The Usability Testing of SSAAT, a Bioinformatic Web Application for DNA Analysis at a Nucleotide Level

Sanger sequencing remains the cornerstone method for Deoxyribonucleic Acid (DNA) sequencing due to its high accuracy in targeting smaller genomic regions in a larger number of samples. The analysis of Sanger sequence DNA data requires powerful and intelligent software tools. Most of the preferred tools are proprietary licensed tools that offer a user-friendly interface and have many features, however, their affordability, especially to individual scientists or students, is limited. On the other hand, a few free and open-source licensed tools are available but have limited features. This study focuses on the usability testing of the developed Sanger Sequence Automatic Analysis Tool (SSAAT), a free and open-source web tool for Sanger sequence analysis. Usability tests were conducted with potential users and the results demonstrate that the participants were able to use the tool easily and accomplish the test tasks at the given time. Moreover, the participants were excited with the easy-to-use interface and agreed that most users could use the tool with no need for technical assistance. However, the participants also identified some issues that require more development effort.

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DNA Analysis Tool on Bioinformatics Applications

SSRN Electronic Journal ◽

10.2139/ssrn.944872 ◽

2006 ◽

Author(s):

Ribhu Mahajan ◽

Sunny Gakhar ◽

Kunal Jaiswal

Keyword(s):

Dna Analysis ◽

Analysis Tool

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PRISMS-Fatigue computational framework for fatigue analysis in polycrystalline metals and alloys

npj Computational Materials ◽

10.1038/s41524-021-00506-8 ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Mohammadreza Yaghoobi ◽

Krzysztof S. Stopka ◽

Aaditya Lakshmanan ◽

Veera Sundararaghavan ◽

John E. Allison ◽

...

Keyword(s):

Open Source ◽

Open Source Software ◽

Large Scale ◽

Metals And Alloys ◽

Analysis Tool ◽

Computational Framework ◽

Crystal Plasticity Finite Element ◽

Polycrystalline Metals ◽

Simulation Based ◽

Open Source Framework

AbstractThe PRISMS-Fatigue open-source framework for simulation-based analysis of microstructural influences on fatigue resistance for polycrystalline metals and alloys is presented here. The framework uses the crystal plasticity finite element method as its microstructure analysis tool and provides a highly efficient, scalable, flexible, and easy-to-use ICME community platform. The PRISMS-Fatigue framework is linked to different open-source software to instantiate microstructures, compute the material response, and assess fatigue indicator parameters. The performance of PRISMS-Fatigue is benchmarked against a similar framework implemented using ABAQUS. Results indicate that the multilevel parallelism scheme of PRISMS-Fatigue is more efficient and scalable than ABAQUS for large-scale fatigue simulations. The performance and flexibility of this framework is demonstrated with various examples that assess the driving force for fatigue crack formation of microstructures with different crystallographic textures, grain morphologies, and grain numbers, and under different multiaxial strain states, strain magnitudes, and boundary conditions.

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Jump Diffusion Process Model Considering Component Dependency in Open Source Project for Development Effort Management

2020 IEEE International Conference on Industrial Engineering and Engineering Management (IEEM) ◽

10.1109/ieem45057.2020.9309990 ◽

2020 ◽

Author(s):

Yoshinobu Tamura ◽

Kodai Sugisaki ◽

Shigeru Yamada

Keyword(s):

Diffusion Process ◽

Open Source ◽

Process Model ◽

Jump Diffusion ◽

Development Effort ◽

Open Source Project ◽

Jump Diffusion Process

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RiboA: a web application to identify ribosome A-site locations in ribosome profiling data

BMC Bioinformatics ◽

10.1186/s12859-021-04068-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Danying Shao ◽

Nabeel Ahmed ◽

Nishant Soni ◽

Edward P. O’Brien

Keyword(s):

