Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample ...processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.
Immersive virtual- and augmented-reality headsets can overlay a flat image against any surface or hang virtual objects in the space around the user. The technology is rapidly improving and may, in ...the long term, replace traditional flat panel displays in many situations. When displays are no longer intrinsically flat, how should we use the space around the user for abstract data visualisation? In this paper, we ask this question with respect to origin-destination flow data in a global geographic context. We report on the findings of three studies exploring different spatial encodings for flow maps. The first experiment focuses on different 2D and 3D encodings for flows on flat maps. We find that participants are significantly more accurate with raised flow paths whose height is proportional to flow distance but fastest with traditional straight line 2D flows. In our second and third experiment we compared flat maps, 3D globes and a novel interactive design we call MapsLink , involving a pair of linked flat maps. We find that participants took significantly more time with MapsLink than other flow maps while the 3D globe with raised flows was the fastest, most accurate, and most preferred method. Our work suggests that careful use of the third spatial dimension can resolve visual clutter in complex flow maps.
Flow visualisation is an attractive topic in data visualisation, offering great challenges for research. Very large data sets must be processed, consisting of multivariate data at large numbers of ...grid points, often arranged in many time steps. Recently, the steadily increasing performance of computers again has become a driving force for new advances in flow visualisation, especially in techniques based on texturing, feature extraction, vector field clustering, and topology extraction.
In this article we present the state of the art in feature‐based flow visualisation techniques. We will present numerous feature extraction techniques, categorised according to the type of feature. Next, feature tracking and event detection algorithms are discussed, for studying the evolution of features in time‐dependent data sets. Finally, various visualisation techniques are demonstrated.
ACM CSS: I.3.8 Computer Graphics—applications
•Identifies a significant lack of research into analytics in operational research orientated publications.•Charts the histories of operational research, analytics and a range of related ...disciplines.•Discussed the relationship between these disciplines and how they are perceived by the wider business community.•Provides suggested routes for future research that can combine key themes in analytics and operational research.
The growing attention and prominence afforded to analytics presents a genuine challenge for the operational research community. Many in the community have recognised this growth and sought to align themselves with analytics. For instance, the US operational research society INFORMS now offers analytics related conferences, certification and a magazine. However, as shown in this research, the volume of analytics-orientated studies in journals associated with operational research is comparatively low. This paper seeks to address this paradox by seeking to better understand what analytics is, and how operational research is related to it. To do so literature from a range of academic disciplines is analysed, in what is conceived as concurrent histories in the shared tradition of a management paradigm spread over the last 100 years. The findings of this analysis reveal new insights as to how operational research exists within an ecosystem shared with several other disciplines, and how interactions and ripple effects diffuse knowledge and ideas between each. Whilst this ecosystem is developed and evolved through interdisciplinary collaborations, individual disciplines are cast into competition for the attention of the same business users. These findings are further explored by discussing the implication this has for operational research, as well as considering what directions future research may take to maximise the potential value of these relationships.
•New topology optimised manifold configurations for uniform cooling with a low-pressure drop.•Performance of compact and adaptable manifold configuration demonstrated experimentally.•Flow ...visualisation shows the influence of inlet vortices on flow distribution.•Printed test section provides a convenient milli-fluidic manufacturing method.•Parameter optimisation improves the extraction of geometries from optimised topologies.
The current study proposes compact and adaptable manifold configurations for achieving uniform flow distribution with minimal pressure drop, for electronics cooling and many other industrial applications. Two-dimensional topology optimisation generates new manifold configurations, referred to as mini-baffle and baffle. Both configurations use proportionately sized obstructions to regulate flow distribution and achieve excellent uniformity. Elliptical pins, with parametrically optimised diameters, are adopted to represent the mini-baffle configuration and tested using a three-dimensional model and flow visualisation experiments. Computational results show that introducing these pins reduces the variation of normalised channel flow rates from 19% to 1% with only an 8% increase in the pressure drop, at a Reynolds number of 200. Experimental results support this, with variation reduced from 20% to 7%, the slight increase due to manufacturing limitations. Results also show the influence of vortices, formed at the inlet, on flow distribution. A test section printed in a single piece demonstrates a streamlined and cost-effective manufacturing method for milli-fluidic devices. Coupling topology with parameter optimisation provides a method for accurately extracting discrete optimised geometries for physical manufacturing.
