{"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}
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.
{"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}
Pub Date : 2020-05-22DOI: 10.20944/preprints202005.0351.v1
T. Dowrick, J. Avery, Mayo Faulkner, D. Holder, K. Aristovich
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).
{"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}
R. Richardson, D. Wright, W. Edeling, V. Jancauskas, J. Lakhlili, P. Coveney
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.
{"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}
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.
ABC-OCT，经济实惠的基于b扫描相机的光学相干断层扫描，使用跨平台c++和OpenCV框架实现实时显示的傅里叶域光学相干断层扫描。该软件可以使用当前版本的GCC for *nix/Mac和Microsoft®Visual Studio for Windows进行编译。ABC-OCT的完整功能需要QHYCCD的相机SDK和一个QHYCCD相机连接;但代码可以很容易地修改，以支持其他摄像头驱动程序，如演示版本所示，它可以使用任何安装的网络摄像头。该代码在MIT许可下提供。该软件可从GitHub (https://github.com/hn-88/FDOCT)获得。资助声明:本研究未获得任何资助。
{"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}
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.
{"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}
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
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)
Zarrar Khan1, Thomas wild1,2, Chris Vernon1, Andy Miller3, Mohamad hejazi1,2, Leon clarke1,4, Fernando miralles - wilhel1,2, Raul Munoz Castillo5, Fekadu Moreda6, Julia Lacal Bereslawski5, Micaela Suriano7和Jose Casado7全球变化联合研究所，太平洋西北国家实验室(PNNL)，马里兰州大学公园，美国2地球系统科学跨学科中心(ESSIC)，马里兰大学，马里兰州，美国3国家和平队协会，华盛顿特区，4 .马里兰大学全球可持续发展中心，马里兰大学帕克分校;5 .美洲开发银行(IDB)，华盛顿特区;6 .三角研究所(RTI)，北卡罗来纳州三角研究园区;7 .阿瓜国家研究所(INA)，阿根廷布宜诺斯艾利斯。通讯作者:Zarrar Khan (zarrar.khan@pnnl.gov)
{"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}
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.
{"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}
{"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}
V. Gónzalez-Pérez, P. Keil, Yachao Li, A. Zülke, R. Burrel, D. Csala, H. Hoster
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.
{"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}
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