Healthy or Not: A Way to Predict Ecosystem Health in GitHub

With the development of open source community, through the interaction of developers, the collaborative development of software, and the sharing of software tools, the formation of open source software ecosystem has matured. Natural ecosystems provide ecological services on which human beings depend. Maintaining a healthy natural ecosystem is a necessity for the sustainable development of mankind. Similarly, maintaining a healthy ecosystem of open source software is also a prerequisite for the sustainable development of open source communities, such as GitHub. This paper takes GitHub as an example to analyze the health condition of open source ecosystem and, also, it is a research area in Symmetry. Firstly, the paper presents the healthy definition of GitHub open source ecosystem health and, then, according to the main components of natural ecosystem health, the paper proposes the health indicators and health indicators evaluation method. Based on the above, the GitHub ecosystem health prediction method is proposed. By analyzing the projects and data collected in GitHub, it is found that, using the proposed evaluation indicators and method, we can analyze the healthy development trend of the GitHub ecosystem and contribute to the stability of ecosystem development

Empirical research on the evaluation model and method of sustainability of the open source ecosystem

The development of open source brings new thinking and production modes to software engineering and computer science, and establishes a software development method and ecological environment in which groups participate. Regardless of investors, developers, participants, and managers, they are most concerned about whether the Open Source Ecosystem can be sustainable to ensure that the ecosystem they choose will serve users for a long time. Moreover, the most important quality of the software ecosystem is sustainability, and it is also a research area in Symmetry. Therefore, it is significant to assess the sustainability of the Open Source Ecosystem. However, the current measurement of the sustainability of the Open Source Ecosystem lacks universal measurement indicators, as well as a method and a model. Therefore, this paper constructs an Evaluation Indicators System, which consists of three levels: The target level, the guideline level and the evaluation level, and takes openness, stability, activity, and extensibility as measurement indicators. On this basis, a weight calculation method, based on information contribution values and a Sustainability Assessment Model, is proposed. The models and methods are used to analyze the factors affecting the sustainability of Stack Overflow (SO) ecosystem. Through the analysis, we find that every indicator in the SO ecosystem is partaking in different development trends. The development trend of a single indicator does not represent the sustainable development trend of the whole ecosystem. It is necessary to consider all of the indicators to judge that ecosystem’s sustainability. The research on the sustainability of the Open Source Ecosystem is helpful for judging software health, measuring development efficiency and adjusting organizational structure. It also provides a reference for researchers who study the sustainability of software engineering

Identification-method research for open-source software ecosystems

In recent years, open-source software (OSS) development has grown, with many developers around the world working on different OSS projects. A variety of open-source software ecosystems have emerged, for instance, GitHub, StackOverflow, and SourceForge. One of the most typical social-programming and code-hosting sites, GitHub, has amassed numerous open-source-software projects and developers in the same virtual collaboration platform. Since GitHub itself is a large open-source community, it hosts a collection of software projects that are developed together and coevolve. The great challenge here is how to identify the relationship between these projects, i.e., project relevance. Software-ecosystem identification is the basis of other studies in the ecosystem. Therefore, how to extract useful information in GitHub and identify software ecosystems is particularly important, and it is also a research area in symmetry. In this paper, a Topic-based Project Knowledge Metrics Framework (TPKMF) is proposed. By collecting the multisource dataset of an open-source ecosystem, project-relevance analysis of the open-source software is carried out on the basis of software-ecosystem identification. Then, we used our Spectral Clustering algorithm based on Core Project (CP-SC) to identify software-ecosystem projects and further identify software ecosystems. We verified that most software ecosystems usually contain a core software project, and most other projects are associated with it. Furthermore, we analyzed the characteristics of the ecosystem, and we also found that interactive information has greater impact on project relevance. Finally, we summarize the Topic-based Project Knowledge Metrics Framework

Visualization of metabolic interaction networks in microbial communities using VisANT 5.0

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues.This work was supported by the National Institutes of Health, R01GM103502-05 to CD, ZH and DS. Partial support was also provided by grants from the Office of Science (BER), U.S. Department of Energy (DE-SC0004962), the Joslin Diabetes Center (Pilot & Feasibility grant P30 DK036836), the Army Research Office under MURI award W911NF-12-1-0390, National Institutes of Health (1RC2GM092602-01, R01GM089978 and 5R01DE024468), NSF (1457695), and Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS), Purchase Request No. HR0011515303, Program Code: TRS-0 Issued by DARPA/CMO under Contract No. HR0011-15-C-0091. Funding for open access charge: National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (R01GM103502-05 - National Institutes of Health; 1RC2GM092602-01 - National Institutes of Health; R01GM089978 - National Institutes of Health; 5R01DE024468 - National Institutes of Health; DE-SC0004962 - Office of Science (BER), U.S. Department of Energy; P30 DK036836 - Joslin Diabetes Center; W911NF-12-1-0390 - Army Research Office under MURI; 1457695 - NSF; HR0011515303 - Defense Advanced Research Projects Agency Biological Technologies Office (BTO), Program: Biological Robustness In Complex Settings (BRICS); HR0011-15-C-0091 - DARPA/CMO; National Institutes of Health)Published versio

