Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine.

BACKGROUND: The last decade has seen a dramatic increase in the availability of scientific data, where human-related biological databases have grown not only in count but also in volume, posing unprecedented challenges in data storage, processing, analysis, exchange, and curation. Next generation sequencing (NGS) advancements have facilitated and accelerated the process of identifying genetic variations. Adopting NGS with Whole-Genome and RNA sequencing in a diagnostic context has the potential to improve disease-risk detection in support of precision medicine and drug discovery. Several bioinformatics pipelines have been developed to strengthen variant interpretation by efficiently processing and analyzing sequence data, whereas many published results show how genomics data can be proactively incorporated into medical practices and improve utilization of clinical information. To utilize the wealth of genomics and health, there is a crucial need to generate appropriate gene-disease annotation repositories accessed through modern technology. RESULTS: Our focus here is to create a comprehensive database with mobile access to actionable genes and classified diseases, considered the foundation for clinical genomics and precision medicine. We present a publicly available iOS app, PAS-Gen, which invites global users to freely download it on iPhone and iPad devices, quickly adopt its easy to use interface, and search for genes and related diseases. PAS-Gen was developed using Swift, XCODE, and PHP scripting that uses Web and MySQL database servers, which includes over 59,000 protein-coding and non-coding genes, and over 90,000 classified gene-disease associations. PAS-Gen is founded on the clinical and scientific premise that easier healthcare and genomics data sharing will accelerate future medical discoveries. CONCLUSIONS: We present a cutting-edge gene-disease database with a smart phone application, integrating information on classified diseases and related genes. The PAS-Gen app will assist researchers, medical practitioners, and pharmacists by providing a broad and view of genes that may be implicated in the likelihood of developing certain diseases. This tool with accelerate users\u27 abilities to understand the genetic basis of human complex diseases and by assimilating genomic and phenotypic data will support future work to identify gene-specific designer drugs, target precise molecular fingerprints for tumors, suggest appropriate drug therapies, predict individual susceptibility to disease, and diagnose and treat rare illnesses

The State of Practice for Security Unit Testing: Towards Data Driven Strategies to Shift Security into Developer\u27s Automated Testing Workflows

The pressing need to “shift security left” in the software development lifecycle has motivated efforts to adapt the iterative and continuous process models used in practice today. Security unit testing is praised by practitioners and recommended by expert groups, usually in the context of DevSecOps and achieving “continuous security”. In addition to vulnerability testing and standards adherence, this technique can help developers verify that security controls are implemented correctly, i.e. functional security testing. Further, the means by which security unit testing can be integrated into developer workflows is unique from other standalone tools as it is an adaptation of practices and infrastructure developers are already familiar with. Yet, software engineering researchers have so far failed to include this technique in their empirical studies on secure development and little is known about the state of practice for security unit testing. This dissertation is motivated by the disconnect between promotion of security unit testing and the lack of empirical evidence on how it is and can be applied. The goal of this work was to address the disconnect towards identifying actionable strategies to promote wider adoption and mitigate observed challenges. Three mixed-method empirical studies were conducted wherein practitioner-authored unit test code, Q&A posts, and grey literature were analyzed through three lenses: Practices (what they do), Perspectives and Guidelines (what and how they think it should be done), and Pain Points (what challenges they face) to incorporate both technical and human factors of this phenomena. Accordingly, this work contributes novel and important insights into how developers write functional unit tests for at least nine security controls, including a taxonomy of 53 authentication unit test cases derived from real code and a detailed analysis of seven unique pain points that developers seek help with from peers on Q&A sites. Recommendations given herein for conducting and adopting security unit testing, including mitigating challenges and addressing gaps between available and needed support, are grounded in the guidelines and perspectives on the benefits, limitations, use cases, and integration strategies shared in grey literature authored by practitioners

An enhanced learning analytics plugin for Moodle: Student engagement and personalised intervention

© ASCILITE 2015 - Australasian Society for Computers in Learning and Tertiary Education, Conference Proceedings.All right reserved. Moodle, an open source Learning Management System (LMS), collects a large amount of data on student interactions within it, including content, assessments, and communication. Some of these data can be used as proxy indicators of student engagement, as well as predictors for performance. However, these data are difficult to interrogate and even more difficult to action from within Moodle. We therefore describe a design-based research narrative to develop an enhanced version of an open source Moodle Engagement Analytics Plugin (MEAP). Working with the needs of unit convenors and student support staff, we sought to improve the available information, the way it is represented, and create affordances for action based on this. The enhanced MEAP (MEAP+) allows analyses of gradebook data, assessment submissions, login metrics, and forum interactions, as well as direct action through personalised emails to students based on these analyses

Network Traffic Analysis Using Local Outlier Factor

The issue that this study addresses is the high rate of false positives, high maintenance, and lack of stability and precision that the existing network intrusion detection algorithm faces. To address this problem, we proposed a Local Outlier Factor (LOF) Algorithm that locates outliers and anomalies by comparing the deviation of one data point with respect to its neighbors. To gather data, we will use DARPA’s KDDCup99 as well as questions towards analysts. This data will help determine whether the LOF algorithm is more effective than existing solutions that are presented in the network intrusion detection space

The Potential for Student Performance Prediction in Small Cohorts with Minimal Available Attributes

The measurement of student performance during their progress through university study provides academic leadership with critical information on each student’s likelihood of success. Academics have traditionally used their interactions with individual students through class activities and interim assessments to identify those “at risk” of failure/withdrawal. However, modern university environments, offering easy on-line availability of course material, may see reduced lecture/tutorial attendance, making such identification more challenging. Modern data mining and machine learning techniques provide increasingly accurate predictions of student examination assessment marks, although these approaches have focussed upon large student populations and wide ranges of data attributes per student. However, many university modules comprise relatively small student cohorts, with institutional protocols limiting the student attributes available for analysis. It appears that very little research attention has been devoted to this area of analysis and prediction. We describe an experiment conducted on a final-year university module student cohort of 23, where individual student data are limited to lecture/tutorial attendance, virtual learning environment accesses and intermediate assessments. We found potential for predicting individual student interim and final assessment marks in small student cohorts with very limited attributes and that these predictions could be useful to support module leaders in identifying students potentially “at risk.”.Peer reviewe

Student Privacy in Learning Analytics: An Information Ethics Perspective

In recent years, educational institutions have started using the tools of commercial data analytics in higher education. By gathering information about students as they navigate campus information systems, learning analytics “uses analytic techniques to help target instructional, curricular, and support resources” to examine student learning behaviors and change students’ learning environments. As a result, the information educators and educational institutions have at their disposal is no longer demarcated by course content and assessments, and old boundaries between information used for assessment and information about how students live and work are blurring. Our goal in this paper is to provide a systematic discussion of the ways in which privacy and learning analytics conflict and to provide a framework for understanding those conflicts. We argue that there are five crucial issues about student privacy that we must address in order to ensure that whatever the laudable goals and gains of learning analytics, they are commensurate with respecting students’ privacy and associated rights, including (but not limited to) autonomy interests. First, we argue that we must distinguish among different entities with respect to whom students have, or lack, privacy. Second, we argue that we need clear criteria for what information may justifiably be collected in the name of learning analytics. Third, we need to address whether purported consequences of learning analytics (e.g., better learning outcomes) are justified and what the distributions of those consequences are. Fourth, we argue that regardless of how robust the benefits of learning analytics turn out to be, students have important autonomy interests in how information about them is collected. Finally, we argue that it is an open question whether the goods that justify higher education are advanced by learning analytics, or whether collection of information actually runs counter to those goods