Analysis, Visualization, and Machine Learning of Epigenomic Data

The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C. These efforts have culminated in two web-based resources from our lab—Factorbook and SCREEN—for the exploration of epigenomic data for both human and mouse. Factorbook is a peak-centric resource presenting data such as motif enrichment and histone modification profiles for transcription factor binding sites computed from ENCODE ChIP-seq data. SCREEN provides an encyclopedia of ~2 million regulatory elements, including promoters and enhancers, identified using ENCODE ChIP-seq and DNase data, with an extensive UI for searching and visualization. While we have successfully utilized the thousands of available ENCODE ChIP-seq experiments to build the Encyclopedia and visualizers, we have also struggled with the practical and theoretical inability to assay every possible experiment on every possible biosample under every conceivable biological scenario. We have used machine learning techniques to predict TF binding sites and enhancers location, and demonstrate machine learning is critical to help decipher functional regions of the genome

API Documentation Generator

The importance of Application Programming Interfaces (APIs) in contemporary software development processes is growing. It can be challenging for developers to rapidly comprehend how to utilize a new API; therefore, good documentation is required. For efficient documentation support, we must understand how developers utilize widely available tools today. We provide the results of an exploratory study that examined the pros and cons of observing programmers as they used a basic application programming interface to find solutions. By utilizing an existing API documentation, you can save time and money by not having to reinvent the wheel when integrating with third-party enterprise systems and devices. This thesis describes and evaluates a unique technique to meeting API documentation requirements. I present a list of standards for the documentation of a selection of API tools based on my analysis of the existing literature and standard industry practice. I compare and contrast the documentation processes of Postman, Redocly, SwaggerHub, JavaDoc, and AutoREST with my own prototype implementation, which includes sample code for interacting with the API. I did a randomized study to establish the optimal method for determining the significance of API documentation requirements and to identify a strategy for simplifying documentation, with a focus on fulfilling the needs of user developers. Using Postman, Redocly, SwaggerHub, JavaDoc, and AutoREST, I found reoccurring difficulties that may be minimized with the suggested documentation

Transforming scientific research and development in precision agriculture : the case of hyperspectral sensing and imaging : a thesis presented in partial fulfilment of the requirements for the degree of Doctor in Philosophy in Agriculture at Massey University, Manawatū, New Zealand. EMBARGOED until 30 September 2023.

Embargoed until 30 September 2023There has been increasing social and academic debate in recent times surrounding the arrival of agricultural big data. Capturing and responding to real world variability is a defining objective of the rapidly evolving field of precision agriculture (PA). While data have been central to knowledge-making in the field since its inception in the 1980s, research has largely operated in a data-scarce environment, constrained by time-consuming and expensive data collection methods. While there is a rich tradition of studying scientific practice within laboratories in other fields, PA researchers have rarely been the explicit focal point of detailed empirical studies, especially in the laboratory setting. The purpose of this thesis is to contribute to new knowledge of the influence of big data technologies through an ethnographic exploration of a working PA laboratory. The researcher spent over 30 months embedded as a participant observer of a small PA laboratory, where researchers work with nascent data rich remote sensing technologies. To address the research question: “How do the characteristics of technological assemblages affect PA research and development?” the ethnographic case study systematically identifies and responds to the challenges and opportunities faced by the science team as they adapt their scientific processes and resources to refine value from a new data ecosystem. The study describes the ontological characteristics of airborne hyperspectral sensing and imaging data employed by PA researchers. Observations of the researchers at work lead to a previously undescribed shift in the science process, where effort moves from the planning and performance of the data collection stage to the data processing and analysis stage. The thesis develops an argument that changing data characteristics are central to this shift in the scientific method researchers are employing to refine knowledge and value from research projects. Importantly, the study reveals that while researchers are working in a rapidly changing environment, there is little reflection on the implications of these changes on the practice of science-making. The study also identifies a disjunction to how science is done in the field, and what is reported. We discover that the practices that provide disciplinary ways of doing science are not established in this field and moments to learn are siloed because of commercial constraints the commercial structures imposed in this case study of contemporary PA research

Librarian skills in the 21st century workplace: the development, running and analysis of a training scheme for non-traditional library work contexts

