Static Plots Research Articles

COMPARING SCIENTIFIC COMPUTING ENVIRONMENTS FOR SIMULATING 2D NON-BUOYANT FLUID PARCEL TRAJECTORY UNDER INERTIAL OSCILLATION: A PRELIMINARY EDUCATIONAL STUDY

This study presents a preliminary numerical investigation of the two-dimensional trajectory of a non-buoyant fluid parcel subjected to inertial oscillations and abrupt external forcing events. The simulations were implemented using Python, GNU Octave, R, Julia, and Fortran open-source scientific computing environments. By running 1,000 iterations in each environment, we evaluated the computational performance of these languages in tackling this idealized problem. The results, visualized through static plots and animation, validate the numerical model's ability to represent the fundamental physics governing fluid motion. Statistical analysis using the Kruskal-Wallis test and Dunn's post-hoc test with Bonferroni correction revealed that Fortran exhibits significantly faster execution times than other environments. However, the choice of programming language should also consider factors such as coding expertise, library availability, and scalability requirements. This study focuses on the performance of scientific computing environments within each language rather than the languages themselves. The observed execution times should be interpreted in the context of the specific environments used, as they often leverage optimized libraries written in lower-level languages. Despite the limitations of this work, such as the simplified 2D model and the use of a single hardware configuration, this study provides valuable insights into selecting appropriate computational tools. It contributes to educational resources for teaching idealized fluid dynamics models. Future studies could explore more complex scenarios, a more comprehensive range of programming environments, and the impact of different numerical schemes and physical parameterizations.

Pietra su pietra: materialità e drammaturgia nella Niobe di Eschilo

This paper analyses “the force of things” (Bennett 2010, 1) in Aeschylus’ Niobe, in particular the function of two material props (in a broader sense): the tomb of Niobe’s children and her mourning veil. These will be examined through both textual evidence and visual representations of the myth. Aristoph. Frogs 911-20 (test. 120 R) describes Niobe as seated, veiled, and silent for half of Aeschylus’ play (cf. also Vit. Aeschyl. 5-6 = test. 1.19-23 R). With such a static plot, material props are crucial; from a cognitive, physical, and psychological point of view they deeply affect the main character, as well as the other characters (including the chorus) and the spectators, who experience Niobe’s feelings through her contact with the material medium. The physical and psychological relationship between Niobe and the tomb affects her communication with the other characters, her own perception of reality and her capability to act. The grave locks Niobe into her grief, preventing her from moving forward – and physically away from it – and even from communicating with the outer world. The mourning veil is the material expression of this interrupted relationship. It acts as a material barrier, preventing communication between Niobe and the other characters: it weakens her physical and cognitive perception of the world, as well as her capacity to act, ‘sealing’ the character in her silence. Moreover, the veil separates Niobe from the world of the living, entrapping her in an exclusive relationship with her dead children.

ShinySyn: a Shiny/R application for the interactive visualization and integration of macro- and micro-synteny data.

Synteny analysis is a widely used framework in comparative genomics studies, which provides valuable information to reveal chromosome collinearity in both intra-species and inter-species. Most analysis pipelines, however, are command line-based, making it challenging for biologists to run the algorithms and visualize the results. Existing visualization tools either provide static plots or can only be run on web-based servers and lack efficient visualization methods for associating macro-synteny blocks with individual gene pairs in a micro-synteny region. We developed ShinySyn, a Shiny/R application built on the MCscan framework that provides an easy-to-use graphic interface for synteny analyses without requiring any programming skills, to reduce technical barriers. ShinySyn not only provides interactive visualization for macro-synteny, micro-synteny and genome-level dot views, but it also creates an intuitive representation with a dynamic zooming feature from macro-synteny to individual homologous genes. The source code and installation instructions for ShinySyn can be accessed via https://github.com/obenno/ShinySyn. A pre-built docker image is also available at https://hub.docker.com/r/obenno/shinysyn. The application can be used locally or seamlessly integrated into any Shiny application server.

Knowledge and Attitudes Among Life Scientists Toward Reproducibility Within Journal Articles: A Research Survey.

