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Full-Text Articles in Physical Sciences and Mathematics
The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor
The Role Of Software Engineering In Bioinformatics, Brendan Sean Lawlor
Theses
This thesis proposes that by applying state-of-the-art software engineering tools, techniques and frameworks to currently recognised challenges in bioinformatics, improved outcomes can be attained in that field. It begins by decomposing software engineering into two categories, namely process and architecture, and choosing two key challenges in the practice of bioinformatics: reproducibility and scalability. The body of the thesis is an exploration of the intersection between these two software engineering categories and these two bioinformatics challenges. The question is asked: Can best practices in professional software engineering be applied to address key issues in the bioinformatics domain, creating positive outcomes? And …
Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh
Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh
Department of Computer Science Publications
One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to …