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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

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
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

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
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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

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
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Description
Access control is necessary for information assurance in many of today's applications such as banking and electronic health record. Access control breaches are critical security problems that can result from unintended and improper implementation of security policies. Security testing can help identify security vulnerabilities early and avoid unexpected expensive cost

Access control is necessary for information assurance in many of today's applications such as banking and electronic health record. Access control breaches are critical security problems that can result from unintended and improper implementation of security policies. Security testing can help identify security vulnerabilities early and avoid unexpected expensive cost in handling breaches for security architects and security engineers. The process of security testing which involves creating tests that effectively examine vulnerabilities is a challenging task. Role-Based Access Control (RBAC) has been widely adopted to support fine-grained access control. However, in practice, due to its complexity including role management, role hierarchy with hundreds of roles, and their associated privileges and users, systematically testing RBAC systems is crucial to ensure the security in various domains ranging from cyber-infrastructure to mission-critical applications. In this thesis, we introduce i) a security testing technique for RBAC systems considering the principle of maximum privileges, the structure of the role hierarchy, and a new security test coverage criterion; ii) a MTBDD (Multi-Terminal Binary Decision Diagram) based representation of RBAC security policy including RHMTBDD (Role Hierarchy MTBDD) to efficiently generate effective positive and negative security test cases; and iii) a security testing framework which takes an XACML-based RBAC security policy as an input, parses it into a RHMTBDD representation and then generates positive and negative test cases. We also demonstrate the efficacy of our approach through case studies.
ContributorsGupta, Poonam (Author) / Ahn, Gail-Joon (Thesis advisor) / Collofello, James (Committee member) / Huang, Dijiang (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Introductory programming courses, also known as CS1, have a specific set of expected outcomes related to the learning of the most basic and essential computational concepts in computer science (CS). However, two of the most often heard complaints in such courses are that (1) they are divorced from the reality

Introductory programming courses, also known as CS1, have a specific set of expected outcomes related to the learning of the most basic and essential computational concepts in computer science (CS). However, two of the most often heard complaints in such courses are that (1) they are divorced from the reality of application and (2) they make the learning of the basic concepts tedious. The concepts introduced in CS1 courses are highly abstract and not easily comprehensible. In general, the difficulty is intrinsic to the field of computing, often described as "too mathematical or too abstract." This dissertation presents a small-scale mixed method study conducted during the fall 2009 semester of CS1 courses at Arizona State University. This study explored and assessed students' comprehension of three core computational concepts - abstraction, arrays of objects, and inheritance - in both algorithm design and problem solving. Through this investigation students' profiles were categorized based on their scores and based on their mistakes categorized into instances of five computational thinking concepts: abstraction, algorithm, scalability, linguistics, and reasoning. It was shown that even though the notion of computational thinking is not explicit in the curriculum, participants possessed and/or developed this skill through the learning and application of the CS1 core concepts. Furthermore, problem-solving experiences had a direct impact on participants' knowledge skills, explanation skills, and confidence. Implications for teaching CS1 and for future research are also considered.
ContributorsBillionniere, Elodie V (Author) / Collofello, James (Thesis advisor) / Ganesh, Tirupalavanam G. (Thesis advisor) / VanLehn, Kurt (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2011
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Description
Machine learning tutorials often employ an application and runtime specific solution for a given problem in which users are expected to have a broad understanding of data analysis and software programming. This thesis focuses on designing and implementing a new, hands-on approach to teaching machine learning by streamlining the process