We constructed a survey to understand how authors and scientists view the issues around reproducibility, focusing on interactive elements such as interactive figures embedded within online publications, as a solution for enabling the reproducibility of experiments. We report the views of 251 researchers, comprising authors who have published in eLIFE Sciences, and those who work at the Norwich Biosciences Institutes (NBI). The survey also outlines to what extent researchers are occupied with reproducing experiments themselves. Currently, there is an increasing range of tools that attempt to address the production of reproducible research by making code, data, and analyses available to the community for reuse. We wanted to collect information about attitudes around the consumer end of the spectrum, where life scientists interact with research outputs to interpret scientific results. Static plots and figures within articles are a central part of this interpretation, and therefore we asked respondents to consider various features for an interactive figure within a research article that would allow them to better understand and reproduce a published analysis. The majority (91%) of respondents reported that when authors describe their research methodology (methods and analyses) in detail, published research can become more reproducible. The respondents believe that having interactive figures in published papers is a beneficial element to themselves, the papers they read as well as to their readers. Whilst interactive figures are one potential solution for consuming the results of research more effectively to enable reproducibility, we also review the equally pressing technical and cultural demands on researchers that need to be addressed to achieve greater success in reproducibility in the life sciences.

Make Interactive Complex Heatmaps in R

Abstract Heatmap is a powerful visualization method on two-dimensional data to reveal patterns shared by subsets of rows and columns. In R, there are many packages that make heatmaps. Among them, ComplexHeatmap provides rich tools for constructing highly customizable heatmaps. It can easily establish connections between information from multiple sources by automatically concatenating and adjusting multiple heatmaps as well as complex annotations, which makes it widely applied in data analysis in various fields, especially in Bioinformatics. Nevertheless, the limit of ComplexHeatmap still exists. It only generates static plots which restricts deeper inspections on complex heatmaps, e.g., to look into a subset of rows and columns when a specific pattern of interest is observed from the heatmap. In this work, we described a new R/Bioconductor package InteractiveComplexHeatmap that brings interactivity to ComplexHeatmap. InteractiveComplexHeatmap is designed with an easy-to-use interface where static complex heatmaps can be directly exported to an interactive Shiny web application only with one extra line of code. The interactive application contains comprehensive tools for manipulating heatmaps. Besides common tools as supported in other interactive heatmap packages, InteractiveComplexHeatmap additionally supports, e.g., selecting over multiple heatmaps and searching heatmaps via row or column labels. Also, InteractiveComplexHeatmap provides methods for exporting static heatmaps from other popular heatmap functions, e.g., heatmap.2() or pheatmap(), to interactive heatmap applications. Finally, InteractiveComplexHeatmap provides flexible functionalities for integrating interactive heatmap widgets into other Shiny applications. InteractiveComplexHeatmap provides a user interface for self-defining response to the selection events on heatmaps, which helps to implement more complex Shiny web applications.

CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing

Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector.

Animated analysis of geoscientific datasets: An interactive graphical application

Geoscientists are required to analyze and draw conclusions from increasingly large volumes of data. There is a need to recognise and characterise features and changing patterns of Earth observables within such large datasets. It is also necessary to identify significant subsets of the data for more detailed analysis.We present an innovative, interactive software tool and workflow to visualise, characterise, sample and tag large geoscientific datasets from both local and cloud-based repositories. It uses an animated interface and human-computer interaction to utilise the capacity of human expert observers to identify features via enhanced visual analytics. ‘Tagger’ enables users to analyze datasets that are too large in volume to be drawn legibly on a reasonable number of single static plots. Users interact with the moving graphical display, tagging data ranges of interest for subsequent attention. The tool provides a rapid pre-pass process using fast GPU-based OpenGL graphics and data-handling and is coded in the Quartz Composer visual programing language (VPL) on Mac OSX. It makes use of interoperable data formats, and cloud-based (or local) data storage and compute.In a case study, Tagger was used to characterise a decade (2000–2009) of data recorded by the Cape Sorell Waverider Buoy, located approximately 10 km off the west coast of Tasmania, Australia. These data serve as a proxy for the understanding of Southern Ocean storminess, which has both local and global implications. This example shows use of the tool to identify and characterise 4 different types of storm and non-storm events during this time. Events characterised in this way are compared with conventional analysis, noting advantages and limitations of data analysis using animation and human interaction. Tagger provides a new ability to make use of humans as feature detectors in computer-based analysis of large-volume geosciences and other data.

La «Fedra» di Seneca-Sanguineti: rilettura di una traduzione per la messinscena

The purpose of this study is to fill a gap about Edoardo Sanguineti’s translations in the current bibliography. Despite the fact that Friedmar Apel’s method brings a sweeping change to research in the field of translation studies and many works about Sanguineti’s activity have been published in recent years, an overall analysis regarding Seneca’s Phaedra still doesn’t exist. The drama was translated for Luca Ronconi’s theatrical production, performed at Teatro Stabile di Roma in 1969. Both play and translation were harshly criticized for their rhetoric, declamation and forceful emphasis: the same critics were directed to the original text. This study tries to show that Sanguineti perfectly knows that in the Seneca’s play – as Eliot said – «the drama is all in the word». Therefore Sanguineti creates a new style of translation, that he calls «oracolese»: its idiosyncratic syntax (caused by reproduction of ordo verborum ), assonances and alliterations, alienating commixture between high literal tradition and colloquial Italian grammar are strictly related to the mise-en-scene. Sanguineti realizes that Seneca’s dramas’ static plot has a special strength and – because «in translation there is no other speaker than translator» – this is the strongest relation with the original, the only point of contact possible.

