scholarly journals Conducting linguistic experiments online with OpenSesame and OSWeb

2021 ◽  
Author(s):  
Sebastiaan Mathot ◽  
Jennifer March
Keyword(s):  
Data Quality ◽  
Open Source ◽  
Viable Alternative ◽  
Graphical Interface ◽  
Technical Expertise ◽  
Behavioral Experiments ◽  
Online Experiments ◽  
Temporal Precision ◽  
Server Software ◽  
User Friendly

In this Methods Showcase, we outline a workflow for running behavioral experiments online, with a focus on linguistic experiments. The workflow that we describe here relies on three tools: OpenSesame/ OSWeb (open source) provides a user-friendly graphical interface for developing experiments; JATOS (open source) is server software for hosting experiments; and Prolific (commercial) is a platform for recruiting participants. These three tools integrate well with each other, and together they provide a workflow that requires little technical expertise. We discuss several challenges that are associated with running online experiments, including temporal precision, the ability to implement counterbalancing, and data quality. We conclude that these problems are real but surmountable, and that in many cases online experiments are a viable alternative to laboratory-based experiments.

Traffic Simulation with Open-Source and Commercial Traffic Microsimulators: A Case Study

2022 ◽  
Vol 24 (2) ◽  
pp. E49-E62
Author(s):  
Nelson Baza-Solares ◽  
Ruben Velasquez-Martínez ◽  
Cristian Torres-Bohórquez ◽  
Yerly Martínez-Estupiñán ◽  
Cristian Poliziani
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Transport Modeling ◽  
Graphical Interface ◽  
Urban Centers ◽  
Output Data ◽  
Computational Tools ◽  
Input And Output ◽  
User Friendly

The analysis of traffic problems in large urban centers often requires the use of computational tools, which give the possibility to make a more detailed analysis of the issue, suggest solutions, predict behaviors and, above all, support efficient decision-making. Transport microsimulation software programs are a handy set of tools for this type of analysis. This research paper shows a case study where functions and limitations of Aimsun version 8.2.0, a commercial-like European software and Sumo version 1.3.1, a European open-source software, are presented. The input and output data are similar in both software and the interpretation of results is quite intuitive for both, as well. However, Aimsun's graphical interface interprets results more user-friendly, because Sumo is an open-access software presented as an effective alternative tool for transport modeling.

scholarly journals LIONESS Lab: a free web-based platform for conducting interactive experiments online

2020 ◽  
Vol 6 (1) ◽  
pp. 95-111 ◽  
Author(s):  
Marcus Giamattei ◽  
Kyanoush Seyed Yahosseini ◽  
Simon Gächter ◽  
Lucas Molleman
Keyword(s):  
Waiting Time ◽  
Graphical Interface ◽  
Online Experiments ◽  
Web Based ◽  
Methodological Challenges ◽  
Online Experimentation ◽  
Key Features ◽  
User Friendly ◽  
Time Form

Abstract LIONESS Lab is a free web-based platform for interactive online experiments. An intuitive, user-friendly graphical interface enables researchers to develop, test, and share experiments online, with minimal need for programming experience. LIONESS Lab provides solutions for the methodological challenges of interactive online experimentation, including ways to reduce waiting time, form groups on-the-fly, and deal with participant dropout. We highlight key features of the software, and show how it meets the challenges of conducting interactive experiments online.

scholarly journals DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 397
Author(s):  
Boyoung Kim
Keyword(s):  
Open Source ◽  
Three Dimensional ◽  
Graphical Interface ◽  
Matlab Toolbox ◽  
Function Generator ◽  
Point Spread ◽  
Spread Function ◽  
Asymmetric Shape ◽  
User Friendly ◽  
Imaging Conditions

To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future.

scholarly journals An open source tool to compute measures of inpatient glycemic control: translating from healthcare analytics research to clinical quality improvement

JAMIA Open ◽  
2021 ◽  
Vol 4 (2) ◽  
Author(s):  
Ying Chen ◽  
Yilin Ning ◽  
Prem Thomas ◽  
Mark Salloway ◽  
Maudrene Luor Shyuan Tan ◽  
...  
Keyword(s):  
Glycemic Control ◽  
Open Source ◽  
Graphical Interface ◽  
Prior Work ◽  
Healthcare Analytics ◽  
Privacy Concerns ◽  
Open Source Tool ◽  
Extended Code ◽  
User Friendly