Machine learning tutorials often employ an application and runtime specific solution for a given problem in which users are expected to have a broad understanding of data analysis and software programming. This thesis focuses on designing and implementing a new, hands-on approach to teaching machine learning by streamlining the process of generating Inertial Movement Unit (IMU) data from multirotor flight sessions, training a linear classifier, and applying said classifier to solve Multi-rotor Activity Recognition (MAR) problems in an online lab setting. MAR labs leverage cloud computing and data storage technologies to host a versatile environment capable of logging, orchestrating, and visualizing the solution for an MAR problem through a user interface. MAR labs extends Arizona State University’s Visual IoT/Robotics Programming Language Environment (VIPLE) as a control platform for multi-rotors used in data collection. VIPLE is a platform developed for teaching computational thinking, visual programming, Internet of Things (IoT) and robotics application development. As a part of this education platform, this work also develops a 3D simulator capable of simulating the programmable behaviors of a robot within a maze environment and builds a physical quadrotor for use in MAR lab experiments.
ContributorsDe La Rosa, Matthew Lee (Author) / Chen, Yinong (Thesis advisor) / Collofello, James (Committee member) / Huang, Dijiang (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The following is a case study composed of three workflow investigations at the open source software development (OSSD) based Apache Software Foundation (Apache). I start with an examination of the workload inequality within the Apache, particularly with regard to requirements writing. I established that the stronger a participant's

The following is a case study composed of three workflow investigations at the open source software development (OSSD) based Apache Software Foundation (Apache). I start with an examination of the workload inequality within the Apache, particularly with regard to requirements writing. I established that the stronger a participant's experience indicators are, the more likely they are to propose a requirement that is not a defect and the more likely the requirement is eventually implemented. Requirements at Apache are divided into work tickets (tickets). In our second investigation, I reported many insights into the distribution patterns of these tickets. The participants that create the tickets often had the best track records for determining who should participate in that ticket. Tickets that were at one point volunteered for (self-assigned) had a lower incident of neglect but in some cases were also associated with severe delay. When a participant claims a ticket but postpones the work involved, these tickets exist without a solution for five to ten times as long, depending on the circumstances. I make recommendations that may reduce the incidence of tickets that are claimed but not implemented in a timely manner. After giving an in-depth explanation of how I obtained this data set through web crawlers, I describe the pattern mining platform I developed to make my data mining efforts highly scalable and repeatable. Lastly, I used process mining techniques to show that workflow patterns vary greatly within teams at Apache. I investigated a variety of process choices and how they might be influencing the outcomes of OSSD projects. I report a moderately negative association between how often a team updates the specifics of a requirement and how often requirements are completed. I also verified that the prevalence of volunteerism indicators is positively associated with work completion but what was surprising is that this correlation is stronger if I exclude the very large projects. I suggest the largest projects at Apache may benefit from some level of traditional delegation in addition to the phenomenon of volunteerism that OSSD is normally associated with.
ContributorsPanos, Ryan (Author) / Collofello, James (Thesis advisor) / Fowler, John (Thesis advisor) / Pan, Rong (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2017
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Description
Affect signals what humans care about and is involved in rational decision-making and action selection. Many technologies may be improved by the capability to recognize human affect and to respond adaptively by appropriately modifying their operation. This capability, named affect-driven self-adaptation, benefits systems as diverse as learning environments, healthcare applications,

Affect signals what humans care about and is involved in rational decision-making and action selection. Many technologies may be improved by the capability to recognize human affect and to respond adaptively by appropriately modifying their operation. This capability, named affect-driven self-adaptation, benefits systems as diverse as learning environments, healthcare applications, and video games, and indeed has the potential to improve systems that interact intimately with users across all sectors of society. The main challenge is that existing approaches to advancing affect-driven self-adaptive systems typically limit their applicability by supporting the creation of one-of-a-kind systems with hard-wired affect recognition and self-adaptation capabilities, which are brittle, costly to change, and difficult to reuse. A solution to this limitation is to leverage the development of affect-driven self-adaptive systems with a manufacturing vision.

This dissertation demonstrates how using a software product line paradigm can jumpstart the development of affect-driven self-adaptive systems with that manufacturing vision. Applying a software product line approach to the affect-driven self-adaptive domain provides a comprehensive, flexible and reusable infrastructure of components with mechanisms to monitor a user’s affect and his/her contextual interaction with a system, to detect opportunities for improvements, to select a course of action, and to effect changes. It also provides a domain-specific architecture and well-documented process guidelines, which facilitate an understanding of the organization of affect-driven self-adaptive systems and their implementation by systematically customizing the infrastructure to effectively address the particular requirements of specific systems.

The software product line approach is evaluated by applying it in the development of learning environments and video games that demonstrate the significant potential of the solution, across diverse development scenarios and applications.