Taming PITCHf/x Data with XML2R and pitchRx

XML2R is a framework that reduces the effort required to transform XML content into tables in a way that preserves parent to child relationships. pitchRx applies XML2R’s grammar for XML manipulation to Major League Baseball Advanced Media (MLBAM)’s Gameday data. With pitchRx, one can easily obtain and store Gameday data in a remote database. The Gameday website hosts a wealth of XML data, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball’s flight path from a pitcher’s hand to home plate. With pitchRx, one can easily create animations and interactive 3D scatterplots of the baseball’s flight path. PITCHf/x data is also commonly used to generate a static plot of baseball locations at the moment they cross home plate. These plots, sometimes called strike-zone plots , can also refer to a plot of event probabilities over the same region. pitchRx provides an easy and robust way to generate strike-zone plots using the ggplot2 package.

29Si-NMR study of antiferromagnet CeRh2Si2 using single crystals

29Si-NMR Study of antiferromagnet CeRh2Si2 with a tetragonal ThCr2Si2-type structure has been performed using single crystals. The Knight shifts along the a and the c axes have been measured as a function of temperatures in the paramagnetic state. At ambient pressure, the Knight shifts show the Ising-type anisotropy along the c axis, which is similar to the magnetic susceptibility. The hyperfine coupling constants for 29Si along the a and the c axes have been determined from Knight shift versus static susceptibility plots.

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization.

Identification and characterization of cancer subtypes are important areas of research that are based on the integrated analysis of multiple heterogeneous genomics datasets. Since there are no tools supporting this process, much of this work is done using ad-hoc scripts and static plots, which is inefficient and limits visual exploration of the data. To address this, we have developed StratomeX, an integrative visualization tool that allows investigators to explore the relationships of candidate subtypes across multiple genomic data types such as gene expression, DNA methylation, or copy number data. StratomeX represents datasets as columns and subtypes as bricks in these columns. Ribbons between the columns connect bricks to show subtype relationships across datasets. Drill-down features enable detailed exploration. StratomeX provides insights into the functional and clinical implications of candidate subtypes by employing small multiples, which allow investigators to assess the effect of subtypes on molecular pathways or outcomes such as patient survival. As the configuration of viewing parameters in such a multi-dataset, multi-view scenario is complex, we propose a meta visualization and configuration interface for dataset dependencies and data-view relationships. StratomeX is developed in close collaboration with domain experts. We describe case studies that illustrate how investigators used the tool to explore subtypes in large datasets and demonstrate how they efficiently replicated findings from the literature and gained new insights into the data.

Interactive and Animated Scalable Vector Graphics andRData Displays

We describe an approach to creating interactive and animated graphical displays using R’s graphics engine and Scalable Vector Graphics, an XML vocabulary for describing two-dimensional graphical displays. We use the svg() graphics device inR and then post-process the resulting XML documents. The post-processing identifies the elements in the SVG that correspond to the different components of the graphical display, e.g., points, axes, labels, lines. One can then annotate these elements to add interactivity and animation effects. One can also use JavaScript to provide dynamic interactive effects to the plot, enabling rich user interactions and compelling visualizations. The resulting SVG documents can be embedded within HTML documents and can involve JavaScript code that integrates the SVG and HTML objects. The functionality is provided via the SVGAnnotation package and makes static plots generated viaR graphics functions available as stand-alone, interactive and animated plots for the Web and other venues.

Thermographic signal reconstruction for vibrothermography

Vibrothermography, also known as thermosonics or sonic infrared, is a method of nondestructive evaluation that finds cracks or delaminations from the heat given off in response to vibration. In vibrothermography, finding cracks requires identifying and localizing pulsed surface and subsurface heat sources from a time sequence of infrared images. Traditionally this identification involves manually stepping through and studying the images. Careful observation of the heating and subsequent cooling is needed to distinguish cracks from false indications. In this paper, we present an algorithm that reduces the entire time sequence to a single static plot. The plot uses only a few coefficients per pixel to reconstruct the original sequence; this is possible because the reduction is based on a physical model. As an added bonus, the algorithm reduces noise and improves sensitivity. A single false-color image summarizes all the information from the entire sequence, simplifying the task of identifying cracks.

