Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

A Study of Concurrency Bugs and Advanced Development Support for Actor-based Programs

The actor model is an attractive foundation for developing concurrent applications because actors are isolated concurrent entities that communicate through asynchronous messages and do not share state. Thereby, they avoid concurrency bugs such as data races, but are not immune to concurrency bugs in general. This study taxonomizes concurrency bugs in actor-based programs reported in literature. Furthermore, it analyzes the bugs to identify the patterns causing them as well as their observable behavior. Based on this taxonomy, we further analyze the literature and find that current approaches to static analysis and testing focus on communication deadlocks and message protocol violations. However, they do not provide solutions to identify livelocks and behavioral deadlocks. The insights obtained in this study can be used to improve debugging support for actor-based programs with new debugging techniques to identify the root cause of complex concurrency bugs.Comment: - Submitted for review - Removed section 6 "Research Roadmap for Debuggers", its content was summarized in the Future Work section - Added references for section 1, section 3, section 4.3 and section 5.1 - Updated citation

A management architecture for active networks

In this paper we present an architecture for network and applications management, which is based on the Active Networks paradigm and shows the advantages of network programmability. The stimulus to develop this architecture arises from an actual need to manage a cluster of active nodes, where it is often required to redeploy network assets and modify nodes connectivity. In our architecture, a remote front-end of the managing entity allows the operator to design new network topologies, to check the status of the nodes and to configure them. Moreover, the proposed framework allows to explore an active network, to monitor the active applications, to query each node and to install programmable traps. In order to take advantage of the Active Networks technology, we introduce active SNMP-like MIBs and agents, which are dynamic and programmable. The programmable management agents make tracing distributed applications a feasible task. We propose a general framework that can inter-operate with any active execution environment. In this framework, both the manager and the monitor front-ends communicate with an active node (the Active Network Access Point) through the XML language. A gateway service performs the translation of the queries from XML to an active packet language and injects the code in the network. We demonstrate the implementation of an active network gateway for PLAN (Packet Language for Active Networks) in a forty active nodes testbed. Finally, we discuss an application of the active management architecture to detect the causes of network failures by tracing network events in time

A management architecture for active networks

In this paper we present an architecture for network and applications management, which is based on the Active Networks paradigm and shows the advantages of network programmability. The stimulus to develop this architecture arises from an actual need to manage a cluster of active nodes, where it is often required to redeploy network assets and modify nodes connectivity. In our architecture, a remote front-end of the managing entity allows the operator to design new network topologies, to check the status of the nodes and to configure them. Moreover, the proposed framework allows to explore an active network, to monitor the active applications, to query each node and to install programmable traps. In order to take advantage of the Active Networks technology, we introduce active SNMP-like MIBs and agents, which are dynamic and programmable. The programmable management agents make tracing distributed applications a feasible task. We propose a general framework that can inter-operate with any active execution environment. In this framework, both the manager and the monitor front-ends communicate with an active node (the Active Network Access Point) through the XML language. A gateway service performs the translation of the queries from XML to an active packet language and injects the code in the network. We demonstrate the implementation of an active network gateway for PLAN (Packet Language for Active Networks) in a forty active nodes testbed. Finally, we discuss an application of the active management architecture to detect the causes of network failures by tracing network events in time

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

Towards quality programming in the automated testing of distributed applications

PhD ThesisSoftware testing is a very time-consuming and tedious activity and accounts for over 25% of the cost of software development. In addition to its high cost, manual testing is unpopular and often inconsistently executed. Software Testing Environments (STEs) overcome the deficiencies of manual testing through automating the test process and integrating testing tools to support a wide range of test capabilities. Most prior work on testing is in single-thread applications. This thesis is a contribution to testing of distributed applications, which has not been well explored. To address two crucial issues in testing, when to stop testing and how good the software is after testing, a statistics-based integrated test environment which is an extension of the testing concept in Quality Programming for distributed applications is presented. It provides automatic support for test execution by the Test Driver, test development by the SMAD Tree Editor and the Test Data Generator, test failure analysis by the Test Results Validator and the Test Paths Tracer, test measurement by the Quality Analyst, test management by the Test Manager and test planning by the Modeller. These tools are integrated around a public, shared data model describing the data entities and relationships which are manipulable by these tools. It enables early entry of the test process into the life cycle due to the definition of the quality planning and message-flow routings in the modelling. After well-prepared modelling and requirements specification are undertaken, the test process and the software design and implementation can proceed concurrently. A simple banking application written using Java Remote Method Invocation (RMI) and Java DataBase Connectivity (JDBC) shows the testing process of fitting it into the integrated test environment. The concept of the automated test execution through mobile agents across multiple platforms is also illustrated on this 3-tier client/server application.The National Science Council, Taiwan: The Ministry of National Defense, Taiwan