Human Factors in the Design and Evaluation of Bioinformatics Tools

Al-Ageel, Naelah; Al-Wabil, Areej; Badr, Ghada; Alomar, Noura

doi:10.1016/j.promfg.2015.07.247

Cited by 14 publications

(8 citation statements)

References 9 publications

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“…Most tools that are developed and published in the area of bioinformatics do not always consider the user perspective and requirements first [41]. One recommendation from the meeting is to start thinking about how to incentivize more user-centered design principles [42].…”

Section: Software and Systemsmentioning

confidence: 99%

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

Jagodnik

Koplev

Jenkins

et al. 2017

Journal of Biomedical Informatics

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The volume and diversity of data in biomedical research has been rapidly increasing in recent years. While such data hold significant promise for accelerating discovery, their use entails many challenges including: the need for adequate computational infrastructure, secure processes for data sharing and access, tools that allow researchers to find and integrate diverse datasets, and standardized methods of analysis. These are just some elements of a complex ecosystem that needs to be built to support the rapid accumulation of these data. The NIH Big Data to Knowledge (BD2K) initiative aims to facilitate digitally enabled biomedical research. Within the BD2K framework, the Commons initiative is intended to establish a virtual environment that will facilitate the use, interoperability, and discoverability of shared digital objects used for research. The BD2K Commons Framework Pilots Working Group (CFPWG) was established to clarify goals and work on pilot projects that would address existing gaps toward realizing the vision of the BD2K Commons. This report reviews highlights from a two-day meeting involving the BD2K CFPWG to provide insights on trends and considerations in advancing Big Data science for biomedical research in the United States.

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Section: Software and Systemsmentioning

confidence: 99%

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

Jagodnik

Koplev

Jenkins

et al. 2017

Journal of Biomedical Informatics

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“…It involves the union of computer science, mathematics, statistics and molecular biology [5]. It is in this context that the area grows exponentially [6][7][8][9]. Studies [7,[9][10][11] indicate a growth in the supply of computational resources in support of the area.…”

Section: Introductionmentioning

confidence: 99%

“…It is in this context that the area grows exponentially [6][7][8][9]. Studies [7,[9][10][11] indicate a growth in the supply of computational resources in support of the area. Nucleic acids' research presents a series of tools, like biological databases (database issue, https://nar.oxfordjournals.org/content/44/D1.toc ) and web-based software resources (web server issue, https://academic.oup.com/nar/issue/44/W1).…”

Section: Introductionmentioning

confidence: 99%

“…Theoretical and empirical research reports demonstrate usability problems in various bioinformatics systems. Studies [9,[11][12][13][14][15][16][17][18][19][20] point out usability limitations in bioinformatics tools such as difficulties related to the high workload required to access information and having to use command line interfaces, commonly used in bioinformatics. Pavelin [21] highlights navigability issues at interfaces.…”

Section: Introductionmentioning

confidence: 99%

“…Considering that how people perceive and interact with bioinformatics tools can influence the understanding of the data and the results of the analysis [16], the study of the factors that affect users' experiences in the use of interactive biological systems is essential [9]. Thus, usability should be a persistent concern in bioinformatics systems given the amount of information they need to handle and visualize using several tools with many different capabilities [17].…”

Section: Introductionmentioning

confidence: 99%

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Usability as the Key Factor to the Design of a Web Server for the CReF Protein Structure Predictor: The wCReF

et al. 2018

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Abstract:Protein structure prediction servers use various computational methods to predict the three-dimensional structure of proteins from their amino acid sequence. Predicted models are used to infer protein function and guide experimental efforts. This can contribute to solving the problem of predicting tertiary protein structures, one of the main unsolved problems in bioinformatics. The challenge is to understand the relationship between the amino acid sequence of a protein and its three-dimensional structure, which is related to the function of these macromolecules. This article is an extended version of the article wCReF: The Web Server for the Central Residue Fragment-based Method (CReF) Protein Structure Predictor, published in the 14th International Conference on Information Technology: New Generations. In the first version, we presented the wCReF, a protein structure prediction server for the central residue fragment-based method. The wCReF interface was developed with a focus on usability and user interaction. With this tool, users can enter the amino acid sequence of their target protein and obtain its approximate 3D structure without the need to install all the multitude of necessary tools. In this extended version, we present the design process of the prediction server in detail, which includes: (A) identification of user needs: aiming at understanding the features of a protein structure prediction server, the end user profiles and the commonly-performed tasks; (B) server usability inspection: in order to define wCReF's requirements and features, we have used heuristic evaluation guided by experts in both the human-computer interaction and bioinformatics domain areas, applied to the protein structure prediction servers I-TASSER, QUARK and Robetta; as a result, changes were found in all heuristics resulting in 89 usability problems; (C) software requirements document and prototype: assessment results guiding the key features that wCReF must have compiled in a software requirements document; from this step, prototyping was carried out; (D) wCReF usability analysis: a glimpse at the detection of new usability problems with end users by adapting the Ssemugabi satisfaction questionnaire; users' evaluation had 80% positive feedback; (E) finally, some specific guidelines for interface design are presented, which may contribute to the design of interactive computational resources for the field of bioinformatics. In addition to the results of the original article, we present the methodology used in wCReF's design and evaluation process (sample, procedures, evaluation tools) and the results obtained.

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