Interactive Graphics: Exemplified with Real Data Applications

Graphics are widely used in modern applied statistics because they are easy to create, convenient to use, and they can present information effectively. Static plots do not allow interacting with graphics. User interaction, on the other hand, is crucial in exploring data. It gives flexibility and control. One can experiment with the data and the displays. One can investigate the data from different perspectives to produce views that are easily interpretable and informative. In this paper, we try to explain interactive graphics and advocate their use as a practical tool. The benefits and strengths of interactive graphics for data exploration and data quality analyses are illustrated systematically with three complex real datasets.

A real-time/non-real-time spectrum analyzer for musical sounds

A color spectrum analyzer specialized for visualization of musical sounds has been developed for the Macintosh Power PC computer. Input samples (monaural or stereo) can be obtained from microphone or CD-ROM input in real time or from a sound file in nonreal time. Spectral analysis can be tuned specifically to the fundamental frequency of the input signal using sample rate conversion (tuned case), or it can be based on a specified window size at the input sample rate (nontuned case). In the tuned case each spectral component corresponds to a harmonic of the input. Several different displays can occur simultaneously: an oscilloscope waveform display; a 1D spectrum, where an amplitude-vs-frequency graph varies as time progresses; a spectral waterfall display; a 2D spectrum showing frequency vs time with amplitude registered as degree of display brightness; a 3D display showing amplitude vs time vs frequency at an arbitrary orientation. In addition to time-varying graphs which are available for both real and nonreal time, static plots are available for preanalyzed file input. For stereo signals it is possible to plot output/input transfer functions. Spectral time averaging is also available for cases where the instantaneous spectrum is unstable

Mechanical Ventilation Strategies for Lung Protection

A large body of animal literature has shown that lungs stretched beyond their normal maximum are likely to be injured and release inflammatory cytokines into the systemic circulation. Moreover, this injury seems to be compounded if alveolar collapse also occurs. This has give rise to the notion that adequate positive end expiratory pressure (PEEP) to prevent derecruitment coupled with a tidal volume-PEEP combination that limits maximal distention to below the normal maximum is the ideal way to provide positive pressure ventilatory support. Some have argued that static pressure-volume plots to describe upper and lower inflection points are particularly important in implementing this approach. Supporting this concept is the recently completed NIH trial showing improved survival in acute respiratory distress syndrome (ARDS) when a small tidal volume strategy was used.

Server-Side Statistics Scripting inPHP

On the UCLA Statistics WWW server there are a large number of demos and calculators that can be used in statistics teaching and research. Some of these demos require substantial amounts of computation, others mainly use graphics. These calculators and demos are implemented in various different ways, reflecting developments in WWW based computing. As usual, one of the main choices is between doing the work on the client-side (i.e. in the browser) or on the server-side (i.e. on our WWW server). Obviously, client-side computation puts fewer demands on the server. On the other hand, it requires that the client downloads Java applets, or installs plugins and/or helpers. If JavaScript is used, client-side computations will generally be slow. We also have to assume that the client is installed properly, and has the required capabilities. Requiring too much on the client-side has caused browsing machines such as Netscape Communicator to grow beyond all reasonable bounds, both in size and RAM requirements. Moreover requiring Java and JavaScript rules out such excellent browsers as Lynx or Emacs W3. For server-side computing, we can configure the server and its resources ourselves, and we need not worry about browser capabilities and configuration. Nothing needs to be downloaded, except the usual HTML pages and graphics. In the same way as on the client side, there is a scripting solution, where code is interpreted, or a ob ject-code solution using compiled code. For the server-side scripting, we use embedded languages, such as PHP/FI. The scripts in the HTML pages are interpreted by a CGI program, and the output of the CGI program is send to the clients. Of course the CGI program is compiled, but the statistics procedures will usually be interpreted, because PHP/FI does not have the appropriate functions in its scripting language. This will tend to be slow, because embedded languages do not deal efficiently with loops and similar constructs. Thus a first step towards greater efficiency is to compile the necessary primitives into the PHP/FI executable. This is easy to do, because the API is quite simple. In the extensions below, we have added the complete ranlib and dcdflib to PHP, plus some additional useful functions. The source code for these extensions, plus Solaris binaries for libranlib.a and libdcdf.a can be obtained from our server. Interpreting a PHP script, even with our new primitives, still requires starting up a CGI process for each page that is read. Again, this can be improved upon. We could use FastCGI to keep the CGI process around on a permanent basis. Instead, we have chosen a more direct method. PHP can be compiled as an Apache module, i.e. it can be compiled into the Apache HTTPD server binary. This means that PHP scripts are interpreted by the WWW server, which is always around, and which will fork additional children if necessary. No CGI processes need to be started. The PHP install process creates a libphp.a and mod_php.c in the Apache source directories, which can be used to build an enhanced server. This has the additional advantage of security, because all security features of the server can be used, and none of the pitfalls of using CGI or Java apply. Using PHP, in combination with the WWW server, also has some disadvantages. Although we can make simple static plots, using the gd library, we cannot use any dynamics, and interaction between the user and the page is somewhat limited. Java, or scripts using a client-side Xlisp-Stat as a helper, are more flexible in this respect. As a consequence, the UCLA Statistics pages still use a combined approach, with server-side PHP and CGI and client-side Xlisp-Stat and Java/JavaScript. Sometime this year, server-side Java scripting will become available, and then it seems advisable to switch as much of the code as possible to the server-side.