Architecture and Information Requirements to Assess and Predict Flight Safety Risks During Highly Autonomous Urban Flight Operations

As aviation adopts new and increasingly complex operational paradigms, vehicle types, and technologies to broaden airspace capability and efficiency, maintaining a safe system will require recognition and timely mitigation of new safety issues as they emerge and before significant consequences occur. A shift toward a more predictive risk mitigation capability becomes critical to meet this challenge. In-time safety assurance comprises monitoring, assessment, and mitigation functions that proactively reduce risk in complex operational environments where the interplay of hazards may not be known (and therefore not accounted for) during design. These functions can also help to understand and predict emergent effects caused by the increased use of automation or autonomous functions that may exhibit unexpected non-deterministic behaviors. The envisioned monitoring and assessment functions can look for precursors, anomalies, and trends (PATs) by applying model-based and data-driven methods. Outputs would then drive downstream mitigation(s) if needed to reduce risk. These mitigations may be accomplished using traditional design revision processes or via operational (and sometimes automated) mechanisms. The latter refers to the in-time aspect of the system concept. This report comprises architecture and information requirements and considerations toward enabling such a capability within the domain of low altitude highly autonomous urban flight operations. This domain may span, for example, public-use surveillance missions flown by small unmanned aircraft (e.g., infrastructure inspection, facility management, emergency response, law enforcement, and/or security) to transportation missions flown by larger aircraft that may carry passengers or deliver products. Caveat: Any stated requirements in this report should be considered initial requirements that are intended to drive research and development (R&D). These initial requirements are likely to evolve based on R&D findings, refinement of operational concepts, industry advances, and new industry or regulatory policies or standards related to safety assurance

PICES Press, Vol. 20, No. 2, Summer 2012

•The 2012 Inter-sessional Science Board Meeting: A Note from Science Board Chairman (pp. 1-4) ◾PICES Interns (p. 4) ◾2012 Inter-sessional Workshop on a Roadmap for FUTURE (pp. 5-8) ◾Second Symposium on “Effects of Climate Change on the World’s Oceans” (pp. 9-13) ◾2012 Yeosu Workshop on “Framework for Ocean Observing” (pp. 14-15) ◾2012 Yeosu Workshop on “Climate Change Projections” (pp. 16-17) ◾2012 Yeosu Workshop on “Coastal Blue Carbon” (pp. 18-20) ◾Polar Comparisons: Summary of 2012 Yeosu Workshop (pp. 21-23) ◾2012 Yeosu Workshop on “Climate Change and Range Shifts in the Oceans" (pp. 24-27) ◾2012 Yeosu Workshop on “Beyond Dispersion” (pp. 28-30) ◾2012 Yeosu Workshop on “Public Perception of Climate Change” (pp. 31, 50) ◾PICES Working Group 20: Accomplishments and Legacy (pp. 32-33) ◾The State of the Western North Pacific in the Second Half of 2011 (pp. 34-35) ◾Another Cold Winter in the Gulf of Alaska (pp. 36-37) ◾The Bering Sea: Current Status and Recent Events (pp. 38-40) ◾PICES/ICES 2012 Conference for Early Career Marine Scientists (pp. 41-43) ◾Completion of the PICES Seafood Safety Project – Indonesia (pp. 44-46) ◾Oceanography Improves Salmon Forecasts (p. 47) ◾2012 GEOHAB Open Science Meeting (p. 48-50) ◾Shin-ichi Ito awarded 2011 Uda Prize (p. 50

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Medical data processing and analysis for remote health and activities monitoring

Recent developments in sensor technology, wearable computing, Internet of Things (IoT), and wireless communication have given rise to research in ubiquitous healthcare and remote monitoring of human\u2019s health and activities. Health monitoring systems involve processing and analysis of data retrieved from smartphones, smart watches, smart bracelets, as well as various sensors and wearable devices. Such systems enable continuous monitoring of patients psychological and health conditions by sensing and transmitting measurements such as heart rate, electrocardiogram, body temperature, respiratory rate, chest sounds, or blood pressure. Pervasive healthcare, as a relevant application domain in this context, aims at revolutionizing the delivery of medical services through a medical assistive environment and facilitates the independent living of patients. In this chapter, we discuss (1) data collection, fusion, ownership and privacy issues; (2) models, technologies and solutions for medical data processing and analysis; (3) big medical data analytics for remote health monitoring; (4) research challenges and opportunities in medical data analytics; (5) examples of case studies and practical solutions