Research suggests that recently graduated librarians are failing to find work in the traditional library context and consequently are seeking employment in related fields; also that internships are recognized as a valuable component of professional training, that students find them useful in developing skills, with demand outstripping supply. This study consisted of setting up, running, and analyzing an experimental intern training programme for MLS students outside the traditional library context. Its aims were to : i) Develop and manage an intern training programme (ITP) specifically focused on mentoring recent graduates and students in the application of their library skills in a non-library work context; ii) Use this model to facilitate students and recent graduates in transferring their library skills to a non-library work context; iii) Gauge whether participants found the ITP effective in preparing them for finding work – either in a traditional library or outside the traditional library setting. Through setting up this programme and running it since 2013, this study has made a primarily applied contribution to the discipline. In this written component of the study the researcher offers the documentation of the programme as a live case study analysed using a combination of tools including surveys, interviews and both qualitative and quantitative methods. Findings show that interns expect to use internships in the job searching process; that they expect to acquire new skills not developed on their MLS programmes; that they would still prefer traditional library jobs but that they expect their careers to involve non-traditional work contexts. Related to this, participants believe the internship has raised awareness of a wider range of suitable jobs. This indicates that they see the nature of librarianship changing – something reinforced by the way they believe librarianship is evolving through, for example, integrating social media into the role of the librarian. This study and its findings contributes to raising awareness in the library sector of the changing nature of the world of work for the next generation of librarians and, in turn, contribute to MLS programmes by indicating how they may adapt as the 21st century workplace continues to evolve.Information ScienceD. Litt. et Phil. (Information Science

Cybersecurity of Digital Service Chains

This open access book presents the main scientific results from the H2020 GUARD project. The GUARD project aims at filling the current technological gap between software management paradigms and cybersecurity models, the latter still lacking orchestration and agility to effectively address the dynamicity of the former. This book provides a comprehensive review of the main concepts, architectures, algorithms, and non-technical aspects developed during three years of investigation; the description of the Smart Mobility use case developed at the end of the project gives a practical example of how the GUARD platform and related technologies can be deployed in practical scenarios. We expect the book to be interesting for the broad group of researchers, engineers, and professionals daily experiencing the inadequacy of outdated cybersecurity models for modern computing environments and cyber-physical systems

Metabolomics Data Processing and Data Analysis—Current Best Practices

Metabolomics data analysis strategies are central to transforming raw metabolomics data files into meaningful biochemical interpretations that answer biological questions or generate novel hypotheses. This book contains a variety of papers from a Special Issue around the theme “Best Practices in Metabolomics Data Analysis”. Reviews and strategies for the whole metabolomics pipeline are included, whereas key areas such as metabolite annotation and identification, compound and spectral databases and repositories, and statistical analysis are highlighted in various papers. Altogether, this book contains valuable information for researchers just starting in their metabolomics career as well as those that are more experienced and look for additional knowledge and best practice to complement key parts of their metabolomics workflows

Strengthening digital engagement to provide intersectional narratives within museums using user generated metadata: a case study at Chicago’s Adler Planetarium and the applications beyond.

Cultural heritage institutions have experienced a technological boom over the last fifty years, and digital access to collections has evolved from searchable catalogues available onsite with the aid of a research staff member, to a variety of modalities ranging from web-based, publicly available databases to interaction through social media platforms. As institutions look to capitalize on the new ways in which their collections are being discovered, cataloguing visual data and expanding metadata are necessary for staying relevant, on trend, and engaged with audiences. Metadata allows people to perform various operations with data, including searching, managing, structuring, preserving, and authenticating resources. Creating metadata is a labor intensive process, and one solution to the need for more extensive cataloguing is crowdsourcing, which over the last two decades has proven not only to increase access points to collections but also to enrich catalogue data. As well, crowdsourcing presents an opportunity for museums to make what has long been an opaque back-end process more transparent, turning metadata creation into a mission-supporting activity. Using an adapted practice-based methodology, this thesis examines projects I devised and led at Chicago’s Adler Planetarium, Tag Along with Adler, as a case study in the benefits of crowdsourcing projects (and metadata tagging projects in particular) within cultural heritage institutions, not as mere outsourcing of labor but rather as participatory, even transformational experiences for an engaged public that also enhance and expand cataloguing. It also explores the successes and shortcomings of this case study and what these results suggest for the field at large with respect to language and metadata production. In particular, it demonstrates that there exists a semantic gap in the language and descriptive styles of museum professionals, on the one hand, and the public, on the other, and that crowdsourcing demonstrates promise to help bridge this gap while also providing an opportunity for the public to engage with museums directly