NUMERICAL ANALYSIS OF MICROMECHANICAL BEHAVIOUR OF GRANULAR MATERIALS

A numerical analysis of the micromechanical behaviour of a granular material is described using a new program MASOM based on Cundall's discrete element method. In the analysis the individual grains which make up the material are taken to be deformable 2D polygons of arbitrary size and shape. Contact forces between the grains are calculated according to Mindlin's solution for frictional contact between elastic bodies. The material in each grain is taken to be linear elastic but limited by the fracture strength of the material. Fracture is permitted along any one of a number of candidate fracture planes if an associated compressive load tending to split the gain reaches a critical level. Fragments of fractured grains are carried until they become too small to track using the explicit time integration algorithm used to advance the solution. The MASOM program is able to consider a number of different classes of elements and different types of contact between the various classes. Thus, in addition to the granular material the program can also model containers and loading devices. The program is used to simulate uniaxial and triaxial compression tests for geological materials. The results are shown to give results for stress‐strain and stress difference versus pressure which are in qualitative agreement with test data. The numerical results reveal a very complex micromechanical behaviour in granular materials, including highly variable and rather unstable load paths and a very inhomogeneous load distribution within a representative sample of the material. A video of the response of a typical frictional material to applied loads shows an interesting localized effect near sample boundaries involving crowding together of grains which cannot be observed using conventional static field plots.

Anatomy of a new medium: Literary and pedagogic uses of advanced linguistic computer structures

The availability of advanced function workstations makes possible a new medium for the manipulation of language which changes in kind as well as in degree the pedagogic and literary potential of the computer. This article presents a structural/functional analysis of the kind of system that, though still unrealized, is becominig increasingly possible to build: an Advanced Language System that includes natural language processing, knowledge representation, discourse structure, and narrative structure. Communicative language learning and the creation of computer-based fiction are both served by the emergence of this medium. Advanced language systems may include: “ako” links, semantic networks, query, “script,” “analogy,” and character/belief structures. For language learning advanced language systems offer greater error correction and research opportunities and more flexibility in presenting communicative and cultural exercises. For the creation of art, they offer the possibility of creating “round” instead of “flat” characters and “dynamic” rather than static plots. Programs which “learn” offer the possibility of creating literary formulae and even interpretive “traditions” on the computer. Literary invention will always be the key to making such systems effective as art or as aids to communicative learning.

Counterpoise in Honglou meng

THAT many of the characters in Honglou meng are conceived in pairs, whether as opposites, doubles, or mutual complements, is immediately obvious even to the most casual reader: the Buddhist monk and the Taoist priest, the Divine Luminescent Stone-inWaiting and the Crimson Pearl Flower, Zhen Shi-yin and Jia Yucun, Zhen Bao-yu andJia Bao-yu, Dai-yu and Bao-chai, and so on, are all introduced in tandem. Such coupling is not confined to the presentation of characters within particular scenes, but extends to the grouping of similar episodes, such as parties, birthdays and love affairs, in which various characters are juxtaposed and events echo one another. The persistent recurrence of pairing of characters and episodes points to a conscious narrative procedure. Such a procedure offers several advantages. The numerous quotidian trivia through which the author seeks to convey the texture of daily life gain significance only in perspective. Characters by mutual implication or refraction illuminate one another. The interplay of comparisons and contrasts not only portrays a kaleidoscopic array of characters, but in effect subtly shapes an implicit system of values, wherein the individual characters find their place. By presenting, either simultaneously or in alternation, the conflicting views of various characters, the author creates an underlying tension that unifies and enlivens an otherwise episodic, often static plot.