Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Subliminally Perceived Odours Modulate Female Intrasexual Competition: An Eye Movement Study

Background: Evidence suggests that subliminal odorants influence human perception and behavior. It has been hypothesized that the human sex-steroid derived compound 4,16-androstadien-3-one (androstadienone) functions as a human chemosignal. The most intensively studied steroid compound, androstadienone is known to be biologically relevant since it seems to convey information about male mate quality to women. It is unclear if the effects of androstadienone are menstrual cycle related. Methodology/Principal Findings: In the first experiment, heterosexual women were exposed to androstadienone or a control compound and asked to view stimuli such as female faces, male faces and familiar objects while their eye movements were recorded. In the second experiment the same women were asked to rate the level of stimuli attractiveness following exposure to the study or control compound. The results indicated that women at high conception risk spent more time viewing the female than the male faces regardless of the compound administered. Women at a low conception risk exhibited a preference for female faces only following exposure to androstadienone. Conclusions/Significance: We contend that a woman’s level of fertility influences her evaluation of potential competitors (e.g., faces of other women) during times critical for reproduction. Subliminally perceived odorants, such as androstadienone, might similarly enhance intrasexual competition strategies in women during fertility phases not critica

A High-Level Language for Rule-Based Modelling

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages