GenomeGraphs: integrated genomic data visualization with R.

BackgroundBiological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses.ResultsWe developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system.ConclusionGenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R

TAE Plus: Transportable Applications Environment Plus tools for building graphic-oriented applications

The Transportable Applications Environment Plus (TAE Plus), developed by NASA's Goddard Space Flight Center, is a portable User Interface Management System (UIMS), which provides an intuitive WYSIWYG WorkBench for prototyping and designing an application's user interface, integrated with tools for efficiently implementing the designed user interface and effective management of the user interface during an application's active domain. During the development of TAE Plus, many design and implementation decisions were based on the state-of-the-art within graphics workstations, windowing system and object-oriented programming languages. Some of the problems and issues experienced during implementation are discussed. A description of the next development steps planned for TAE Plus is also given

Sketchy rendering for information visualization

We present and evaluate a framework for constructing sketchy style information visualizations that mimic data graphics drawn by hand. We provide an alternative renderer for the Processing graphics environment that redefines core drawing primitives including line, polygon and ellipse rendering. These primitives allow higher-level graphical features such as bar charts, line charts, treemaps and node-link diagrams to be drawn in a sketchy style with a specified degree of sketchiness. The framework is designed to be easily integrated into existing visualization implementations with minimal programming modification or design effort. We show examples of use for statistical graphics, conveying spatial imprecision and for enhancing aesthetic and narrative qualities of visual- ization. We evaluate user perception of sketchiness of areal features through a series of stimulus-response tests in order to assess users’ ability to place sketchiness on a ratio scale, and to estimate area. Results suggest relative area judgment is compromised by sketchy rendering and that its influence is dependent on the shape being rendered. They show that degree of sketchiness may be judged on an ordinal scale but that its judgement varies strongly between individuals. We evaluate higher-level impacts of sketchiness through user testing of scenarios that encourage user engagement with data visualization and willingness to critique visualization de- sign. Results suggest that where a visualization is clearly sketchy, engagement may be increased and that attitudes to participating in visualization annotation are more positive. The results of our work have implications for effective information visualization design that go beyond the traditional role of sketching as a tool for prototyping or its use for an indication of general uncertainty

Building real-time embedded applications on QduinoMC: a web-connected 3D printer case study

Single Board Computers (SBCs) are now emerging with multiple cores, ADCs, GPIOs, PWM channels, integrated graphics, and several serial bus interfaces. The low power consumption, small form factor and I/O interface capabilities of SBCs with sensors and actuators makes them ideal in embedded and real-time applications. However, most SBCs run non-realtime operating systems based on Linux and Windows, and do not provide a user-friendly API for application development. This paper presents QduinoMC, a multicore extension to the popular Arduino programming environment, which runs on the Quest real-time operating system. QduinoMC is an extension of our earlier single-core, real-time, multithreaded Qduino API. We show the utility of QduinoMC by applying it to a specific application: a web-connected 3D printer. This differs from existing 3D printers, which run relatively simple firmware and lack operating system support to spool multiple jobs, or interoperate with other devices (e.g., in a print farm). We show how QduinoMC empowers devices with the capabilities to run new services without impacting their timing guarantees. While it is possible to modify existing operating systems to provide suitable timing guarantees, the effort to do so is cumbersome and does not provide the ease of programming afforded by QduinoMC.http://www.cs.bu.edu/fac/richwest/papers/rtas_2017.pdfAccepted manuscrip

Tools for modelling support and construction of optimization applications

We argue the case for an open systems approach towards modelling and application support. We discuss how the 'usability' and 'skills' analysis naturally leads to a viable strategy for integrating application construction with modelling tools and optimizers. The role of the implementation environment is also seen to be critical in that it is retained as a building block within the resulting system

Realtime 3D graphics programming using the Quake3 engine

We present a lab assignment that accompanies a complete module called Real-time Graphics . The students task is to get familiar with content creation and programming a (previously) commercial 3D engine. In a first task, students have to create 3D content, which is integrated into the Quake3 engine. In a second task, the students have to implement a simple animation and finally add an impressive 3D graphics effect to the Quake3 engine. The lecture has been taught four times from 2004 to 2007. We present the assignment and report on experiences that we have gained

