed for biomedical applications in Electrical Impedance Tomography (EIT) to address the need for custom, non-linear refinement in certain areas (e.g. around electrodes), EIT-MESHER can also be used in other fields where custom FEM refinement is required, such as Diffuse Optical Tomography (DOT).","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45475007","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: 1
EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing EasyVVUQ:一个用于高性能计算的验证、验证和不确定度量化的库
Journal of Open Research Software Pub Date : 2020-04-29 DOI: 10.5334/jors.303
R. Richardson, D. Wright, W. Edeling, V. Jancauskas, J. Lakhlili, P. Coveney
{"title":"EasyVVUQ: A Library for Verification, Validation and Uncertainty Quantification in High Performance Computing","authors":"R. Richardson, D. Wright, W. Edeling, V. Jancauskas, J. Lakhlili, P. Coveney","doi":"10.5334/jors.303","DOIUrl":"https://doi.org/10.5334/jors.303","url":null,"abstract":"EasyVVUQ is an open source Python library ( https://github.com/UCL-CCS/EasyVVUQ ) designed to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations. The goal of EasyVVUQ is to make it as easy as possible to implement advanced VVUQ techniques for existing application codes or workflows. Our aim is to expose these features in an accessible way for users of scientific software, in particular for simulation codes running on high performance computers. Funding statement: We acknowledge funding support from the European Union’s Horizon 2020 research and innovation programme under grant agreement 800925 (VECMA project, www.vecma.eu) and the UK Consortium on Mesoscale Engineering Sciences (UK-COMES, http://www.ukcomes.org), EPSRC reference EP/L00030X/1.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"8 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2020-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46826356","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: 33
ABC-OCT – A Cross-Platform Implementation of Real-Time Fourier-Domain Optical Coherence Tomography 实时傅里叶域光学相干层析成像的跨平台实现
Journal of Open Research Software Pub Date : 2020-03-30 DOI: 10.5334/JORS.272
H. Nandakumar, S. Srivastava
{"title":"ABC-OCT – A Cross-Platform Implementation of Real-Time Fourier-Domain Optical Coherence Tomography","authors":"H. Nandakumar, S. Srivastava","doi":"10.5334/JORS.272","DOIUrl":"https://doi.org/10.5334/JORS.272","url":null,"abstract":"ABC-OCT, Affordable B-scan Camera-based Optical Coherence Tomography, implements Fourier-Domain Optical Coherence Tomography with real-time display using cross-platform C++ and the OpenCV framework. The software can be compiled using current versions of GCC for *nix/Mac and Microsoft®Visual Studio for Windows. Full functionality of ABC-OCT needs the camera SDK from QHYCCD and a QHYCCD camera to be connected; but the code can be easily modified to support other camera drivers, as is shown by an included demo version which can use any installed webcam. The code is made available under the MIT license. The software is available from GitHub ( https://github.com/hn-88/FDOCT ). Funding statement: This work has not been funded by any grants.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43342177","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: 0
An Open Source Toolbox for Integrating Freshwater Social-Ecological Indicators in Basin Management 流域管理中淡水社会生态指标集成的开源工具箱
Journal of Open Research Software Pub Date : 2020-03-30 DOI: 10.5334/jors.291
K. Shaad, H. Alt
{"title":"An Open Source Toolbox for Integrating Freshwater Social-Ecological Indicators in Basin Management","authors":"K. Shaad, H. Alt","doi":"10.5334/jors.291","DOIUrl":"https://doi.org/10.5334/jors.291","url":null,"abstract":"The Freshwater Health Index (FHI) toolbox is an open source software in C# developed to guide ecological management of freshwater systems. It provides functionality to calculate basin-level freshwater socialecological indicators, with algorithms for selected indicators also integrated with support for processing geospatial datasets. The toolbox archives the data necessary for calculating the indicators and can serve as a collaborative platform in a basin by providing users with the ability to initiate, edit and share a common freshwater basin database. Now available at GitHub and through the FHI website, the FHI toolbox offers a convenient yet rigorous way for basin-level freshwater management to maintain continuity and reproducibility amid numerous indicators assessed for freshwater basins.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42246437","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: 0
Metis – A Tool to Harmonize and Analyze Multi-Sectoral Data and Linkages at Variable Spatial Scales Metis -一个在可变空间尺度上协调和分析多部门数据和联系的工具
Journal of Open Research Software Pub Date : 2020-03-29 DOI: 10.5334/jors.292
J. Casado, M. Suriano, J. L. Bereslawski, F. Moreda, Raúl Muñoz Castillo, F. Miralles-Wilhelm, L. Clarke, M. Hejazi, Andy Miller, C. Vernon, T. Wild, Z. Khan
