A Behavioral Characterization of Plausible Priors

One of the last great novels of José Saramago, Death with Interruptions, begins with an epigraph taken from Ludwig Wittgenstein: “If, for example, you were to think more deeply about death, then it would be truly strange if, in so doing, you did not encounter new images, new linguistic fields”. The aim of my paper is to ponder on what kind of a new language game the Portuguese writer is offering us in his book and how to interpret his investigations from the angle of another contemporary literary and philosophical thanatological discourses.One of the last great novels of José Saramago, Death with Interruptions, begins with an epigraph taken from Ludwig Wittgenstein: “If, for example, you were to think more deeply about death, then it would be truly strange if, in so doing, you did not encounter new images, new linguistic fields”. The aim of my paper is to ponder on what kind of a new language game the Portuguese writer is offering us in his book and how to interpret his investigations from the angle of another contemporary literary and philosophical thanatological discourses

Phenotype ontologies for mouse and man: bridging the semantic gap

A major challenge of the post-genomic era is coding phenotype data from humans and model organisms such as the mouse, to permit the meaningful translation of phenotype descriptions between species. This ability is essential if we are to facilitate phenotype-driven gene function discovery and empower comparative pathobiology. Here, we review the current state of the art for phenotype and disease description in mice and humans, and discuss ways in which the semantic gap between coding systems might be bridged to facilitate the discovery and exploitation of new mouse models of human diseases

Prospects for Declarative Mathematical Modeling of Complex Biological Systems

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation program, in a general-purpose programming language. Examples of such computations on models include model analysis, relatively general-purpose model-reduction maps, and the initial phases of model implementation, all of which should preserve or approximate the mathematical semantics of a complex biological model. The potential advantages are particularly relevant in the case of developmental modeling, wherein complex spatial structures exhibit dynamics at molecular, cellular, and organogenic levels to relate genotype to multicellular phenotype. Multiscale modeling can benefit from both the expressive power of declarative modeling languages and the application of model reduction methods to link models across scale. Based on previous work, here we define declarative modeling of complex biological systems by defining the operator algebra semantics of an increasingly powerful series of declarative modeling languages including reaction-like dynamics of parameterized and extended objects; we define semantics-preserving implementation and semantics-approximating model reduction transformations; and we outline a "meta-hierarchy" for organizing declarative models and the mathematical methods that can fruitfully manipulate them