Version control of pathway models using XML patches

<p>Background: Computational modelling has become an important tool in understanding biological systems such as signalling pathways. With an increase in size complexity of models comes a need for techniques to manage model versions and their relationship to one another. Model version control for pathway models shares some of the features of software version control but has a number of differences that warrant a specific solution.</p> <p>Results: We present a model version control method, along with a prototype implementation, based on XML patches. We show its application to the EGF/RAS/RAF pathway.</p> <p>Conclusion: Our method allows quick and convenient storage of a wide range of model variations and enables a thorough explanation of these variations. Trying to produce these results without such methods results in slow and cumbersome development that is prone to frustration and human error.</p&gt

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

http://dx.doi.org/10.1093/bib/bbn026Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ..

Texas Business Review, August 1967

The Business Situation in Texas; Climatology at Work in Texas; Texas Building Construction, January-June 1967; Texas Retail Sales, January-June 1967Bureau of Business Researc

In-work poverty in the East Midlands

Research that explores the nature and scale of in-work poverty in the East Midlands, using several established measures

Decomposing the Univalence Axiom

This paper investigates Voevodsky's univalence axiom in intensional Martin-Löf type theory. In particular, it looks at how univalence can be derived from simpler axioms. We first present some existing work, collected together from various published and unpublished sources; we then present a new decomposition of the univalence axiom into simpler axioms. We argue that these axioms are easier to verify in certain potential models of univalent type theory, particularly those models based on cubical sets. Finally we show how this decomposition is relevant to an open problem in type theory

Far infrared and submillimeter brightness temperatures of the giant planets

The brightness temperatures of Jupiter, Saturn, Uranus, and Neptune in the range 35 to 1000 micron. The effective temperatures derived from the measurements, supplemented by shorter wavelength Voyager data for Jupiter and Saturn, are 126.8 + or - 4.5 K, 93.4 + or - 3.3 K, 58.3 + or - 2.0 K, and 60.3 + or - 2.0 K, respectively. The implications of the measurements for bolometric output and for atmospheric structure and composition are discussed. The temperature spectrum of Jupiter shows a strong peak at approx. 350 microns followed by a deep valley at approx. 450 to 500 microns. Spectra derived from model atmospheres qualitatively reproduced these features but do not fit the data closely