Integer Programming ◽

Web Application ◽

Stop Codon ◽

Ribosome Profiling ◽

Programming Method ◽

Analysis Tool ◽

Site Location ◽

Link Type ◽

Wide Range ◽

A Site

Abstract Background Translation is a fundamental process in gene expression. Ribosome profiling is a method that enables the study of transcriptome-wide translation. A fundamental, technical challenge in analyzing Ribo-Seq data is identifying the A-site location on ribosome-protected mRNA fragments. Identification of the A-site is essential as it is at this location on the ribosome where a codon is translated into an amino acid. Incorrect assignment of a read to the A-site can lead to lower signal-to-noise ratio and loss of correlations necessary to understand the molecular factors influencing translation. Therefore, an easy-to-use and accurate analysis tool is needed to accurately identify the A-site locations. Results We present RiboA, a web application that identifies the most accurate A-site location on a ribosome-protected mRNA fragment and generates the A-site read density profiles. It uses an Integer Programming method that reflects the biological fact that the A-site of actively translating ribosomes is generally located between the second codon and stop codon of a transcript, and utilizes a wide range of mRNA fragment sizes in and around the coding sequence (CDS). The web application is containerized with Docker, and it can be easily ported across platforms. Conclusions The Integer Programming method that RiboA utilizes is the most accurate in identifying the A-site on Ribo-Seq mRNA fragments compared to other methods. RiboA makes it easier for the community to use this method via a user-friendly and portable web application. In addition, RiboA supports reproducible analyses by tracking all the input datasets and parameters, and it provides enhanced visualization to facilitate scientific exploration. RiboA is available as a web service at https://a-site.vmhost.psu.edu/. The code is publicly available at https://github.com/obrien-lab/aip_web_docker under the MIT license.

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An open-source R-package and web application for high-quality probabilistic predictions in hydrology

10.5194/egusphere-egu21-8549 ◽

2021 ◽

Author(s):

Jason Hunter ◽

Mark Thyer ◽

Dmitri Kavetski ◽

David McInerney

Keyword(s):

Open Source ◽

Web Application ◽

R Package ◽

Error Model ◽

Objective Functions ◽

High Quality ◽

Wide Range ◽

Probabilistic Error

Probabilistic predictions provide crucial information regarding the uncertainty of hydrological predictions, which are a key input for risk-based decision-making. However, they are often excluded from hydrological modelling applications because suitable probabilistic error models can be both challenging to construct and interpret, and the quality of results are often reliant on the objective function used to calibrate the hydrological model.We present an open-source R-package and an online web application that achieves the following two aims. Firstly, these resources are easy-to-use and accessible, so that users need not have specialised knowledge in probabilistic modelling to apply them. Secondly, the probabilistic error model that we describe provides high-quality probabilistic predictions for a wide range of commonly-used hydrological objective functions, which it is only able to do by including a new innovation that resolves a long-standing issue relating to model assumptions that previously prevented this broad application. &#160;We demonstrate our methods by comparing our new probabilistic error model with an existing reference error model in an empirical case study that uses 54 perennial Australian catchments, the hydrological model GR4J, 8 common objective functions and 4 performance metrics (reliability, precision, volumetric bias and errors in the flow duration curve). The existing reference error model introduces additional flow dependencies into the residual error structure when it is used with most of the study objective functions, which in turn leads to poor-quality probabilistic predictions. In contrast, the new probabilistic error model achieves high-quality probabilistic predictions for all objective functions used in this case study.The new probabilistic error model and the open-source software and web application aims to facilitate the adoption of probabilistic predictions in the hydrological modelling community, and to improve the quality of predictions and decisions that are made using those predictions. In particular, our methods can be used to achieve high-quality probabilistic predictions from hydrological models that are calibrated with a wide range of common objective functions.

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MarkUs: An Open-Source Web Application to Annotate Student Papers On-Line

Volume 4: Advanced Manufacturing Processes; Biomedical Engineering; Multiscale Mechanics of Biological Tissues; Sciences, Engineering and Education; Multiphysics; Emerging Technologies for Inspection ◽

10.1115/esda2012-82141 ◽

2012 ◽

Author(s):

Morgan Magnin ◽

Guillaume Moreau ◽

Nelle Varoquaux ◽

Benjamin Vialle ◽

Karen Reid ◽

...