{"title":"Metis – A Tool to Harmonize and Analyze Multi-Sectoral Data and Linkages at Variable Spatial Scales","authors":"J. Casado, M. Suriano, J. L. Bereslawski, F. Moreda, Raúl Muñoz Castillo, F. Miralles-Wilhelm, L. Clarke, M. Hejazi, Andy Miller, C. Vernon, T. Wild, Z. Khan","doi":"10.5334/jors.292","DOIUrl":"https://doi.org/10.5334/jors.292","url":null,"abstract":"Zarrar Khan1, Thomas Wild1,2, Chris Vernon1, Andy Miller3, Mohamad Hejazi1,2, Leon Clarke1,4, Fernando Miralles-Wilhelm1,2, Raul Munoz Castillo5, Fekadu Moreda6, Julia Lacal Bereslawski5, Micaela Suriano7 and Jose Casado7 1 Joint Global Change Research institute, Pacific Northwest National Laboratory (PNNL), College Park, MD, US 2 Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, College Park, MD, US 3 National Peace Corps Association, Washington, DC, US 4 Center for Global Sustainability, University of Maryland, College Park, MD, US 5 Inter-American Development Bank (IDB), Washington, DC, US 6 Research Triangle Institute (RTI), Research Triangle Park, NC, US 7 Instituto Nacional del Agua (INA), Buenos Aires, AR Corresponding author: Zarrar Khan (zarrar.khan@pnnl.gov)","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70681195","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: 13
PowNet: A Network-Constrained Unit Commitment/Economic Dispatch Model for Large-Scale Power Systems Analysis PowNet：一个用于大型电力系统分析的网络约束机组组合/经济调度模型
Journal of Open Research Software Pub Date : 2020-03-12 DOI: 10.5334/jors.302
A. Chowdhury, J. Kern, Thanh Duc Dang, S. Galelli
{"title":"PowNet: A Network-Constrained Unit Commitment/Economic Dispatch Model for Large-Scale Power Systems Analysis","authors":"A. Chowdhury, J. Kern, Thanh Duc Dang, S. Galelli","doi":"10.5334/jors.302","DOIUrl":"https://doi.org/10.5334/jors.302","url":null,"abstract":"PowNet is a free modelling tool for simulating the Unit Commitment/Economic Dispatch of large-scale power systems. PowNet is specifically conceived for systems characterized by the presence of variable renewable resources (e.g., hydropower, solar, and wind), whose penetration on the grid is strongly influenced by climatic variability and constrained by the availability of transmission capacity. To help users effectively capture the nuances of power system dynamics, PowNet is equipped with features that enable accuracy, transferability, and computational efficiency over large spatial and temporal domains. Specifically, the model (i) accounts for the techno-economic constraints of both generating units and transmission networks, (ii) can be easily coupled with models that estimate the status of generating units as a function of the climatic conditions, and (iii) explicitly includes import/export nodes, which are useful in representing cross-border systems. PowNet is implemented in Python and is compatible with any standard optimization solver (e.g., Gurobi, CPLEX). Its functionality is demonstrated on the Cambodian power system.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45683734","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: 10
High Precision Particle Swarm Optimization Algorithm (HiPPSO) 高精度粒子群优化算法
Journal of Open Research Software Pub Date : 2020-03-09 DOI: 10.5334/jors.282
Alexander Raß
{"title":"High Precision Particle Swarm Optimization Algorithm (HiPPSO)","authors":"Alexander Raß","doi":"10.5334/jors.282","DOIUrl":"https://doi.org/10.5334/jors.282","url":null,"abstract":"","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46656157","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: 1
A Python Package to Preprocess the Data Produced by Novonix High-Precision Battery-Testers 一个用于预处理Novonix高精度电池测试仪数据的Python包
Journal of Open Research Software Pub Date : 2020-03-04 DOI: 10.5334/jors.281
V. Gónzalez-Pérez, P. Keil, Yachao Li, A. Zülke, R. Burrel, D. Csala, H. Hoster
{"title":"A Python Package to Preprocess the Data Produced by Novonix High-Precision Battery-Testers","authors":"V. Gónzalez-Pérez, P. Keil, Yachao Li, A. Zülke, R. Burrel, D. Csala, H. Hoster","doi":"10.5334/jors.281","DOIUrl":"https://doi.org/10.5334/jors.281","url":null,"abstract":"We present preparenovonix, a Python package that handles common issues encountered in data fles generated with a range of software versions from the Novonix battery-testers. This package can also add extra information that makes easier coulombic counting and relating a measurement to the experimental protocol. The package provides a master function that can run at once the cleaning and adding derived information, with fexibility to choose only some features. There is a separate function to simply read a column by its given name. The usage of all the functions is documented in the code including examples. The code presented here can be installed either as a python package or from a GitHub repository.","PeriodicalId":37323,"journal":{"name":"Journal of Open Research Software","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41555233","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: 0
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