Peer-reviewed Articles

8 downloads
146 views

Background Software maintenance is an important activity in the development process where maintenance team members leave and new members join over time. The identification of files which are changed together frequently has been proposed several times. Yet, existing...

["Data Science","Software Engineering"]
doi:10.7717/peerj-cs.135
26 downloads
219 views

User eXperience (UX) is a key factor in the success of software systems. Many software companies face challenges in their work with UX. Existing research does not analyze UX practices and challenges in relation to other software quality characteristics or, in particular,...

["Human-Computer Interaction","Software Engineering"]
doi:10.7717/peerj-cs.130
73 downloads
271 views

GitHub is a widely used online collaborative software development environment. In this paper, we describe curation projects as a new category of GitHub project that collects, evaluates, and preserves resources for software developers. We investigate: (1) what motivates...

["Human-Computer Interaction","Software Engineering"]
doi:10.7717/peerj-cs.134
26 downloads
209 views

Cataloging mutated driver genes that confer a selective growth advantage for tumor cells from sporadic passenger mutations is a critical problem in cancer genomic research. Previous studies have reported that some driver genes are not highly frequently mutated...

["Bioinformatics","Computational Biology"]
doi:10.7717/peerj-cs.133
52 downloads
418 views

Purpose This paper introduces the Research Articles in Simplified HTML (or RASH), which is a Web-first format for writing HTML-based scholarly papers; it is accompanied by the RASH Framework, a set of tools for interacting with RASH-based articles. The paper also...

["Digital Libraries","World Wide Web and Web Science"]
doi:10.7717/peerj-cs.132
70 downloads
695 views

Software engineering education is under constant pressure to provide students with industry-relevant knowledge and skills. Educators must address issues beyond exercises and theories that can be directly rehearsed in small settings. Industry training has similar...

["Computer Education","Software Engineering"]
doi:10.7717/peerj-cs.131
61 downloads
574 views

Background Mass Spectrometry (MS) based chemoproteomics has recently become a main tool to identify and quantify cellular target protein interactions with ligands/drugs in drug discovery. The complexity associated with these new types of data requires scientists...

["Bioinformatics"]
doi:10.7717/peerj-cs.129
135 downloads
945 views

Gathering up-to-date information on food prices is critical in developing regions, as it allows policymakers and development practitioners to rely on accurate data on food security. This study explores the feasibility of utilizing social media as a new data source...

["Data Science","Network Science and Online Social Networks","Social Computing"]
doi:10.7717/peerj-cs.126
99 downloads
631 views

Virtual reality (VR) applications have disseminated throughout several fields, with a special quest for immersion. The avatar is one of the key constituents of immersive applications, and avatar resemblance can provoke diverse emotional responses from the user....

["Human-Computer Interaction","Emerging Technologies"]
doi:10.7717/peerj-cs.128
195 downloads
1,378 views

We present a CUDA-based implementation of a decision tree construction algorithm within the gradient boosting library XGBoost. The tree construction algorithm is executed entirely on the graphics processing unit (GPU) and shows high performance with a variety of...

["Artificial Intelligence","Data Mining and Machine Learning","Data Science"]
doi:10.7717/peerj-cs.127
201 downloads
807 views

Background The availability of large databases containing high resolution three-dimensional (3D) models of proteins in conjunction with functional annotation allows the exploitation of advanced supervised machine learning techniques for automatic protein function...

["Bioinformatics","Computational Biology","Data Mining and Machine Learning"]
doi:10.7717/peerj-cs.124
51 downloads
666 views

CodonGenie, freely available from http://codon.synbiochem.co.uk, is a simple web application for designing ambiguous codons to support protein mutagenesis applications. Ambiguous codons are derived from specific heterogeneous nucleotide mixtures, which create sequence...

["Bioengineering","Bioinformatics","Biotechnology","Computational Biology","Synthetic Biology"]
doi:10.7717/peerj-cs.120
51 downloads
541 views

The unit of experimental measurement in a variety of scientific applications is the one-dimensional (1D) continuum: a dependent variable whose value is measured repeatedly, often at regular intervals, in time or space. A variety of software packages exist for computing...

["Scientific Computing and Simulation","Programming Languages"]
doi:10.7717/peerj-cs.125
99 downloads
535 views

Objects of more than three dimensions can be used to model geographic phenomena that occur in space, time and scale. For instance, a single 4D object can be used to represent the changes in a 3D object’s shape across time or all its optimal representations at various...

["Graphics","Scientific Computing and Simulation","Spatial and Geographic Information Systems"]
doi:10.7717/peerj-cs.123
80 downloads
719 views

Despite recent algorithmic improvements, learning the optimal structure of a Bayesian network from data is typically infeasible past a few dozen variables. Fortunately, domain knowledge can frequently be exploited to achieve dramatic computational savings, and...

["Artificial Intelligence","Data Mining and Machine Learning","Data Science","Distributed and Parallel Computing"]
doi:10.7717/peerj-cs.122

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