39 research outputs found

    Programming with models: modularity and abstraction provide powerful capabilities for systems biology

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    Mathematical models are increasingly used to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations presents a fundamental barrier to progress. Overcoming this requires modularity, enabling sub-systems to be specified independently and combined incrementally, and abstraction, enabling generic properties of biological processes to be specified independently of specific instances. These, in turn, require models to be represented as programs rather than as datatypes. Programmable modularity and abstraction enables libraries of modules to be created, which can be instantiated and reused repeatedly in different contexts with different components. We have developed a computational infrastructure that accomplishes this. We show here why such capabilities are needed, what is required to implement them and what can be accomplished with them that could not be done previously

    Multiple voices: A virtual discussion

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    Directional sensitivity of the retina: 75 years of Stiles–Crawford effect

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    The reduction of the brightness when a light beam's entry into the eye is shifted from the centre to the edge of the pupil has from the outset been shown to be due to a change in luminous efficiency of radiation when it is incident obliquely on the retina. The phenomenon is most prominent in photopic vision and this has concentrated attention on the properties of retinal cones, where responsibility has yet to be assigned to factors such as differences in shape, fine structure and configuration, and membrane anchoring of photopigment molecules. Geometrical optics and waveguide formulations have been applied to the question of how light is guided in receptors, but details of their geometry and optical parameters even if they become available will make calculations complex and of only moderate generality. In practice, the diminution of oblique light helps visual performance by reducing deleterious influence of ocular aberrations and of glare caused by light scattering when the pupil is wide. Receptor orientation can come into play in ocular conditions due to mechanical disturbance and has been shown to have potentiality as a tool for clinical diagnosis. Currently, open questions include microanatomical and molecular differences between rods and cones, the coupling of the optical image of the eye with the transducing apparatus in the photoreceptors, possible phototropism and more convincing methods of estimating the actual spatial distribution of photon events as it affects visual resolution
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