Background Bioinformatics software tools are often created ad hoc, frequently by people
without extensive training in software development. In particular, for beginners, the barrier to …

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 …

Background Life scientists routinely face massive and heterogeneous data analysis tasks
and must find and access the most suitable databases or software in a jungle of web …

Software design and sustainable software engineering are essential for the long-term
development of bioinformatics software. Typical challenges in an academic environment are …

Motivation: The analysis of large biological datasets often requires complex processing
pipelines that run for a long time on large computational infrastructures. We designed and …

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life
sciences, has played a crucial role in advancing data-driven research since the 2010s. As …

Background There is a huge demand on bioinformaticians to provide their biologists with
user friendly and scalable software infrastructures to capture, exchange, and exploit the …

Motivation A challenge for computational biologists is to make our analyses reproducible—
ie to rerun, combine, and share, with the assurance that equivalent runs will generate …

Most bioinformatics tools available today were not written by professional software
developers, but by people that wanted to solve their own problems, using computational …

Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for
scientists from many disciplines. Installing and starting applications on the command-line …