The key contributions of this work include extending self-adaptive system modeling, implementing a reusable infrastructure, and leveraging the use of patterns to exploit the commonalities between systems in the affect-driven self-adaptation domain.
ContributorsGonzalez-Sanchez, Javier (Author) / Burleson, Winslow (Thesis advisor) / Collofello, James (Thesis advisor) / Garlan, David (Committee member) / Sarjoughian, Hessam S. (Committee member) / Atkinson, Robert (Committee member) / Arizona State University (Publisher)
Created2016
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Description
The complexity of the systems that software engineers build has continuously grown since the inception of the field. What has not changed is the engineers' mental capacity to operate on about seven distinct pieces of information at a time. The widespread use of UML has led to more abstract software

The complexity of the systems that software engineers build has continuously grown since the inception of the field. What has not changed is the engineers' mental capacity to operate on about seven distinct pieces of information at a time. The widespread use of UML has led to more abstract software design activities, however the same cannot be said for reverse engineering activities. The introduction of abstraction to reverse engineering will allow the engineer to move farther away from the details of the system, increasing his ability to see the role that domain level concepts play in the system. In this thesis, we present a technique that facilitates filtering of classes from existing systems at the source level based on their relationship to concepts in the domain via a classification method using machine learning. We showed that concepts can be identified using a machine learning classifier based on source level metrics. We developed an Eclipse plugin to assist with the process of manually classifying Java source code, and collecting metrics and classifications into a standard file format. We developed an Eclipse plugin to act as a concept identifier that visually indicates a class as a domain concept or not. We minimized the size of training sets to ensure a useful approach in practice. This allowed us to determine that a training set of 7:5 to 10% is nearly as effective as a training set representing 50% of the system. We showed that random selection is the most consistent and effective means of selecting a training set. We found that KNN is the most consistent performer among the learning algorithms tested. We determined the optimal feature set for this classification problem. We discussed two possible structures besides a one to one mapping of domain knowledge to implementation. We showed that classes representing more than one concept are simply concepts at differing levels of abstraction. We also discussed composite concepts representing a domain concept implemented by more than one class. We showed that these composite concepts are difficult to detect because the problem is NP-complete.
ContributorsCarey, Maurice (Author) / Colbourn, Charles (Thesis advisor) / Collofello, James (Thesis advisor) / Davulcu, Hasan (Committee member) / Sarjoughian, Hessam S. (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Software Managed Manycore (SMM) architectures - in which each core has only a scratch pad memory (instead of caches), - are a promising solution for scaling memory hierarchy to hundreds of cores. However, in these architectures, the code and data of the tasks mapped to the cores must be explicitly

Software Managed Manycore (SMM) architectures - in which each core has only a scratch pad memory (instead of caches), - are a promising solution for scaling memory hierarchy to hundreds of cores. However, in these architectures, the code and data of the tasks mapped to the cores must be explicitly managed in the software by the compiler. State-of-the-art compiler techniques for SMM architectures require inter-procedural information and analysis. A call graph of the program does not have enough information, and Global CFG, i.e., combining all the control flow graphs of the program has too much information, and becomes too big. As a result, most new techniques have informally defined and used GCCFG (Global Call Control Flow Graph) - a whole program representation which captures the control-flow as well as function call information in a succinct way - to perform inter-procedural analysis. However, how to construct it has not been shown yet. We find that for several simple call and control flow graphs, constructing GCCFG is relatively straightforward, but there are several cases in common applications where unique graph transformation is needed in order to formally and correctly construct the GCCFG. This paper fills this gap, and develops graph transformations to allow the construction of GCCFG in (almost) all cases. Our experiments show that by using succinct representation (GCCFG) rather than elaborate representation (GlobalCFG), the compilation time of state-of-the-art code management technique [4] can be improved by an average of 5X, and that of stack management [20] can be improved by an average of 4X.
ContributorsHolton, Bryce (Author) / Shrivastava, Aviral (Thesis advisor) / Collofello, James (Committee member) / Richa, Andrea (Committee member) / Arizona State University (Publisher)
Created2014