Automated robotic liquid handling assembly of modular DNA devices

Recent advances in modular DNA assembly techniques have enabled synthetic biologists to test significantly more of the available "design space" represented by "devices" created as combinations of individual genetic components. However, manual assembly of such large numbers of devices is time-intensive, error-prone, and costly. The increasing sophistication and scale of synthetic biology research necessitates an efficient, reproducible way to accommodate large-scale, complex, and high throughput device construction. Here, a DNA assembly protocol using the Type-IIS restriction endonuclease based Modular Cloning (MoClo) technique is automated on two liquid-handling robotic platforms. Automated liquid-handling robots require careful, often times tedious optimization of pipetting parameters for liquids of different viscosities (e.g. enzymes, DNA, water, buffers), as well as explicit programming to ensure correct aspiration and dispensing of DNA parts and reagents. This makes manual script writing for complex assemblies just as problematic as manual DNA assembly, and necessitates a software tool that can automate script generation. To this end, we have developed a web-based software tool, http://mocloassembly.com, for generating combinatorial DNA device libraries from basic DNA parts uploaded as Genbank files. We provide access to the tool, and an export file from our liquid handler software which includes optimized liquid classes, labware parameters, and deck layout. All DNA parts used are available through Addgene, and their digital maps can be accessed via the Boston University BDC ICE Registry. Together, these elements provide a foundation for other organizations to automate modular cloning experiments and similar protocols. The automated DNA assembly workflow presented here enables the repeatable, automated, high-throughput production of DNA devices, and reduces the risk of human error arising from repetitive manual pipetting. Sequencing data show the automated DNA assembly reactions generated from this workflow are ~95% correct and require as little as 4% as much hands-on time, compared to manual reaction preparation

ChimpCheck: Property-Based Randomized Test Generation for Interactive Apps

We consider the problem of generating relevant execution traces to test rich interactive applications. Rich interactive applications, such as apps on mobile platforms, are complex stateful and often distributed systems where sufficiently exercising the app with user-interaction (UI) event sequences to expose defects is both hard and time-consuming. In particular, there is a fundamental tension between brute-force random UI exercising tools, which are fully-automated but offer low relevance, and UI test scripts, which are manual but offer high relevance. In this paper, we consider a middle way---enabling a seamless fusion of scripted and randomized UI testing. This fusion is prototyped in a testing tool called ChimpCheck for programming, generating, and executing property-based randomized test cases for Android apps. Our approach realizes this fusion by offering a high-level, embedded domain-specific language for defining custom generators of simulated user-interaction event sequences. What follows is a combinator library built on industrial strength frameworks for property-based testing (ScalaCheck) and Android testing (Android JUnit and Espresso) to implement property-based randomized testing for Android development. Driven by real, reported issues in open source Android apps, we show, through case studies, how ChimpCheck enables expressing effective testing patterns in a compact manner.Comment: 20 pages, 21 figures, Symposium on New ideas, New Paradigms, and Reflections on Programming and Software (Onward!2017

Automatically Discovering, Reporting and Reproducing Android Application Crashes

Mobile developers face unique challenges when detecting and reporting crashes in apps due to their prevailing GUI event-driven nature and additional sources of inputs (e.g., sensor readings). To support developers in these tasks, we introduce a novel, automated approach called CRASHSCOPE. This tool explores a given Android app using systematic input generation, according to several strategies informed by static and dynamic analyses, with the intrinsic goal of triggering crashes. When a crash is detected, CRASHSCOPE generates an augmented crash report containing screenshots, detailed crash reproduction steps, the captured exception stack trace, and a fully replayable script that automatically reproduces the crash on a target device(s). We evaluated CRASHSCOPE's effectiveness in discovering crashes as compared to five state-of-the-art Android input generation tools on 61 applications. The results demonstrate that CRASHSCOPE performs about as well as current tools for detecting crashes and provides more detailed fault information. Additionally, in a study analyzing eight real-world Android app crashes, we found that CRASHSCOPE's reports are easily readable and allow for reliable reproduction of crashes by presenting more explicit information than human written reports.Comment: 12 pages, in Proceedings of 9th IEEE International Conference on Software Testing, Verification and Validation (ICST'16), Chicago, IL, April 10-15, 2016, pp. 33-4