Computer Science Education: A Game to Teach Children about Programming

abstract: Computational thinking, the fundamental way of thinking in computer science, including information sourcing and problem solving behind programming, is considered vital to children who live in a digital era. Most of current educational games designed to teach children about coding either rely on external curricular materials or are too complicated to work well with young children. In this thesis project, Guardy, an iOS tower defense game, was developed to help children over 8 years old learn about and practice using basic concepts in programming. The game is built with the SpriteKit, a graphics rendering and animation infrastructure in Apple’s integrated development environment Xcode. It simplifies switching among different game scenes and animating game sprites in the development. In a typical game, a sequence of operations is arranged by players to destroy incoming enemy minions. Basic coding concepts like looping, sequencing, conditionals, and classification are integrated in different levels. In later levels, players are required to type in commands and put them in an order to keep playing the game. To reduce the difficulty of the usability testing, a method combining questionnaires and observation was conducted with two groups of college students who either have no programming experience or are familiar with coding. The results show that Guardy has the potential to help children learn programming and practice computational thinking.Dissertation/ThesisMasters Thesis Computer Science 201

Critters in the Classroom: A 3D Computer-Game-Like Tool for Teaching Programming to Computer Animation Students

The brewing crisis threatening computer science education is a well documented fact. To counter this and to increase enrolment and retention in computer science related degrees, it has been suggested to make programming "more fun" and to offer "multidisciplinary and cross-disciplinary programs" [Carter 2006]. The Computer Visualisation and Animation undergraduate degree at the National Centre for Computer Animation (Bournemouth University) is such a programme. Computer programming forms an integral part of the curriculum of this technical arts degree, and as educators we constantly face the challenge of having to encourage our students to engage with the subject. We intend to address this with our C-Sheep system, a reimagination of the "Karel the Robot" teaching tool [Pattis 1981], using modern 3D computer game graphics that today's students are familiar with. This provides a game-like setting for writing computer programs, using a task-specific set of instructions which allow users to take control of virtual entities acting within a micro world, effectively providing a graphical representation of the algorithms used. Whereas two decades ago, students would be intrigued by a 2D top-down representation of the micro world, the lack of the visual gimmickry found in modern computer games for representing the virtual world now makes it extremely difficult to maintain the interest of students from today's "Plug&Play generation". It is therefore especially important to aim for a 3D game-like representation which is "attractive and highly motivating to today's generation of media-conscious students" [Moskal et al. 2004]. Our system uses a modern, platform independent games engine, capable of presenting a visually rich virtual environment using a state of the art rendering engine of a type usually found in entertainment systems. Our aim is to entice students to spend more time programming, by providing them with an enjoyable experience. This paper provides a discussion of the 3D computer game technology employed in our system and presents examples of how this can be exploited to provide engaging exercises to create a rewarding learning experience for our students

Do Robots Dream of Virtual Sheep: Rediscovering the "Karel the Robot" Paradigm for the "Plug&Play Generation"

We introduce ”C-Sheep”, an educational system designed to teach students the fundamentals of computer programming in a novel and exciting way. Recent studies suggest that computer science education is fast approaching a crisis - application numbers for degree courses in the area of computer programming are down, and potential candidates are put off the subject which they do not fully understand. We address this problem with our system by providing the visually rich virtual environment of ”The Meadow”, where the user writes programs to control the behaviour of a sheep using our ”CSheep” programming language. This combination of the ”Karel the Robot” paradigm with modern 3D computer graphics techniques, more commonly found in computer games, aims to help students to realise that computer programming can be an enjoyable and rewarding experience and intends to help educators with the teaching of computer science fundamentals. Our mini-language-like system for computer science education uses a state of the art rendering engine offering features more commonly found in entertainment systems. The scope of the mini-language is designed to fit in with the curriculum for the first term of an introductory computer program ming course (using the C programming language)