Big Data is an emerging paradigm and has currently become a strong attractor of global interest, specially within the transportation industry. The combination of disruptive technologies and new ...concepts such as the Smart City upgrades the transport data life cycle. In this context, Big Data is considered as a new pledge for the transportation industry to effectively manage all data this sector required for providing safer, cleaner and more efficient transport means, as well as for users to personalize their transport experience. However, Big Data comes along with its own set of technological challenges, stemming from the multiple and heterogeneous transportation/mobility application scenarios. In this survey we analyze the latest research efforts revolving on Big Data for the transportation and mobility industry, its applications, baselines scenarios, fields and use case such as routing, planning, infrastructure monitoring, network design, among others. This analysis will be done strictly from the Big Data perspective, focusing on those contributions gravitating on techniques, tools and methods for modeling, processing, analyzing and visualizing transport and mobility Big Data. From the literature review a set of trends and challenges is extracted so as to provide researchers with an insightful outlook on the field of transport and mobility.
Three‐dimensional (3D) representations of anatomical specimens are increasingly used as learning resources. Photogrammetry is a well‐established technique that can be used to generate 3D models and ...has only been recently applied to produce visualisations of cadaveric specimens. This study has developed a semi‐standardised photogrammetry workflow to produce photorealistic models of human specimens. Eight specimens, each with unique anatomical characteristics, were successfully digitised into interactive 3D models using the described workflow and the strengths and limitations of the technique are described. Various tissue types were reconstructed with apparent preservation of geometry and texture which visually resembled the original specimen. Using this workflow, an institution could digitise their existing cadaveric resources, facilitating the delivery of novel educational experiences.
This paper presents a workflow for using photogrammetry as a method by which to reproduce photorealistic, three‐dimensional (3D) cadaveric specimens with high resolution. The paper guides the anatomist through the photogrammetry process, from selection and staging of cadaveric specimens through to equipment and lighting, image acquisition and 3D reconstruction.
•A deep learning approach to quantify discriminatory leaf is proposed.•Shape is not a dominant feature for leaf but rather the different orders of venation.•Deep learning reveals transformation of ...leaf features from general to specific types.•Findings archived fit with the hierarchical botanical definitions of leaf characters.•Features learned using deep learning can improve plant recognition performance.
Plant identification systems developed by computer vision researchers have helped botanists to recognize and identify unknown plant species more rapidly. Hitherto, numerous studies have focused on procedures or algorithms that maximize the use of leaf databases for plant predictive modeling, but this results in leaf features which are liable to change with different leaf data and feature extraction techniques. In this paper, we learn useful leaf features directly from the raw representations of input data using Convolutional Neural Networks (CNN), and gain intuition of the chosen features based on a Deconvolutional Network (DN) approach. We report somewhat unexpected results: (1) different orders of venation are the best representative features compared to those of outline shape, and (2) we observe multi-level representation in leaf data, demonstrating the hierarchical transformation of features from lower-level to higher-level abstraction, corresponding to species classes. We show that these findings fit with the hierarchical botanical definitions of leaf characters. Through these findings, we gained insights into the design of new hybrid feature extraction models which are able to further improve the discriminative power of plant classification systems. The source code and models are available at: https://github.com/cs-chan/Deep-Plant.
In December 2014, computational biologist Lior Pachter posted the results of his “tongue in cheek” in silico genome experiment on his personal blog, where he declared his discovery that “the perfect ...human is Puerto Rican.” In this article, I analyze the “perfect human” experiment. I argue that despite the use of 21st-century, cutting-edge technology in computing and genomics, Pachter’s experiment and his use of visualization can be usefully juxtaposed with earlier modes of visualizing heredity, namely the development of composite portraiture in the late-19th century and late-20th century technologies of “morphing.” I temper the celebration of Pachter’s creation of a “mixed race” perfect human in silico with a challenge to its ostensibly progressive stance. I instead suggest that it must be understood in the broader context of eugenic hauntings and contemporary tensions around questions of sex, sexuality, race, nation, and indigeneity. I argue that the scientific, specifically genomic, stories that we tell, can be productively read in light of critiques of biogenetic kinship and the naturalization of heterosexual love. I conclude by arguing that the perfect human experiment makes a particular kind of argument about what it means to be human and perfect and what constitutes legitimate and cognizable modes of relationality.
As astronomy becomes increasingly invested in large surveys the ample representation of an individual target becomes a significant challenge. Tabulations of basic properties can convey the message in ...an absolute sense but not within the context of the sample from which the individual is drawn. We present a novel but simple plot that simultaneously visualises the properties of the sample and the individual. Numbers and characters are kept at an absolute minimum to enable the stacking of such plots without introducing too much verbal information. Once the user becomes accustomed to their appearance, a set of starfish diagrams provides a direct representation of the individual within a sample, or between various samples. The utility and versatility of the plot is demonstrated through its application to astrophysical data (SAMI Galaxy Survey) and sports statistics. We provide a brief description of the concept and the source code, which is simple to adapt to any statistical dataset, be it descriptive of physics, demographics, finance, and more.
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