Matching Items (76)
Description
Biological systems are complex in many dimensions as endless transportation and communication networks all function simultaneously. Our ability to intervene within both healthy and diseased systems is tied directly to our ability to understand and model core functionality. The progress in increasingly accurate and thorough high-throughput measurement technologies has provided a deluge of data from which we may attempt to infer a representation of the true genetic regulatory system. A gene regulatory network model, if accurate enough, may allow us to perform hypothesis testing in the form of computational experiments. Of great importance to modeling accuracy is the acknowledgment of biological contexts within the models -- i.e. recognizing the heterogeneous nature of the true biological system and the data it generates. This marriage of engineering, mathematics and computer science with systems biology creates a cycle of progress between computer simulation and lab experimentation, rapidly translating interventions and treatments for patients from the bench to the bedside. This dissertation will first discuss the landscape for modeling the biological system, explore the identification of targets for intervention in Boolean network models of biological interactions, and explore context specificity both in new graphical depictions of models embodying context-specific genomic regulation and in novel analysis approaches designed to reveal embedded contextual information. Overall, the dissertation will explore a spectrum of biological modeling with a goal towards therapeutic intervention, with both formal and informal notions of biological context, in such a way that will enable future work to have an even greater impact in terms of direct patient benefit on an individualized level.
ContributorsVerdicchio, Michael (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Stolovitzky, Gustavo (Committee member) / Collofello, James (Committee member) / Arizona State University (Publisher)
Created2013
Description
The focus of this document is the examination of a new robot simulator developed to aid students in learning robotics programming and provide the ability to test their programs in a simulated world. The simulator, accessed via a website, provides a simulated environment, programming interface, and the ability to control a simulated robot. The simulated environment consists of a user-customizable maze and a robot, which can be controlled manually, via Web service, or by utilizing the Web programming interface. The Web programming interface provides dropdown boxes from which the users may select various options to program their implementations. It is designed to aid new students in the learning of basic skills and thought processes used to program robots. Data was collected and analyzed to determine how effective this system is in helping students learn. This included how quickly students were able to program the algorithms assigned to them and how many lines of code were used to implement them. Students' performance was also monitored to determine how well they were able to use the program and if there were any significant problems. The students also completed surveys to communicate how well the website helped them learn and understand various concepts. The data collected shows that the website was a helpful learning tool for the students and that they were able to use the programming interface quickly and effectively.
ContributorsDrown, Garrett (Author) / Tsai, Wei-Tek (Thesis advisor) / Chen, Yinong (Thesis advisor) / Claveau, David (Committee member) / Arizona State University (Publisher)
Created2012
Description
Laboratory automation systems have seen a lot of technological advances in recent times. As a result, the software that is written for them are becoming increasingly sophisticated. Existing software architectures and standards are targeted to a wider domain of software development and need to be customized in order to use them for developing software for laboratory automation systems. This thesis proposes an architecture that is based on existing software architectural paradigms and is specifically tailored to developing software for a laboratory automation system. The architecture is based on fairly autonomous software components that can be distributed across multiple computers. The components in the architecture make use of asynchronous communication methodologies that are facilitated by passing messages between one another. The architecture can be used to develop software that is distributed, responsive and thread-safe. The thesis also proposes a framework that has been developed to implement the ideas proposed by the architecture. The framework is used to develop software that is scalable, distributed, responsive and thread-safe. The framework currently has components to control very commonly used laboratory automation devices such as mechanical stages, cameras, and also to do common laboratory automation functionalities such as imaging.
ContributorsKuppuswamy, Venkataramanan (Author) / Meldrum, Deirdre (Thesis advisor) / Collofello, James (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Johnson, Roger (Committee member) / Arizona State University (Publisher)
Created2012
Description
The Open Services Gateway initiative (OSGi) framework is a standard of module system and service platform that implements a complete and dynamic component model. Currently most of OSGi implementations are implemented by Java, which has similarities of Android language. With the emergence of Android operating system, due to the similarities between Java and Android, the integration of module system and service platform from OSGi to Android system attracts more and more attention. How to make OSGi run in Android is a hot topic, further, how to find a mechanism to enable communication between OSGi and Android system is a more advanced area than simply making OSGi running in Android. This paper, which aimed to fulfill SOA (Service Oriented Architecture) and CBA (Component Based Architecture), proposed a solution on integrating Felix OSGi platform with Android system in order to build up Distributed OSGi framework between mobile phones upon XMPP protocol. And in this paper, it not only successfully makes OSGi run on Android, but also invents a mechanism that makes a seamless collaboration between these two platforms.
ContributorsDong, Xinyi (Author) / Huang, Dijiang (Thesis advisor) / Dasgupta, Partha (Committee member) / Chen, Yinong (Committee member) / Arizona State University (Publisher)
Created2012
Description
The pay-as-you-go economic model of cloud computing increases the visibility, traceability, and verifiability of software costs. Application developers must understand how their software uses resources when running in the cloud in order to stay within budgeted costs and/or produce expected profits. Cloud computing's unique economic model also leads naturally to an earn-as-you-go profit model for many cloud based applications. These applications can benefit from low level analyses for cost optimization and verification. Testing cloud applications to ensure they meet monetary cost objectives has not been well explored in the current literature. When considering revenues and costs for cloud applications, the resource economic model can be scaled down to the transaction level in order to associate source code with costs incurred while running in the cloud. Both static and dynamic analysis techniques can be developed and applied to understand how and where cloud applications incur costs. Such analyses can help optimize (i.e. minimize) costs and verify that they stay within expected tolerances. An adaptation of Worst Case Execution Time (WCET) analysis is presented here to statically determine worst case monetary costs of cloud applications. This analysis is used to produce an algorithm for determining control flow paths within an application that can exceed a given cost threshold. The corresponding results are used to identify path sections that contribute most to cost excess. A hybrid approach for determining cost excesses is also presented that is comprised mostly of dynamic measurements but that also incorporates calculations that are based on the static analysis approach. This approach uses operational profiles to increase the precision and usefulness of the calculations.
