Software Supply Chain Development and Application

Motivation: Free Libre Open Source Software (FLOSS) has become a critical componentin numerous devices and applications. Despite its importance, it is not clear why FLOSS ecosystem works so well or if it may cease to function. Majority of existing research is focusedon studying a specific software project or a portion of an ecosystem, but FLOSS has not been investigated in its entirety. Such view is necessary because of the deep and complex technical and social dependencies that go beyond the core of an individual ecosystem and tight inter-dependencies among ecosystems within FLOSS.Aim: We, therefore, aim to discover underlying relations within and across FLOSS projects and developers in open source community, mitigate potential risks induced by the lack of such knowledge and enable systematic analysis over entire open source community through the lens of supply chain (SC).Method: We utilize concepts from an area of supply chains to model risks of FLOSS ecosystem. FLOSS, due to the distributed decision making of software developers, technical dependencies, and copying of the code, has similarities to traditional supply chain. Unlike in traditional supply chain, where data is proprietary and distributed among players, we aim to measure open-source software supply chain (OSSC) by operationalizing supply chain concept in software domain using traces reconstructed from version control data.Results: We create a very large and frequently updated collection of version control data in the entire FLOSS ecosystems named World of Code (WoC), that can completely cross-reference authors, projects, commits, blobs, dependencies, and history of the FLOSS ecosystems, and provide capabilities to efficiently correct, augment, query, and analyze that data. Various researches and applications (e.g., software technology adoption investigation) have been successfully implemented by leveraging the combination of WoC and OSSC.Implications: With a SC perspective in FLOSS development and the increased visibility and transparency in OSSC, our work provides potential opportunities for researchers to conduct wider and deeper studies on OSS over entire FLOSS community, for developers to build more robust software and for students to learn technologies more efficiently and improve programming skills

Scenarios for Educational and Game Activities using Internet of Things Data

Raising awareness among young people and changing their behavior and habits concerning energy usage and the environment is key to achieving a sustainable planet. The goal to address the global climate problem requires informing the population on their roles in mitigation actions and adaptation of sustainable behaviors. Addressing climate change and achieve ambitious energy and climate targets requires a change in citizen behavior and consumption practices. IoT sensing and related scenario and practices, which address school children via discovery, gamification, and educational activities, are examined in this paper. Use of seawater sensors in STEM education, that has not previously been addressed, is included in these educational scenaria

Formalization of molecular interaction maps in systems biology; Application to simulations of the relationship between DNA damage response and circadian rhythms

Quantitative exploration of biological pathway networks must begin with a qualitative understanding of them. Often researchers aggregate and disseminate experimental data using regulatory diagrams with ad hoc notations leading to ambiguous interpretations of presented results. This thesis has two main aims. First, it develops software to allow researchers to aggregate pathway data diagrammatically using the Molecular Interaction Map (MIM) notation in order to gain a better qualitative understanding of biological systems. Secondly, it develops a quantitative biological model to study the effect of DNA damage on circadian rhythms. The second aim benefits from the first by making use of visual representations to identify potential system boundaries for the quantitative model. I focus first on software for the MIM notation - a notation to concisely visualize bioregulatory complexity and to reduce ambiguity for readers. The thesis provides a formalized MIM specification for software implementation along with a base layer of software components for the inclusion of the MIM notation in other software packages. It also provides an implementation of the specification as a user-friendly tool, PathVisio-MIM, for creating and editing MIM diagrams along with software to validate and overlay external data onto the diagrams. I focus secondly on the application of the MIM software to the quantitative exploration of the poorly understood role of SIRT1 and PARP1, two NAD+-dependent enzymes, in the regulation of circadian rhythms during DNA damage response. SIRT1 and PARP1 participate in the regulation of several key DNA damage-repair proteins and are the subjects of study as potential cancer therapeutic targets. In this part of the thesis, I present an ordinary differential equation (ODE) model that simulates the core circadian clock and the involvement of SIRT1 in both the positive and negative arms of circadian regulation. I then use this model is then used to predict a potential role for the competition for NAD+ supplies by SIRT1 and PARP1 leading to the observed behavior of primarily phase advancement of circadian oscillations during DNA damage response. The model further predicts a potential mechanism by which multiple forms of post-transcriptional modification may cooperate to produce a primarily phase advancement

Sustainability Index Development for Manufacturing Industry

Manufacturing industries are adopting new techniques and philosophies to address the acute shortage of non-renewable energy. Many of these manufacturing industries are focusing on achieving sustainability in every possible stage of their production, from raw material to the recycling of waste. Thus, the significance of using renewable energy, properly handling waste, and progressively conserving the environment is increasing day by day. In this research, the definition of sustainability is quite specific: being productive while making little to no impact on non-replenishable resources. The objective of the research is to determine the sustainability index of manufacturing plants. Since the topic has a broad scope, this research is limited to small and medium scale industries, which have common sets of operation and defined process plans. Besides, the focus goes into the nonhazardous waste and while doing so the indicators of the index are selected with respect to energy efficiency, workers\u27 health and safety and waste management. An interactive model is prepared to collect the responses. The interactive model has a series of questions that have to be answered. Based on the sustainable index, the model is able to provide suggestions to improve sustainability as well as carbon footprint consumption. The research has used datasets from various projects of Industrial Assessment Center (IAC) at West Virginia University to build the knowledge database. The interactive model system is executed by a software. The software uses the JavaRTM language and is validated by case studies from IAC. The outcome of this research is a software that can immensely help the industries identify their shortcomings in achieving sustainability, determine the carbon footprint reduction potential, and compare the sustainability index among different manufacturing industries