Abstract Objectives The objective of this study is to facilitate monitoring of the quality of inpatient glycemic control by providing an open-source tool to compute glucometrics. To allay regulatory and privacy concerns, the tool is usable locally; no data are uploaded to the internet. Materials and Methods We extended code, initially developed for healthcare analytics research, to serve the clinical need for quality monitoring of diabetes. We built an application, with a graphical interface, which can be run locally without any internet connection. Results We verified that our code produced results identical to prior work in glucometrics. We extended the prior work by including additional metrics and by providing user customizability. The software has been used at an academic healthcare institution. Conclusion We successfully translated code used for research methods into an open source, user-friendly tool which hospitals may use to expedite quality measure computation for the management of inpatients with diabetes.

scholarly journals Canary: An NLP Platform for Clinicians and Researchers

2017 ◽  
Vol 08 (02) ◽  
pp. 447-453 ◽  
Author(s):  
Shervin Malmasi ◽  
Nicolae Sandor ◽  
Naoshi Hosomura ◽  
Matt Goldberg ◽  
Stephen Skentzos ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Language Processing ◽  
Extraction Methods ◽  
Free Software ◽  
Graphical Interface ◽  
Technical Expertise ◽  
Major Barrier ◽  
Critical Knowledge ◽  
Medical Researchers ◽  
User Friendly

SummaryInformation Extraction methods can help discover critical knowledge buried in the vast repositories of unstructured clinical data. However, these methods are underutilized in clinical research, potentially due to the absence of free software geared towards clinicians with little technical expertise. The skills required for developing/using such software constitute a major barrier for medical researchers wishing to employ these methods. To address this, we have developed Canary, a free and open-source solution designed for users without natural language processing (NLP) or software engineering experience. It was designed to be fast and work out of the box via a user-friendly graphical interface. Citation: Malmasi S, Sandor NL, Hosomura N, Goldberg M, Skentzos S, Turchin A. Canary: an NLP platform for clinicians and researchers. Appl Clin Inform 2017; 8: 447–453 https://doi.org/10.4338/ACI-2017-01-IE-0018

MackDroid - An Android based Application to monitor devices

2016 ◽  
Vol 9 ◽  
pp. 1
Author(s):  
Maaz Sirkhot ◽  
Ekta Sirwani ◽  
Aishwarya Kourani ◽  
Akshit Batheja ◽  
Kajal Jethanand Jewani
Keyword(s):  
Operating System ◽  
Open Source ◽  
Vital Role ◽  
Mobile Users ◽  
Android Application ◽  
Web Page ◽  
Technological World ◽  
Monitoring Service ◽  
User Friendly

In this technological world, smartphones can be considered as one of the most far-reaching inventions. It plays a vital role in connecting people socially. The number of mobile users using an Android based smartphone has increased rapidly since last few years resulting in organizations, cyber cell departments, government authorities feeling the need to monitor the activities on certain targeted devices in order to maintain proper functionality of their respective jobs. Also with the advent of smartphones, Android became one of the most popular and widely used Operating System. Its highlighting features are that it is user friendly, smartly designed, flexible, highly customizable and supports latest technologies like IoT. One of the features that makes it exclusive is that it is based on Linux and is Open Source for all the developers. This is the reason why our project Mackdroid is an Android based application that collects data from the remote device, stores it and displays on a PHP based web page. It is primarily a monitoring service that analyzes the contents and distributes it in various categories like Call Logs, Chats, Key logs, etc. Our project aims at developing an Android application that can be used to track, monitor, store and grab data from the device and store it on a server which can be accessed by the handler of the application.

scholarly journals An Interactive WebGIS Framework for Coastal Erosion Risk Management

2021 ◽  
Vol 9 (6) ◽  
pp. 567
Author(s):  
Alessandra Capolupo ◽  
Cristina Monterisi ◽  
Alessandra Saponieri ◽  
Fabio Addona ◽  
Leonardo Damiani ◽  
...  
Keyword(s):  
Open Source ◽  
3D Visualization ◽  
Erosion Risk ◽  
Innovative Strategies ◽  
Web Mapping ◽  
Natural Processes ◽  
Multi Scale ◽  
Interactive Interface ◽  
Multi Temporal ◽  
User Friendly

The Italian coastline stretches over about 8350 km, with 3600 km of beaches, representing a significant resource for the country. Natural processes and anthropic interventions keep threatening its morphology, moulding its shape and triggering soil erosion phenomena. Thus, many scholars have been focusing their work on investigating and monitoring shoreline instability. Outcomes of such activities can be largely widespread and shared with expert and non-expert users through Web mapping. This paper describes the performances of a WebGIS prototype designed to disseminate the results of the Italian project Innovative Strategies for the Monitoring and Analysis of Erosion Risk, known as the STIMARE project. While aiming to include the entire national coastline, three study areas along the regional coasts of Puglia and Emilia Romagna have already been implemented as pilot cases. This WebGIS was generated using Free and Open-Source Software for Geographic information systems (FOSS4G). The platform was designed by combining Apache http server, Geoserver, as open-source server and PostgreSQL (with PostGIS extension) as database. Pure javascript libraries OpenLayers and Cesium were implemented to obtain a hybrid 2D and 3D visualization. A user-friendly interactive interface was programmed to help users visualize and download geospatial data in several formats (pdf, kml and shp), in accordance with the European INSPIRE directives, satisfying both multi-temporal and multi-scale perspectives.

