Towards an Algebra for Cascade Effects

We introduce a new class of (dynamical) systems that inherently capture cascading effects (viewed as consequential effects) and are naturally amenable to combinations. We develop an axiomatic general theory around those systems, and guide the endeavor towards an understanding of cascading failure. The theory evolves as an interplay of lattices and fixed points, and its results may be instantiated to commonly studied models of cascade effects. We characterize the systems through their fixed points, and equip them with two operators. We uncover properties of the operators, and express global systems through combinations of local systems. We enhance the theory with a notion of failure, and understand the class of shocks inducing a system to failure. We develop a notion of mu-rank to capture the energy of a system, and understand the minimal amount of effort required to fail a system, termed resilience. We deduce a dual notion of fragility and show that the combination of systems sets a limit on the amount of fragility inherited.Comment: 31 page

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure