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SPOT: Open Source framework for scientific data repository and interactive visualization [article]

Faruk Diblen, Jisk Attema, Rena Bakhshi, Sascha Caron, Luc Hendriks, Bob Stienen
2018 arXiv   pre-print
SPOT is an open source and free visual data analytics tool for multi-dimensional data-sets. Its web-based interface allows a quick analysis of complex data interactively.  ...  It follows FAIR principles to allow reuse and comparison of the published data-sets. The software also support PostgreSQL database for scalability.  ...  The aim of SPOT [1] is to provide a flexible data visualization framework to visualize such data.  ... 
arXiv:1809.08893v1 fatcat:gz5227znbfasrpikgreja6ibxi

spot: Open Source framework for scientific data repository and interactive visualization

Faruk Diblen, Jisk Attema, Rena Bakhshi, Sascha Caron, Luc Hendriks, Bob Stienen
2019 SoftwareX  
spot is an open source and free visual data analytics tool for multi-dimensional data-sets. Its web-based interface enables user to do a quick and interactive analysis of complex data.  ...  It follows FAIR principles to allow reuse and comparison of the published data-sets.  ...  The frontend is built on a number of open-source JavaScript packages, such as Chart.js, Vis.js, and Sigma.js for animated plots, and Ampersand.js and Material Design Lite for the interface.  ... 
doi:10.1016/j.softx.2019.04.006 fatcat:lcqormywpbcjlez5h7olfo5ohu

D5.4 SPOT Data Management Plan [article]

Šťastná Milada, Chvorostov Alexander, Zloch Jan
2020 Zenodo  
The objective of D5.4 (the Data Management Plan) is to describe what data the SPOT project will collect and proceed, whether and how it will be exploited or made accessible for verification and reuse and  ...  data will be collected, processed and/or generated, • which methodology & standards will be applied, • whether data will be shared/made open access, and • how data will be curated & preserved (including  ...  The data files to be included in an open data repository will be made openly available through the ZENODO which is the open access repository of the Open Access Infrastructure for Research in Europe (https  ... 
doi:10.5281/zenodo.4456417 fatcat:4qckq35xenajzbewlc37amuwxe

Shedding Light on Blind Spots: Developing a Reference Architecture to Leverage Video Data for Process Mining [article]

Wolfgang Kratsch, Fabian Koenig, Maximilian Roeglinger
2021 arXiv   pre-print
In recent years, numerous methods have been proposed for analyzing structured process data.  ...  Yet, in many cases, it is only the digitized parts of processes that are directly captured from process-aware information systems, and manual activities often result in blind spots.  ...  Thanks to our realworld evaluation, we also make it easier to implement such a system by providing an end-to-end example of how to use open-source frameworks to most efficiently instantiate the proposed  ... 
arXiv:2010.11289v2 fatcat:acdpo2mznjbztoww7h7pvvj5ma

Libraries Fight Disinformation: An Analysis of Online Practices to Help Users' Generations in Spotting Fake News

Paula Herrero-Diz, Clara López-Rufino
2021 Societies  
To help citizens, these entities have developed a wide range of actions that range from online seminars, to learning how to evaluate the quality of a source, to video tutorials or the creation of repositories  ...  Among the actions carried out to counteract misinformation, open-access materials that favor self-learning stand out.  ...  Data Availability Statement: Not applicable. Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/soc11040133 fatcat:shslyzqqzrbqtc6dgjv3o3dqde

Pepper Bacterial Spot Control by Bacillus velezensis: Bioprocess Solution

Ivana Pajčin, Vanja Vlajkov, Marcus Frohme, Sergii Grebinyk, Mila Grahovac, Marija Mojićević, Jovana Grahovac
2020 Microorganisms  
Pepper bacterial spot is one of the most severe plant diseases in terms of infection persistence and economic losses when it comes to fresh pepper fruits used in nutrition and industrial processing.  ...  The bioprocess solution developed at the laboratory scale investigated in this study represents a promising strategy for production of pepper bacterial spot biocontrol agent based on B. velezensis IP22  ...  Acknowledgments: Identification of Xanthomonas strains was conducted in the Laboratory for seed testing at the Institute of Field and Vegetable Crops (Novi Sad, Serbia) with kind assistance of Maja Ignjatov  ... 
doi:10.3390/microorganisms8101463 pmid:32987624 fatcat:pvrm7e4oubhjvnu6k4ke4teevq

Capture Knowledge on the Spot: Toward the Autonomous and Pervasive Service of Context-Rich Knowledge

Keedong Yoo
2013 Automatika  
data.  ...  This paper proposes a methodology to capture knowledge on the spot in an autonomous and pervasive manner by deploying the Smartphone as a sensor to monitor and gather dialogue-based knowledge and context  ...  Therefore the word stemming and vector creating tool of Yale [14] , a free open-source environment for KDD and machine learning, was employed.  ... 
doi:10.7305/automatika.54-4.411 fatcat:j5pytvbnibannd4pb43simpwcu

Interactive Web-Based Visualization of Multidimensional Physical and Astronomical Data

Faruk Diblen, Luc Hendriks, Bob Stienen, Sascha Caron, Rena Bakhshi, Jisk Attema
2021 Frontiers in Big Data  
The implementation of interactive web-based visualizations enables quick and convenient reanalysis and comparisons of phenomenological data.  ...  In this article, we propose expanding the use of scientific repositories such as Zenodo and HEP data, in particular, to better study multiparametric solutions of physical models.  ...  The SPOT framework provides classes for datasets, data views, partitions, aggregation, and filtering.  ... 
doi:10.3389/fdata.2021.626998 pmid:34250466 pmcid:PMC8264300 fatcat:f3il3fknpzc7vpy64lvtwyw6h4

