Righting Web Development

The web browser is the most important application runtime today, encompassing all types of applications on practically every Internet-connected device. Browsers power complete office suites, media players, games, and augmented and virtual reality experiences, and they integrate with cameras, microphones, GPSes, and other sensors available on computing devices. Many apparently native mobile and desktop applications are secretly hybrid apps that contain a mix of native and browser code. History has shown that when new devices, sensors, and experiences appear on the market, the browser will evolve to support them. Despite the browser\u27s importance, developing web applications is exceedingly difficult. Web browsers organically evolved from a document viewer into a ubiquitous program runtime. The browser\u27s scripting language for web designers, JavaScript, has grown into the only universally supported programming language in the browser. Unfortunately, JavaScript is notoriously difficult to write and debug. The browser\u27s high-level and event-driven I/O interfaces make it easy to add simple interactions to webpages, but these same interfaces lead to nondeterministic bugs and performance issues in larger applications. These bugs are challenging for developers to reason about and fix. This dissertation revisits web development and provides developers with a complete set of development tools with full support for the browser environment. McFly is the first time-traveling debugger for the browser, and lets developers debug web applications and their visual state during time-travel; components of this work shipped in Microsoft\u27s ChakraCore JavaScript engine. BLeak is the first system for automatically debugging memory leaks in web applications, and provides developers with a ranked list of memory leaks along with the source code responsible for them. BCause constructs a causal graph of a web application\u27s events, which helps developers understand their code\u27s behavior. Doppio lets developers run code written in conventional languages in the browser, and Browsix brings Unix into the browser to enable unmodified programs expecting a Unix-like environment to run directly in the browser. Together, these five systems form a solid foundation for web development

Physics Lab Toolbox - Collisions Lab

This IQP aimed to discover methods to improve physics lab experiments by taking an existing collisions lab and modifying it to make it more engaging and educational for the students. A new web page-based instructions template was developed to achieve this, complete with extra content panels that address software and physics concept issues. Along the way, issues with Logger Pro, the software used to conduct labs, were identified and compensated for. Surveys were administered to determine whether or not this approach succeeded, and a preliminary data analysis indicated that it did. This data can be used for further research, or inspire new phases of research to make more conclusions

Progress in the development of a recombinant vaccine for human hookworm disease: The Human Hookworm Vaccine Initiative

Hookworm infection is one of the most important parasitic infections of humans, possibly outranked only by malaria as a cause of misery and suffering. An estimated 1.2 billion people are infected with hookworm in areas of rural poverty in the tropics and subtropics. Epidemiological data collected in China, Southeast Asia, and Brazil indicate that, unlike other soil-transmitted helminth infections, the highest hookworm burdens typically occur in adult populations, including the elderly. Emerging data on the host cellular immune responses of chronically infected populations suggest that hookworms induce a state of host anergy and immune hyporesponsiveness. These features account for the high rates of hookworm reinfection following treatment with anthelminthic drugs and therefore, the failure of anthelminthics to control hookworm. Despite the inability of the human host to develop naturally acquired immune responses to hookworm, there is evidence for the feasibility of developing a vaccine based on the successes of immunizing laboratory animals with either attenuated larval vaccines or antigens extracted from the alimentary canal of adult blood-feeding stages. The major antigens associated with each of these larval and adult hookworm vaccines have been cloned and expressed in prokaryotic and eukaryotic systems. However, only eukaryotic expression systems (e.g., yeast, baculovirus, and insect cells) produce recombinant proteins that immunologically resemble the corresponding native antigens. A challenge for vaccinologists is to formulate selected eukaryotic antigens with appropriate adjuvants in order to elicit high antibody titers. In some cases, antigen-specific IgE responses are required to mediate protection. Another challenge will be to produce anti-hookworm vaccine antigens at high yield low cost suitable for immunizing large impoverished populations living in the developing nations of the tropics

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype

Publisher Correction: Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper

SurroundWeb: Mitigating Privacy Concerns in a 3D Web Browser

Abstract-Immersive experiences that mix digital and real-world objects are becoming reality, but they raise serious privacy concerns as they require real-time sensor input. These experiences are already present on smartphones and game consoles via Kinect, and will eventually emerge on the web platform. However, browsers do not expose the display interfaces needed to render immersive experiences. Previous security research focuses on controlling application access to sensor input alone, and do not deal with display interfaces. Recent research in human computer interactions has explored a variety of high-level rendering interfaces for immersive experiences, but these interfaces reveal sensitive data to the application. Bringing immersive experiences to the web requires a high-level interface that mitigates privacy concerns. This paper presents SurroundWeb, the first 3D web browser, which provides the novel functionality of rendering web content onto a room while tackling many of the inherent privacy challenges. Following the principle of least privilege, we propose three abstractions for immersive rendering: 1) the room skeleton lets applications place content in response to the physical dimensions and locations of renderable surfaces in a room; 2) the detection sandbox lets applications declaratively place content near recognized objects in the room without revealing if the object is present; and 3) satellite screens let applications display content across devices registered with SurroundWeb. Through user surveys, we validate that these abstractions limit the amount of revealed information to an acceptable degree. In addition, we show that a wide range of immersive experiences can be implemented with acceptable performance