Better bioinformatics through usability analysis

Motivation: Improving the usability of bioinformatics resources enables researchers to find, interact with, share, compare and manipulate important information more effectively and efficiently. It thus enables researchers to gain improved insights into biological processes with the potential, ultimately, of yielding new scientific results. Usability ‘barriers' can pose significant obstacles to a satisfactory user experience and force researchers to spend unnecessary time and effort to complete their tasks. The number of online biological databases available is growing and there is an expanding community of diverse users. In this context there is an increasing need to ensure the highest standards of usability. Results: Using ‘state-of-the-art' usability evaluation methods, we have identified and characterized a sample of usability issues potentially relevant to web bioinformatics resources, in general. These specifically concern the design of the navigation and search mechanisms available to the user. The usability issues we have discovered in our substantial case studies are undermining the ability of users to find the information they need in their daily research activities. In addition to characterizing these issues, specific recommendations for improvements are proposed leveraging proven practices from web and usability engineering. The methods and approach we exemplify can be readily adopted by the developers of bioinformatics resources. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Enhancing the Informatics Evaluation Toolkit with Remote Usability Testing

Developing functional clinical informatics products that are also usable remains a challenge. Despite evidence that usability testing should be incorporated into the lifecycle of health information technologies, rarely does this occur. Challenges include poor standards, a lack of knowledge around usability practices, and the expense involved in rigorous testing with a large number of users. Remote usability testing may be a solution for many of these challenges. Remotely testing an application can greatly enhance the number of users who can iteratively interact with a product, and it can reduce the costs associated with usability testing. A case study presents the experiences with remote usability testing when evaluating a Web site designed for health informatics knowledge dissemination. The lessons can inform others seeking to enhance their evaluation toolkits for clinical informatics products

User Interface Design for Searching Biomedical Literature

Biomedical bibliographic sources are crucial resources for the work of physicians, biologists, and bioinformatics. Many of the genetic-medical diagnoses depend on the findings in these bibliographic sources. Despite the importance and value of the information stored in these repositories, the user interface (UI) of these resources does not provide the adequate mechanisms to interact with the content, converting the query and interpretation of the information into complex and time-consuming tasks. In this sense, improving the usability of these UIs becomes a challenge since this means facilitating the interaction, analysis and comparison of biomedical information, and, consequently, improving the productivity of professionals in this domain. This paper presents a UI design for the search of biomedical bibliography that incorporates solutions to the usability problems documented and detected by a study of the literature. The proposed design becomes a usability heuristic for UI designers facing the development of UIs in this domain

Usabilidad en servicios web bioinformáticos: una revisión de literatura

Bioinformática es la aplicación de tecnologías computacionales y la estadística a la gestión y análisis de datos biológicos como lo son las secuencias de ADN y de proteínas (Can, 2014). En esta área se ha evidenciado una creciente necesidad de usabilidad en las herramientas utilizadas para la investigación, con el fin de conseguir un manejo adecuado de la gran cantidad de información que se utiliza (Bolchini et al., 2009). Además, actualmente es evidente la escasez de investigaciones sobre usabilidad en servicios web bioinformáticos (Bolchini et al., 2009). Estos servicios presentan características particulares que los diferencian de otros tipos de software. Además, sus usuarios presentan necesidades distintas. Por ejemplo, las barreras de usabilidad pueden inhibir la satisfacción de la experiencia de usuario y forzar a los investigadores a desperdiciar tiempo y energía en realizar tareas cotidianas en sus trabajos (Bolchini et al., 2009). Es por ello que, en este trabajo de investigación, se busca realizar una revisión de literatura que permita conocer los trabajos relacionados a la usabilidad en servicios web bioinformáticos.Trabajo de investigació

Evaluation of the Usability of Admission and Medical Record Information System: A Heuristic Evaluation