Interactive web-based visualization of multi-dimensional physical and astronomical data [article]

Faruk Diblen, Luc Hendriks, Bob Stienen, Sascha Caron, Rena Bakhshi, Jisk Attema
2020 arXiv   pre-print
The implementation of interactive web-based visualizations enables fast and comfortable re-analysis and comparisons of phenomenological data.  ...  In this manuscript, we propose to expand the use of scientific repositories such as Zenodo and HEP Data, in particular in order to better examine multi-parametric solutions of physical models.  ...  A demonstration of interactive visualization phenoMLdata is an online interactive plotting interface to a database of publicly available data sets, based on the open-source SPOT framework.  ... 
arXiv:2011.03801v1 fatcat:dfprjomf2zesbpoxc2j4f5nw5a

FISH-quant v2: a scalable and modular analysis tool for smFISH image analysis [article]

Arthur Imbert, Wei Ouyang, Adham Safieddine, Emeline Coleno, Christophe Zimmer, Edouard Bertrand, Thomas Walter, Florian Mueller
2021 biorxiv/medrxiv   pre-print
Recent progress in experimental techniques provides larger data-sets, requiring adequate tools for data analysis and exploration.  ...  Our package allows the user to detect isolated and clustered mRNA spots, segment nuclei and cells, quantify RNA localization patterns and visualize these results at the single-cell level.  ...  FISH-quant v2 enjoys a better integration to other open source tools and frameworks, from data analysis to web-based user interaction.  ... 
doi:10.1101/2021.07.20.453024 fatcat:wttfbqs3qvembbu4i6h3my3lyq

Cloud-Native Repositories for Big Scientific Data

Ryan Abernathey, Tom Augspurger, Anderson Banihirwe, Charles Blackmon-Luca, Tim Crone, Chelle Gentemann, Joe Hamman, Naomi Henderson, Chiara Lepore, Theo Mccaie, Niall Robinson, Rich Signell
2021 Computing in science & engineering (Print)  
The Pangeo Project has developed a prototype implementation of these principles by using open-source scientific Python tools.  ...  These objectives motivate a set of best practices for cloud-native data repositories: analysis-ready data, cloudoptimized (ARCO) formats, and loose coupling with data-proximate computing.  ...  Cloud-based science platforms built on open architecture require many elements: software for interactive data analysis, machine learning, and visualization; elastically scaled computing resources; and  ... 
doi:10.1109/mcse.2021.3059437 fatcat:gbyixgevmzbgfathdbcx4vsvvq

Hitting the sweet spot of complexity: Reasons why the development of new custom-tailored models is still warranted and should be encouraged in aquatic sciences

Gregorio A. López Moreira M., Marco Toffolon, Franz Hölker
2021 Journal of Limnology  
This is true for both laboratory experiments and those carried out outdoors, under semi-controlled conditions.  ...  processes and inform policy and decision making in environmental management.  ...  of global data and code repositories, libraries of models, equations and parameter values, wider adoption of ensemble modelling approaches, etc.  ... 
doi:10.4081/jlimnol.2021.2035 fatcat:a5df262ecjdv5bivfjlns5kqpm

Seagrass excretes sugars to their rhizosphere making them the sweet spots in the sea [article]

Emilia Margaret Sogin, Dolma Michellod, Harald Gruber-Vodicka, Patric Bourceau, Benedikt Geier, Dimitri Meier, Michael Seidel, Philipp Hach, Gabriele Procaccini, Nicole Dubilier, Manuel Liebeke
2019 bioRxiv   pre-print
Despite the growing attention to the link between plant production, microbial communities, and the carbon cycle in terrestrial ecosystems, these processes remain enigmatic in the sea.  ...  Despite covering less than 0.1 % of coastal regions, they have the capacity to bury up to 10 % of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests.  ...  Acknowledgements We thank Tora Gulstad, Kristopher Caspersen, Marvin Weinhold, Frantisek Fojt, Janine Beckmann, Silke Wetzel, and Miriam Sadowski (Max Planck Institute for Marine Microbiology-certified  ... 
doi:10.1101/797522 fatcat:loeil25ambevjl4wzlvm7inw3y

Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: a statistical phylogeographic study using a low-dispersal organism

M Álvarez-Presas, A Sánchez-Gracia, F Carbayo, J Rozas, M Riutort
2014 Heredity  
We conclude that extant SAF biodiversity originated and has been shaped by complex interactions between ancient geological events and more recent evolutionary processes, whereas Pleistocene climate changes  ...  The relative importance of the processes that generate and maintain biodiversity is a major and controversial topic in evolutionary biology with large implications for conservation management.  ...  We conducted two different analyses (combining COI and ITS-1 data) in the ABC framework.  ... 
doi:10.1038/hdy.2014.3 pmid:24549112 pmcid:PMC4023448 fatcat:r2kstpvqojav7hyposr2betr4i

Grant Proposal: "Phinch: An interactive, exploratory data visualization framework for environmental -Omics datasets"

Holly Bik
2017 Figshare  
Sloan Foundation, focused on the Phinch data visualization framework - http://phinch.org  ...  illustrating the Phinch visualization toolkit, and c) external software development that has incorporated Phinch's open source code and data visualizations.  ...  Finally, we aim to build a community of open source contributors to the Phinch framework, by specifically engaging with the Center for Open Science (https://cos.io/) and the Mozilla Science Lab's "Working  ... 
doi:10.6084/m9.figshare.5471809.v1 fatcat:ibts53tfcbcwjlxtxhup3kli4i
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