scholarly journals BREC: an R package/Shiny app for automatically identifying heterochromatin boundaries and estimating local recombination rates along chromosomes

2021 ◽  
Vol 22 (S6) ◽  
Author(s):  
Yasmine Mansour ◽  
Annie Chateau ◽  
Anna-Sophie Fiston-Lavier
Keyword(s):  
Data Quality ◽  
Data Science ◽  
Fruit Fly ◽  
R Package ◽  
Model Organisms ◽  
Data Quality Control ◽  
Recombination Rates ◽  
Functional Dynamics ◽  
Shiny App ◽  
User Friendly

Abstract Background Meiotic recombination is a vital biological process playing an essential role in genome's structural and functional dynamics. Genomes exhibit highly various recombination profiles along chromosomes associated with several chromatin states. However, eu-heterochromatin boundaries are not available nor easily provided for non-model organisms, especially for newly sequenced ones. Hence, we miss accurate local recombination rates necessary to address evolutionary questions. Results Here, we propose an automated computational tool, based on the Marey maps method, allowing to identify heterochromatin boundaries along chromosomes and estimating local recombination rates. Our method, called BREC (heterochromatin Boundaries and RECombination rate estimates) is non-genome-specific, running even on non-model genomes as long as genetic and physical maps are available. BREC is based on pure statistics and is data-driven, implying that good input data quality remains a strong requirement. Therefore, a data pre-processing module (data quality control and cleaning) is provided. Experiments show that BREC handles different markers' density and distribution issues. Conclusions BREC's heterochromatin boundaries have been validated with cytological equivalents experimentally generated on the fruit fly Drosophila melanogaster genome, for which BREC returns congruent corresponding values. Also, BREC's recombination rates have been compared with previously reported estimates. Based on the promising results, we believe our tool has the potential to help bring data science into the service of genome biology and evolution. We introduce BREC within an R-package and a Shiny web-based user-friendly application yielding a fast, easy-to-use, and broadly accessible resource. The BREC R-package is available at the GitHub repository https://github.com/GenomeStructureOrganization.

scholarly journals CWDAT—An Open-Source Tool for the Visualization and Analysis of Community-Generated Water Quality Data

2021 ◽  
Vol 10 (4) ◽  
pp. 207
Author(s):  
Annie Gray ◽  
Colin Robertson ◽  
Rob Feick
Keyword(s):  
Water Quality ◽  
Data Quality ◽  
Capacity Building ◽  
Open Source ◽  
Citizen Science ◽  
Water Resource ◽  
Water Quality Monitoring ◽  
Quality Monitoring ◽  
User Engagement ◽  
Community Based

Citizen science initiatives span a wide range of topics, designs, and research needs. Despite this heterogeneity, there are several common barriers to the uptake and sustainability of citizen science projects and the information they generate. One key barrier often cited in the citizen science literature is data quality. Open-source tools for the analysis, visualization, and reporting of citizen science data hold promise for addressing the challenge of data quality, while providing other benefits such as technical capacity-building, increased user engagement, and reinforcing data sovereignty. We developed an operational citizen science tool called the Community Water Data Analysis Tool (CWDAT)—a R/Shiny-based web application designed for community-based water quality monitoring. Surveys and facilitated user-engagement were conducted among stakeholders during the development of CWDAT. Targeted recruitment was used to gather feedback on the initial CWDAT prototype’s interface, features, and potential to support capacity building in the context of community-based water quality monitoring. Fourteen of thirty-two invited individuals (response rate 44%) contributed feedback via a survey or through facilitated interaction with CWDAT, with eight individuals interacting directly with CWDAT. Overall, CWDAT was received favourably. Participants requested updates and modifications such as water quality thresholds and indices that reflected well-known barriers to citizen science initiatives related to data quality assurance and the generation of actionable information. Our findings support calls to engage end-users directly in citizen science tool design and highlight how design can contribute to users’ understanding of data quality. Enhanced citizen participation in water resource stewardship facilitated by tools such as CWDAT may provide greater community engagement and acceptance of water resource management and policy-making.

SIR2004: an improved tool for crystal structure determination and refinement

2005 ◽  
Vol 38 (2) ◽  
pp. 381-388 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Determination ◽  
Protein Structures ◽  
Medium Size ◽  
Graphical Interface ◽  
Asymmetric Unit ◽  
Density Maps ◽  
Data Resolution ◽  
User Friendly

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

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