Viewpoint consistency in Z and LOTOS: A case study

Specification by viewpoints is advocated as a suitable method of specifying complex systems. Each viewpoint describes the envisaged system from a particular perspective, using concepts and specification languages best suited for that perspective. Inherent in any viewpoint approach is the need to check or manage the consistency of viewpoints and to show that the different viewpoints do not impose contradictory requirements. In previous work we have described a range of techniques for consistency checking, refinement, and translation between viewpoint specifications, in particular for the languages LOTOS and Z. These two languages are advocated in a particular viewpoint model, viz. that of the Open Distributed Processing (ODP) reference model. In this paper we present a case study which demonstrates how all these techniques can be combined in order to show consistency between a viewpoint specified in LOTOS and one specified in Z. Keywords: Viewpoints; Consistency; Z; LOTOS; ODP

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account. Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method

Precision measurements of large scale structure with future type Ia supernova surveys

Type Ia supernovae are currently the best known standard candles at cosmological distances. In addition to providing a powerful probe of dark energy they are an ideal source of information about the peculiar velocity field of the local universe. Even with the very small number of supernovae presently available it has been possible to measure the dipole and quadrupole of the local velocity field out to z~0.025. With future continuous all-sky surveys like the LSST project the luminosity distances of tens of thousands of nearby supernovae will be measured accurately. This will allow for a determination of the local velocity structure of the universe as a function of redshift with unprecedented accuracy, provided the redshifts of the host galaxies are known. Using catalogues of mock surveys we estimate that future low redshift supernova surveys will be able to probe sigma-8 to a precision of roughly 5% at 95% C.L. This is comparable to the precision in future galaxy and weak lensing surveys and with a relatively modest observational effort it will provide a crucial cross-check on future measurements of the matter power spectrum.Comment: 18 pages, 9 figures, submitted to JCA