ContributorsBuell, Kevin, Ph.D (Author) / Collofello, James (Thesis advisor) / Davulcu, Hasan (Committee member) / Lindquist, Timothy (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2012
Description
Education in computer science is a difficult endeavor, with learning a new programing language being a barrier to entry, especially for college freshman and high school students. Learning a first programming language requires understanding the syntax of the language, the algorithms to use, and any additional complexities the language carries. Often times this becomes a deterrent from learning computer science at all. Especially in high school, students may not want to spend a year or more simply learning the syntax of a programming language. In order to overcome these issues, as well as to mitigate the issues caused by Microsoft discontinuing their Visual Programming Language (VPL), we have decided to implement a new VPL, ASU-VPL, based on Microsoft's VPL. ASU-VPL provides an environment where users can focus on algorithms and worry less about syntactic issues. ASU-VPL was built with the concepts of Robot as a Service and workflow based development in mind. As such, ASU-VPL is designed with the intention of allowing web services to be added to the toolbox (e.g. WSDL and REST services). ASU-VPL has strong support for multithreaded operations, including event driven development, and is built with Microsoft VPL users in mind. It provides support for many different robots, including Lego's third generation robots, i.e. EV3, and any open platform robots. To demonstrate the capabilities of ASU-VPL, this paper details the creation of an Intel Edison based robot and the use of ASU-VPL for programming both the Intel based robot and an EV3 robot. This paper will also discuss differences between ASU-VPL and Microsoft VPL as well as differences between developing for the EV3 and for an open platform robot.
ContributorsDe Luca, Gennaro (Author) / Chen, Yinong (Thesis director) / Cheng, Calvin (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2015-12
Description
Many psychology-rooted studies into the games industry seek to identify emotions players experience during gameplay. However, there is a need to extend this kind of research beyond the realm of emotion into more long-term concepts, like satisfaction. This experiment tested whether a specific game mechanic was enjoyable. Other literature has established a way to describe and quantify enjoyability. Using a survey based on that work, this study evaluated the addition of a 'gel gun' to a platforming game. The fun was found to significantly increase players' affective experiences, concentration, and sense of control, all being components of an enjoyable experience. It also exposed some conflicts within the survey that merit investigation. It was concluded that the 'gel gun' feature increased gameplay enjoyability without significantly diminishing any other enjoyable factors. Future work may explore the connections between this feature and specific elements of enjoyment.
ContributorsMints, John (Author) / Meuth, Ryan (Thesis director) / Chen, Yinong (Committee member) / Barrett, The Honors College (Contributor)
Created2014-12
Description
Gamification is the process of adding game mechanics to non game activities, thus creating a more engaging environment. Loyals provides a gamification API which can be consumed to add Loyals (achievements) to any website, application, or mobile app. Loyals are used in two major ways: (1) to create an interactive environment where users are rewarded for completing tasks and (2) as contextual information useful for analyzing user interaction with the application. The interactive environment inspires users to continue using an application while the contextual information can be used for improving the application to draw in new loyal visitors, ad targeting, creating user profiles, and much more.
ContributorsClaxton, Joshua Allen (Author) / Chen, Yinong (Thesis director) / Collofello, James (Committee member) / Irwin, Don (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-05
Description
Smartphones have become increasingly common over the past few years, and mobile games continue to be the most common type of application (Apple, Inc., 2013). For many people, the social aspect of gaming is very important, and thus most mobile games include support for playing with multiple players. However, there is a lack of common knowledge about which implementation of this functionality is most favorable from a development standpoint. In this study, we evaluate three different types of multiplayer gameplay (pass-and-play, Bluetooth, and GameCenter) via development cost and user interviews. We find that pass-and-play, the most easily-implemented mode, is not favored by players due to its inconvenience. We also find that GameCenter is not as well favored as expected due to latency of GameCenter's servers, and that Bluetooth multiplayer is the most well favored for social play due to its similarity to real-life play. Despite there being a large overhead in developing and testing Bluetooth and GameCenter multiplayer due to Apple's development process, this is irrelevant since professional developers must enroll in this process anyway. Therefore, the most effective multiplayer mode to develop is mostly determined by whether Internet play is desirable: Bluetooth if not, GameCenter if so. Future studies involving more complete development work and more types of multiplayer modes could yield more promising results.
ContributorsBradley, Michael Robert (Author) / Collofello, James (Thesis director) / Wilkerson, Kelly (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-12
Description
Our goals in our project are to enable management of distributed systems from one central location, record system logs and audit system based on these logs, and to demonstrate feasibility of platform-independent management of distributed systems based on CIM schema. In order to achieve these goals, we will have to overcome research challenges such as identifying meaningful CIM classes and attributes that could help to achieve this goal, how to gather managed objects of these CIM classes to collect such attributes on a given platform, and to research whether a platform's implementation of CIM is complete or incomplete so as to decide which platform would be the best to implement our solution. Even if a platform's implementation of CIM is incomplete, would we be able to create our own solution to a missing attribute and perhaps provide our own extension of the implementation? One major practical accomplishment will include developing a tool to allow distributed systems management regardless of a target system's platform. However, our research accomplishments will include having found the CIM classes that would be advantageous for system management and determining which platform would be best to work with managed objects of these classes.
ContributorsTrang, Patrick D (Author) / Ahn, Gail-Joon (Thesis director) / Chen, Yinong (Committee member) / Wilson, Adrian (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2013-05