Streaming visualisation of quantitative mass spectrometry data based on a novel raw signal decomposition method

As data rates rise, there is a danger that informatics for high-throughput LC-MS becomes more opaque and inaccessible to practitioners. It is therefore critical that efficient visualisation tools are available to facilitate quality control, verification, validation, interpretation, and sharing of raw MS data and the results of MS analyses. Currently, MS data is stored as contiguous spectra. Recall of individual spectra is quick but panoramas, zooming and panning across whole datasets necessitates processing/memory overheads impractical for interactive use. Moreover, visualisation is challenging if significant quantification data is missing due to data-dependent acquisition of MS/MS spectra. In order to tackle these issues, we leverage our seaMass technique for novel signal decomposition. LC-MS data is modelled as a 2D surface through selection of a sparse set of weighted B-spline basis functions from an over-complete dictionary. By ordering and spatially partitioning the weights with an R-tree data model, efficient streaming visualisations are achieved. In this paper, we describe the core MS1 visualisation engine and overlay of MS/MS annotations. This enables the mass spectrometrist to quickly inspect whole runs for ionisation/chromatographic issues, MS/MS precursors for coverage problems, or putative biomarkers for interferences, for example. The open-source software is available from http://seamass.net/viz/

Visualisation for validation

Animation is a multiple graphical view of a process in action. Animation has been successfully employed in programming for designing, developing and debugging programs or monitoring their performance. This paper advocates that many benefits can be accrued from the use of visualisation techniques for the purpose of validating conceptual specifications during Requirements Engineering. To this end, the paper describes a visualisation system which makes use of three interrelated conceptual models and their metamodel represented uniformly in a repository and an animation algorithm which generates graphical views corresponding to the behaviour of an application domain as specified by the conceptual models

PyZX: Large Scale Automated Diagrammatic Reasoning

The ZX-calculus is a graphical language for reasoning about ZX-diagrams, a type of tensor networks that can represent arbitrary linear maps between qubits. Using the ZX-calculus, we can intuitively reason about quantum theory, and optimise and validate quantum circuits. In this paper we introduce PyZX, an open source library for automated reasoning with large ZX-diagrams. We give a brief introduction to the ZX-calculus, then show how PyZX implements methods for circuit optimisation, equality validation, and visualisation and how it can be used in tandem with other software. We end with a set of challenges that when solved would enhance the utility of automated diagrammatic reasoning.Comment: In Proceedings QPL 2019, arXiv:2004.1475

E-BioFlow: Different Perspectives on Scientific Workflows

We introduce a new type of workflow design system called\ud e-BioFlow and illustrate it by means of a simple sequence alignment workflow. E-BioFlow, intended to model advanced scientific workflows, enables the user to model a workflow from three different but strongly coupled perspectives: the control flow perspective, the data flow perspective, and the resource perspective. All three perspectives are of\ud equal importance, but workflow designers from different domains prefer different perspectives as entry points for their design, and a single workflow designer may prefer different perspectives in different stages of workflow design. Each perspective provides its own type of information, visualisation and support for validation. Combining these three perspectives in a single application provides a new and flexible way of modelling workflows

Requirements for Topology in 3D GIS

Topology and its various benefits are well understood within the context of 2D Geographical Information Systems. However, requirements in three-dimensional (3D) applications have yet to be defined, with factors such as lack of users' familiarity with the potential of such systems impeding this process. In this paper, we identify and review a number of requirements for topology in 3D applications. The review utilises existing topological frameworks and data models as a starting point. Three key areas were studied for the purposes of requirements identification, namely existing 2D topological systems, requirements for visualisation in 3D and requirements for 3D analysis supported by topology. This was followed by analysis of application areas such as earth sciences and urban modelling which are traditionally associated with GIS, as well as others including medical, biological and chemical science. Requirements for topological functionality in 3D were then grouped and categorised. The paper concludes by suggesting that these requirements can be used as a basis for the implementation of topology in 3D. It is the aim of this review to serve as a focus for further discussion and identification of additional applications that would benefit from 3D topology. © 2006 The Authors. Journal compilation © 2006 Blackwell Publishing Ltd

Analysis and evaluation of uncertainty for conducted and radiated emissions tests

Whenever an EMC measurement is made, there are numerous uncertainties in different parts of the measurement system and even in the EMC performance of the equipment under test (EUT) which is being measured. It is important to be able to estimate the overall uncertainty, in particular, the test setup and measurement equipment uncertainty. However, making repetitive measurements can reduce the measurement uncertainty, but often economics of time do not permit that. Therefore, a practical process, which is used to evaluate uncertainty in EMC measurement a, according to the principle of uncertainty and conditions in EMC measurement is presented. In this study, an efficient analysis of uncertainty for both radiated and conducted emissions tests is performed. The uncertainty of each contributor had been calculated and evaluating the reported expanded uncertainty of measurement is stated as the standard uncertainty of measurement. This standard uncertainty is multiplied by the coverage factor k=2, which for a normal distribution corresponds to a coverage probability of approximately 95%. The result of calculating the uncertainty for both conducted and radiated emission tests showed that the overall uncertainty of the system is high and it must be lowered by reducing the expanded uncertainty for the dominant contributors for both tests. In addition, the result of applying the concept of CISPR uncertainty for both conducted and radiated emission tests showed that non-compliance is deemed to occur for both EUT of both tests. This is due to the result that the measured disturbances increased by ( ), above the disturbance limit

UK Research Information Shared Service (UKRISS) Final Report, July 2014

The reporting of research information is a complex and expensive activity for research organisations (ROs). There is little alignment between funders of the reporting requests made to institutions and requests made to individual researchers about their research outputs and outcomes. This inevitably results in duplication and increased costs across the sector, whilst limiting the potential sharing and reuse of the information. The UK Research Information Shared Service (UKRISS) project conducted a feasibility and scoping study for the reporting of research information at a national level based on CERIF (Common European Research Information Format), with the objective of increasing efficiency, productivity and quality across the sector. The aim was to define and prototype solutions which are compelling, easy to use, have a low entry barrier, and support innovative information sharing and benchmarking. CERIF has emerged as the preferred format for expressing research information across Europe. To date, CERIF has been piloted for specific applications, but not as a format for reporting requirements across all UK ROs. The final report presents the work carried out by the UKRISS project, including requirements gathering, modelling and prototyping, as well as recommendation for sustainability. UKRISS was divided into two phases. Phase 1, mapping the reporting landscape, ran from March 2012 to December 2012. Phase 2, exploring delivery of potential solutions, began in February 2013 and ended in December 2013

Experimental Test Rig For The Visualisation Study Of The Transcritical Flow In The Two-Phase R744 Ejectors

Recent studies have provided the significant number of approaches to enhance the performance of a twophase ejector, especially for transcritical CO2 cycles. However, the investigation of the mixing process is still challenging matter due to the highspeed fluid flow coupled with mixing of vapour and partially evaporated liquid stream. On the other hand, these phenomena directly influence the ejector efficiency. The behaviour of the aforementioned processes would be valuable for validation the numerical models as well as a required control of the system operation. Hence, in this work, the laboratory test rig for visualisation of the CO2 ejector mixing processes along suction nozzle, premixing chamber and diffuser was developed and manufactured. The visualisation techniques used for this study include the highspeed camera recordings and PIV measurements. The work consists of installation description, including the measurement approaches, solution predicted by the computational model for the transparent construction of the ejector and visualisation procedures. The selected onand offdesign operating points were described having regard ejector performance factors and its correlation with the output of the visualisation procedure