Introduction: Admission and medical record system (AMRS) is one of the most important subsystems of hospital information system, which is used by many users in admission, discharge, and health information management. Interface usability problems can reduce user speed, precision, and efficiency in user-system interaction. This study aimed to identify the usability problems of AMRS in a hospital information system. Method: In this descriptive cross-sectional study, five health information technology experts evaluated AMRS in a hospital information system using heuristic evaluation. Then, the system usability problems were categorized according to Nielsen's 10 usability principles and their severity were determined. Results: Totally, 62 unique usability problems were detected. The most frequent problems were related to "consistency and standards" (n=9) and ''recognition rather than recall" (n=9), and the least frequent ones was related to "flexibility and efficiency of use" (n=1). 59.7% of the identified problems were categorized as big and severe problems. The highest average severity of problems belonged to "system’s visibility" and "aesthetic and minimalist design", and the least average severity belonged to "error prevention". Conclusion: Using heuristic evaluation, a large number of usability problems in AMRS were identified. According to experts' opinions, most of the HIS interface problems were big and severe, and they need to be modified by designers and developers of these systems

A Preliminary Usability Study of the Dryad Database of Biological Data

This paper reports on a usability test (n=10) that evaluated the web interface of the Dryad repository of biological data. Participants, mostly biologists, were asked to find information about the database, find and download data, and upload data. These three workflows were tested with a card sorting procedure and a think-aloud protocol. The results suggest that biologists interact with online database systems much like non- biologists; color, placement, and size of buttons and text were important determiners of recognition and acknowledgement. However, while most web users prefer browsing to seek information on new websites, participants in this study preferred searching. Most participants did not arrive at the website at the homepage, and thus reported a lack of information about Dryad at their initial entry point. Recommendations for enhancing Dryad specifically and web database interfaces in general are included.Master of Science in Information Scienc

BioCreative III interactive task: an overview

The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested

Proposing electronic health record usability requirements based on enriched ISO 9241 metric usability model

Abstract Introduction: System usability assessment is among the important aspects in assessing the quality of clinical information technology, especially when the end users of the system are concerned. This study aims at providing a comprehensive list of system usability. Methods: This research is a descriptive cross-sectional one conducted using Delphi technique in three phases in 2013. After experts’ ideas were concluded, the final version of the questionnaire including 163 items in three phases was presented to 40 users of information systems in hospitals. The grading ranged from 0-4. Data analysis was conducted using SPSS software. Those requirements with a mean point of three or higher were finally confirmed. Results: The list of system usability requirements for electronic health record was designed and confirmed in nine areas including suitability for the task (24 items), self-descriptiveness (22 items), controllability (19 questions), conformity with user expectations (25 items), error tolerance (21 items), suitability for individualization (7 items), suitability for learning (19 items), visual clarity (18 items) and auditory presentation (8 items). Conclusion: A relatively comprehensive model including useful requirements for using EHR was presented which can increase functionality, effectiveness and users’ satisfaction. Thus, it is suggested that the present model be adopted by system designers and healthcare system institutions to assess those systems. Keywords: Electronic Health Records, Information System, Information Technolog

Bioinformática de circRNAS : análise em modelos animais do Transtorno do Espectro Autista e desenvolvimento de um método de avaliação da usabilidade dos softwares utilizados para identificação