Keyword(s):

Higher Education ◽

Open Source ◽

Web Application ◽

Online System ◽

Important Benefit ◽

Special Cases ◽

Assessment Time ◽

On Line ◽

Active Pedagogy ◽

Further Development

A critical component of the learning process lies in the feedback that students receive on their work that validates their progress, identifies flaws in their thinking, and identifies skills that still need to be learned. Many higher-education institutions have developed an active pedagogy that gives students opportunities for different forms of assessment and feedback. This means that students have numerous lab exercises, assignments, and projects. Both instructors and students thus require effective tools to efficiently manage the submission, assessment, and individualized feedback of students’ work. The open-source web application MarkUs aims at meeting these needs: it facilitates the submission and assessment of students’ work. Students directly submit their work using MarkUs, rather than printing it, or sending it by email. The instructors or teaching assistants use MarkUs’s interface to view the students’ work, annotate it, and fill in a marking rubric. Students use the same interface to read the annotations and learn from the assessment. Managing the students’ submissions and the instructors assessments within a single online system, has led to several positive pedagogical outcomes: the number of late submissions has decreased, the assessment time has been drastically reduced, students can access their results and read the instructor’s feedback immediately after the grading process is completed. Using MarkUs has also significantly reduced the time that instructors spend collecting assignments, creating the marking schemes, passing them on to graders, handling special cases, and returning work to the students. In this paper, we introduce MarkUs’ features, and illustrate their benefits for higher education through our own teaching experiences and that of our colleagues. We also describe an important benefit of the fact that the tool itself is open-source. MarkUs has been developed entirely by students giving them a valuable learning opportunity as they work on a large software system that real users depend on. Virtuous circles indeed arise, with former users of MarkUs becoming developers and then supervisors of further development. We will conclude by drawing perspectives about forthcoming features and use, both technically and pedagogically.

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An Open-Source Web-Based Tool for Resource-Agnostic Interactive Translation Prediction

Prague Bulletin of Mathematical Linguistics ◽

10.2478/pralin-2014-0015 ◽

2014 ◽

Vol 102 (1) ◽

pp. 69-80 ◽

Cited By ~ 2

Author(s):

Torregrosa Daniel ◽

Forcada Mikel L. ◽

Pérez-Ortiz Juan Antonio

Keyword(s):

Open Source ◽

Machine Translation ◽

Web Application ◽

Statistical Machine Translation ◽

Black Box ◽

Translation System ◽

Web Tool ◽

Web Based ◽

Strongly Coupled ◽

Machine Translation System

Abstract We present a web-based open-source tool for interactive translation prediction (ITP) and describe its underlying architecture. ITP systems assist human translators by making context-based computer-generated suggestions as they type. Most of the ITP systems in literature are strongly coupled with a statistical machine translation system that is conveniently adapted to provide the suggestions. Our system, however, follows a resource-agnostic approach and suggestions are obtained from any unmodified black-box bilingual resource. This paper reviews our ITP method and describes the architecture of Forecat, a web tool, partly based on the recent technology of web components, that eases the use of our ITP approach in any web application requiring this kind of translation assistance. We also evaluate the performance of our method when using an unmodified Moses-based statistical machine translation system as the bilingual resource.

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Usability Evaluation of Encyclopedia Websites

International Journal of Innovative Computing ◽

10.11113/ijic.v11n1.282 ◽

2021 ◽

Vol 11 (1) ◽

pp. 21-25

Author(s):

Nor Azman Ismail ◽

Fadzrul Izwan Jamaluddin ◽

Akmal Harraz Hamidan ◽

Ahmad Fariz Ali ◽

Su Elya Mohamed ◽

...

Keyword(s):

Standard Form ◽

Usability Testing ◽

Cost Effective ◽

Usability Evaluation ◽

Web Performance ◽

Testing Tools ◽

Usability Tests ◽

Website Analysis ◽

User Friendly

Usability is an important aspect that every website should focus more. It tells us how well and success website will function with real users. Many people often think usability tests are expensive and time-consuming. It can be a cost-effective and time saver with usability testing instead of spending more time fixing an unusable website. This study evaluates the usability of encyclopedia websites by using automated usability testing tools and questionnaire methods. The questionnaire was developed based on a standard form called Website Analysis and Measurement Inventory (WAMMI) that identified 20 common usability questions divided into five categories. Each category deals with one aspect of usability. Simultaneously, the automated usability testing tools used in this study were Pingdom and GT Metrix to calculate and analyse the website performance of selected encyclopedia websites based on website components including page load time, media size and overall web performance grades. This study could help web designer, developer, and practitioners design better and more user-friendly encyclopedia websites.

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