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Publications

Publications by CRACS

2022

Automating microsatellite screening and primer design from multi-individual libraries using Micro-Primers

Authors
Alves, F; Martins, FMS; Areias, M; Munoz Merida, A;

Publication
SCIENTIFIC REPORTS

Abstract
Analysis of intra- and inter-population diversity has become important for defining the genetic status and distribution patterns of a species and a powerful tool for conservation programs, as high levels of inbreeding could lead into whole population extinction in few generations. Microsatellites (SSR) are commonly used in population studies but discovering highly variable regions across species' genomes requires demanding computation and laboratorial optimization. In this work, we combine next generation sequencing (NGS) with automatic computing to develop a genomic-oriented tool for characterizing SSRs at the population level. Herein, we describe a new Python pipeline, named Micro-Primers, designed to identify, and design PCR primers for amplification of SSR loci from a multi-individual microsatellite library. By combining commonly used programs for data cleaning and microsatellite mining, this pipeline easily generates, from a fastq file produced by high-throughput sequencing, standard information about the selected microsatellite loci, including the number of alleles in the population subset, and the melting temperature and respective PCR product of each primer set. Additionally, potential polymorphic loci can be identified based on the allele ranges observed in the population, to easily guide the selection of optimal markers for the species. Experimental results show that Micro-Primers significantly reduces processing time in comparison to manual analysis while keeping the same quality of the results. The elapsed times at each step can be longer depending on the number of sequences to analyze and, if not assisted, the selection of polymorphic loci from multiple individuals can represent a major bottleneck in population studies.

2022

A primer on gamification standardization

Authors
de Queiros, RAP; Pinto, M; Simões, A; Portela, CF;

Publication
Research Anthology on Game Design, Development, Usage, and Social Impact

Abstract
Computer science education has always been a challenging topic for both sides of the trench: educators and learners. Nowadays, with the pandemic state that we are facing, these challenges are even greater, leading educators to look for strategies that promote effective virtual learning. One of such strategies includes the use of game mechanics to improve student engagement and motivation. This design strategy is typically called gamification. Nowadays, gamification is being seen as the solution to solve most of the issues related to demotivation, complexity, or tedious tasks. In the latest years, we saw thousands of educational applications being created with gamification in mind. Nevertheless, this has been an unsustainable growth with ad hoc designs and implementations of educational gamified applications, hampering interoperability and the reuse of good practices. This chapter presents a systematic study on gamification standardization aiming to characterize the status of the field, namely describing existing frameworks, languages, services, and platforms.

2022

Virtual and Augmented Reality Awareness Tools for Universal Design

Authors
Coelho, LP; Freitas, I; Kaminska, DU; Queirós, R; Laska-Lesniewicz, A; Zwolinski, G; Raposo, R; Vairinhos, M; Pereira, ET; Haamer, E; Anbarjafari, G;

Publication
Emerging Advancements for Virtual and Augmented Reality in Healthcare - Advances in Medical Technologies and Clinical Practice

Abstract
This chapter will be focused on contributing to the increase of universal design competencies of future engineers, educators, and designers through the use of mixed reality technologies, closing the gap between theory and field application of principles, towards a more inclusive world and promoting health and wellbeing for all. The experience of a situation where limitations arise in relation to what is taken for granted is an important experience that leads to a personal knowledge of the difficulties. By the use of simulators, especially virtual (VR) and mixed reality (MR) technologies, it is possible to create such experiences. Training based on MR can prepare future and current professionals for up-to-date requirements of the labor market. In addition, it can ensure that the standards such as barrier-free concepts, broader accessibility, adaptive and assistive technology will be familiar to trainees.

2022

WebPuppet - A Tiny Automated Web UI Testing Tool

Authors
Queirós, R;

Publication
Third International Computer Programming Education Conference, ICPEC 2022, June 2-3, 2022, Polytechnic Institute of Cávado and Ave (IPCA), Barcelos, Portugal.

Abstract
One of the most important phases in the Web development cycle is testing. There are several types of tests, different approaches to their use and a wide range of tools. However, most of them are not open source, require coding and do not have a pedagogical nature. This article introduces WebPuppet as an automated Web UI testing tool. The tool is distributed as a small Node package and can be easily integrated into any learning environment in the web development domain. In addition, it does not require coding in any language, just use a very simple domain-specific language that will generate a test script to run in client applications. In order to exemplify its use, a simple test scenario based on a login page is presented. © Queiros, Ricardo; licensed under Creative Commons License CC-BY 4.0

2022

Integration of a Learning Playground into a LMS

Authors
de Queirós, RAP;

Publication
ITiCSE 2022: Innovation and Technology in Computer Science Education, Dublin, Ireland, July 8 - 13, 2022, Volume 2

Abstract
There are lot of interactive environments that encourage the practice of computer programming. Despite their usefulness, these systems are naturally disconnected from the schools' educational environments, forcing teachers and students to alternate between tools. This work integrates Agni - a computer programming learning playground - with Moodle Learning Management System (LMS). Unlike the plugins' strategy to link applications to specific LMS, this integration uses a broader approach, through the IMS LTI standard which defines a set of specifications that allows the connection of any LTI-compliant LMS to external tools. © 2022 Owner/Author.

2022

The Dangers of Gamification

Authors
Queirós, R; Pinto, M;

Publication
Advanced Research in Technologies, Information, Innovation and Sustainability - Second International Conference, ARTIIS 2022, Santiago de Compostela, Spain, September 12-15, 2022, Revised Selected Papers, Part I

Abstract

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