Overcoming Language Dichotomies: Toward Effective Program Comprehension for Mobile App Development

Mobile devices and platforms have become an established target for modern software developers due to performant hardware and a large and growing user base numbering in the billions. Despite their popularity, the software development process for mobile apps comes with a set of unique, domain-specific challenges rooted in program comprehension. Many of these challenges stem from developer difficulties in reasoning about different representations of a program, a phenomenon we define as a "language dichotomy". In this paper, we reflect upon the various language dichotomies that contribute to open problems in program comprehension and development for mobile apps. Furthermore, to help guide the research community towards effective solutions for these problems, we provide a roadmap of directions for future work.Comment: Invited Keynote Paper for the 26th IEEE/ACM International Conference on Program Comprehension (ICPC'18

Translating Video Recordings of Mobile App Usages into Replayable Scenarios

Screen recordings of mobile applications are easy to obtain and capture a wealth of information pertinent to software developers (e.g., bugs or feature requests), making them a popular mechanism for crowdsourced app feedback. Thus, these videos are becoming a common artifact that developers must manage. In light of unique mobile development constraints, including swift release cycles and rapidly evolving platforms, automated techniques for analyzing all types of rich software artifacts provide benefit to mobile developers. Unfortunately, automatically analyzing screen recordings presents serious challenges, due to their graphical nature, compared to other types of (textual) artifacts. To address these challenges, this paper introduces V2S, a lightweight, automated approach for translating video recordings of Android app usages into replayable scenarios. V2S is based primarily on computer vision techniques and adapts recent solutions for object detection and image classification to detect and classify user actions captured in a video, and convert these into a replayable test scenario. We performed an extensive evaluation of V2S involving 175 videos depicting 3,534 GUI-based actions collected from users exercising features and reproducing bugs from over 80 popular Android apps. Our results illustrate that V2S can accurately replay scenarios from screen recordings, and is capable of reproducing $\approx$ 89% of our collected videos with minimal overhead. A case study with three industrial partners illustrates the potential usefulness of V2S from the viewpoint of developers.Comment: In proceedings of the 42nd International Conference on Software Engineering (ICSE'20), 13 page

Recent Developments in the Design, Capabilities and Autonomous Operations of a Lightweight Surface Manipulation System and Test-bed

The first generation of a versatile high performance device for performing payload handling and assembly operations on planetary surfaces, the Lightweight Surface Manipulation System (LSMS), has been designed and built. Over the course of its development, conventional crane type payload handling configurations and operations have been successfully demonstrated and the range of motion, types of operations and the versatility greatly expanded. This enhanced set of 1st generation LSMS hardware is now serving as a laboratory test-bed allowing the continuing development of end effectors, operational techniques and remotely controlled and automated operations. This paper describes the most recent LSMS and test-bed development activities, that have focused on two major efforts. The first effort was to complete a preliminary design of the 2nd generation LSMS that has the capability for limited mobility and can reposition itself between lander decks, mobility chassis, and fixed base locations. A major portion of this effort involved conducting a study to establish the feasibility of, and define, the specifications for a lightweight cable-drive waist joint. The second effort was to continue expanding the versatility and autonomy of large planetary surface manipulators using the 1st generation LSMS as a test-bed. This has been accomplished by increasing manipulator capabilities and efficiencies through both design changes and tool and end effector development. A software development effort has expanded the operational capabilities of the LSMS test-bed to include; autonomous operations based on stored paths, use of a vision system for target acquisition and tracking, and remote command and control over a communications bridge