[show abstract][hide abstract] ABSTRACT: This paper explores the issues around the construction of large-scale complex
systems which are built as 'systems of systems' and suggests that there are
fundamental reasons, derived from the inherent complexity in these systems, why
our current software engineering methods and techniques cannot be scaled up to
cope with the engineering challenges of constructing such systems. It then goes
on to propose a research and education agenda for software engineering that
identifies the major challenges and issues in the development of large-scale
complex, software-intensive systems. Central to this is the notion that we
cannot separate software from the socio-technical environment in which it is
Dave Cliff added a full-text to this article and 2 others.
[show abstract][hide abstract] ABSTRACT: Biologists are increasingly confronted with the challenge of quickly understanding genome-wide biological data, which usually involve a large number of genomic coordinates (e.g. genes) but a much smaller number of samples. To meet the need for data of this shape, we present an open-source package called 'supraHex' for training, analysing and visualising omics data. This package devises a supra-hexagonal map to self-organise the input data, offers scalable functionalities for post-analysing the map, and more importantly, allows for overlaying additional data to explore possible relationships, via the specific application to DNA replication timing data of mouse embryogenesis, we demonstrate that supraHex is capable of simultaneously carrying out gene clustering and sample correlation, providing intuitive visualisation at each step of the analysis. By overlaying CpG and expression data onto the trained replication-timing map, we also show that supraHex is able to intuitively capture an inherent relationship between late replication of low CpG density promoters and low expression levels. As part of the Bioconductor project, supraHex makes accessible to a wide community in a simple way, what would otherwise be a complex framework for the ultrafast understanding of any tabular omics data, both scientifically and artistically. This package can run on Windows, Mac and Linux, and is freely available together with many tutorials on featuring real examples at http://supfam.org/SUPERFAMILY/dcGO/supraHex.html.
Biochemical and Biophysical Research Communications 12/2013;