O Transtorno do Espectro Autista (TEA) é um transtorno do neurodesenvolvimento caracterizado por prejuízos na comunicação e interação social, comportamentos repetitivos e interesses restritos. Estima-se que, mundialmente, 1% da população é afetada pela condição. A etiologia do TEA é desconhecida, porém sabe-se que existe uma contribuição complexa de fatores ambientais e genéticos para o desenvolvimento do transtorno. Alterações transcritômicas são consistentemente observadas no sistema nervoso central de indivíduos com TEA e não estão restritas a expressão de genes codificantes. Uma classe de RNAs não-codificantes de interesse especialmente recente é a dos RNAs circulares (circRNAs). Os circRNAs são abundantes no encéfalo e podem desempenhar funções variadas como competir pela ligação de miRNAs, estimular a transcrição do gene parental e ser traduzido em proteínas funcionais. O envolvimento dos circRNAs no TEA ainda é pouco explorado. Recentemente foram feitas as primeiras observações de circRNAs diferencialmente expressos (CDE) no córtex cerebral de indivíduos com TEA. Adicionalmente, CDE também foram observados em dois modelos animais de TEA. Modelos animais são essenciais para o estudo de transtornos do neurodesenvolvimento e podem auxiliar os pesquisadores a investigar a etiologia e os mecanismos biológicos subjacentes. A detecção em massa e a descoberta de novos circRNAs depende quase exclusivamente de softwares de identificação de circRNA. Entretanto, possíveis problemas na usabilidade dessas ferramentas são relatados na literatura e podem prejudicar os usuários ao consumir tempo e dificultar a reprodutibilidade das análises. Considerando o potencial envolvimento de circRNAs no TEA e a dependência metodológica de softwares para identificação, a presente tese analisa por bioinformática a expressão gênica de circRNAs no encéfalo de diferentes modelos animais de TEA, assim como desenvolver um método de avaliação e melhoramento da usabilidade das ferramentas de bioinformática utilizadas para a identificação dos circRNAs. No Capítulo I, identificamos milhares de circRNAs em diferentes modelos animais de TEA em camundongos e demonstramos que as alterações na expressão estão relacionadas principalmente às funcionalidades sinápticas. No Capítulo II, identificamos parcialmente a sequência do circRNA ciRS-7 no modelo animal de ratos induzidos por ácido valproico. Demonstramos que a expressão de ciRS-7 está elevada, assim como encontrada nos modelos Ash1L, BTBR e Kmt5b no Capítulo I, e que funções sinápticas estão entre os possíveis grupos funcionais afetados. Por fim, no Capítulo III, identificamos os problemas de usabilidade das ferramentas de identificação de circRNAs utilizadas nos Capítulos I e II. Também criamos um conjunto de regras para auxiliar os desenvolvedores desse tipo de software para criarem ferramentas mais utilizáveis para os usuários finais. Em conjunto, os resultados apresentam um panorama do envolvimento de circRNAs no TEA a partir de modelos animais. Além disso, apresentamos um novo método de avaliação de usabilidade de software que deve possibilitar que futuras análises estejam alinhadas com as necessidades e expectativas de uso de ferramentas de identificação de circRNAs.Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in communication and social interaction, repetitive behaviors, and restricted interests. It is estimated that the condition affects 1% of the population worldwide. The etiology of ASD is unknown, but it is known that there is a complex contribution of environmental and genetic factors to the development of the disorder. Transcriptomic alterations are consistently observed in the central nervous system of individuals with ASD and are not restricted to the expression of coding genes. Circular RNAs (circRNAs) are a class of noncoding RNAs of recent interest. CircRNAs are abundant in the brain and can perform varied functions, such as competing for binding miRNAs, stimulating parental gene transcription, and being translated into functional proteins. The involvement of circRNAs in ASD is still poorly explored. Recently, the first observations of differentially expressed circRNAs (DECs) were made in the cerebral cortex of individuals with ASD. Additionally, DECs were also observed in two animal models of ASD. Animal models are essential for studying neurodevelopmental disorders and can help researchers investigate the etiology and underlying biological mechanisms. The mass detection and discovery of novel circRNAs rely almost exclusively on circRNA identification software. However, potential problems in the usability of these tools are reported in the literature and may harm users by consuming time and hindering the reproducibility of analyses. Considering the potential involvement of circRNAs in ASD and the methodological dependence on software for identification, this thesis analyzes by bioinformatics the gene expression of circRNAs in the brain of different animal models of ASD, as well as develops a method to evaluate and improve the usability of bioinformatics tools used for circRNA identification. In Chapter I, we identify thousands of circRNAs in different animal models of ASD in mice and demonstrate that the changes in expression are mainly related to synaptic functionalities. In Chapter II, we partially identify the sequence of the circRNA ciRS-7 in the valproic acid-induced rat model. We demonstrate that ciRS- 7 expression is elevated, as found in the Ash1L, BTBR, and Kmt5b models in Chapter I, and that synaptic functions are among the possible functional groups affected. Finally, in Chapter III, we identify the usability problems of the circRNAs identification tools used in Chapters I and II. We also create a set of rules to assist developers of such software in creating more usable tools for end users. Taken together, the results present an overview of the involvement of circRNAs in ASD from the perspective of animal models. In addition, we present a new software usability evaluation method that should enable future analyses to be aligned with the needs and expectations of using circRNAs identification tools