15 papers · ranked by Valyu relevance
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma + 3 more
'Jason Papadopoulos' 'Kevin Bealer' 'Thomas L Madden'] Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or…
Sofien Gannouni, Kais Belwafi, Mohammad Reshood Al-Sulmi, Meshal Dawood Al-Farhood + 5 more
'Meshal Dawood Al-Farhood' 'Omar Ali Al-Obaid' 'Abdullah Mohammed Al-Awadh' 'Hatim Aboalsamh' 'Abdelfettah Belghith' 'Saugat Bhattacharyya'] There are many applications controlled by the brain signals to bridge the gap in the digital divide between the disabled and the non-disabled people. The deployment of novel…
Dario Beraldi, John Hancock
The visualization of next generation sequencing data is a fundamental part of genomics enabling the analyst to assess the quality of the results and generate hypotheses. Accordingly, several programs for browsing genomic data are widely popular amongst the genomics community, for example, IGV () or Artemis () are…
Neil Loftus, Husnu S. Narman, Hai Dong
Cybersecurity is a complex subject for students to pursue. Hands-on online learning through labs and simulations can help students become more familiar with the subject at security classes to pursue cybersecurity education. There are several online tools and simulation platforms for cybersecurity education. However…
Torsten Seemann
Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I…
Florian Rupprecht, Jason Kai, Biraj Shrestha, Steven Giavasis + 4 more
'Ting Xu' 'Tristan Glatard' 'Michael P Milham' 'Gregory Kiar'] In numerous scientific domains, established tools have often been developed with complex command-line interfaces. Such is the case for brain imaging and bioinformatics, making the use of powerful legacy tools in modern workflow paradigms challenging. We…
Markus Joppich, Ralf Zimmer, Joseph Gillespie
Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface…
Stanislav A. Listopad, Trina M. Norden-Krichmar
Background Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/regions (DMPs/DMRs), across multiple pairwise comparisons. Large biological studies can involve…
Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas + 7 more
Background Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with…
Paul Hodor, Amandeep Chawla, Andrew Clark, Lauren Neal
Summary: One of the solutions proposed for addressing the challenge of the overwhelming abundance of genomic sequence and other biological data is the use of the Hadoop computing framework. Appropriate tools are needed to set up computational environments that facilitate research of novel bioinformatics methodology…
Ahmed Ibrahem Hafez, Beatriz Soriano, Aya Allah Elsayed, Ricardo Futami + 15 more
'Ricardo Futami' 'Raquel Ceprian' 'Ricardo Ramos-Ruiz' 'Genis Martinez' 'Francisco Jose Roig' 'Miguel Angel Torres-Font' 'Fernando Naya-Catala' 'Josep Alvar Calduch-Giner' 'Lucia Trilla-Fuertes' 'Angelo Gamez-Pozo' 'Vicente Arnau' 'Jose Maria Sempere-Luna' 'Jaume Perez-Sanchez' 'Toni Gabaldon' 'Carlos Llorens' 'Stefano…
Sebastian Beyvers, Lukas Jelonek, Alexander Goesmann, Oliver Schwengers
'Oliver Schwengers'] Title: Abstract The Bakta command line application is widely used and one of the most established tools for bacterial genome annotation. It balances comprehensive annotation with computational efficiency via alignment-free sequence identifications. However, the usage of command line software tools…
Natay Aberra, Aswathy Sebastian, Aaron P. Maloy, Christopher B. Rees + 2 more
'Meredith L. Bartron' 'Istvan Albert'] Background Bioinformaticians collaborating with life scientists need software that allows them to involve their collaborators in the process of data analysis. Results We have developed a web application that allows researchers to publish and execute data analysis scripts. Within…
Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi + 6 more
'Vijini Mallawaarachchi' 'Bhavya Papudeshi' 'Scott A. Handley' 'C. Titus Brown' 'Nathan S. Watson-Haigh' 'Robert A. Edwards' 'Scott Markel'] Introduction As bioinformatics analyses increase in size and complexity, workflow managers are becoming more popular for building pipelines [1-3]. Workflow managers, such as…
Tjelvar S.G. Olsson, Matthew Hartley, Todd Vision
The explosion in volumes and types of data has led to substantial challenges in data management. These challenges are often faced by front-line researchers who are already dealing with rapidly changing technologies and have limited time to devote to data management. There are good high-level guidelines for managing and…