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  1. Harris, F. ; Wu, R. ; Redei, A. (Ed.)
    Networks are pervasive in society: infrastructures (e.g., telephone), commercial sectors (e.g., banking), and biological and genomic systems can be represented as networks. Con- sequently, there are software libraries that analyze networks. Containers (e.g., Docker, Singularity), which hold both runnable codes and their execution environments, are in- creasingly utilized by analysts to run codes in a platform-independent fashion. Portability is further enhanced by not only providing software library methods, but also the driver code (i.e., main() method) for each library method. In this way, a user only has to know the invocation for the main() method that is in the container.more »In this work, we describe an automated approach for generating a main() method for each software library method. A single intermediate representation (IR) format is used for all library methods, and one IR instance is populated for one library method by parsing its comments and method signature. An IR for the main() method is generated from that for the library method. A source code generator uses the main() method IR and a set of small, hand-generated source code templates|with variables in the templates that are automatically customized for a particular library method|to produce the source code main() method. We apply our approach to two widely used software libraries, SNAP and NetworkX, as examplars, which combined have over 400 library methods.« less
    Free, publicly-accessible full text available January 1, 2022
  2. The COVID-19 pandemic brought to the forefront an unprecedented need for experts, as well as citizens, to visualize spatio-temporal disease surveillance data. Web application dashboards were quickly developed to fill this gap, including those built by JHU, WHO, and CDC, but all of these dashboards supported a particular niche view of the pandemic (ie, current status or specific regions). In this paper1, we describe our work developing our own COVID-19 Surveillance Dashboard, available at https://nssac.bii.virginia.edu/covid19/dashboard/, which offers a universal view of the pandemic while also allowing users to focus on the details that interest them. From the beginning, our goalmore »was to provide a simple visual way to compare, organize, and track near-real-time surveillance data as the pandemic progresses. Our dashboard includes a number of advanced features for zooming, filtering, categorizing and visualizing multiple time series on a single canvas. In developing this dashboard, we have also identified 6 key metrics we call the 6Cs standard which we propose as a standard for the design and evaluation of real-time epidemic science dashboards. Our dashboard was one of the first released to the public, and remains one of the most visited and highly used. Our group uses it to support federal, state and local public health authorities, and it is used by people worldwide to track the pandemic evolution, build their own dashboards, and support their organizations as they plan their responses to the pandemic. We illustrate the utility of our dashboard by describing how it can be used to support data story-telling – an important emerging area in data science.« less
  3. Abstract—Networks have entered the mainstream lexicon over the last ten years. This coincides with the pervasive use of networks in a host of disciplines of interest to industry and academia, including biology, neurology, genomics, psychology, social sciences, economics, psychology, and cyber-physical systems and infrastructure. Several dozen journals and conferences regularly contain articles related to networks. Yet, there are no general purpose cyberinfrastructures (CI) that can be used across these varied disciplines and domains. Furthermore, while there are scientific gateways that include some network science capabilities for particular domains (e.g., biochemistry, genetics), there are no general-purpose network-based scientific gateways. In thismore »work, we introduce net.science, a CI for Network Engineering and Science, that is designed to be a community resource. This paper provides an overview of net.science, addressing key requirements and concepts, CI components, the types of applications that our CI will support, and various dimensions of our evaluation process. Index Terms—cyberinfrastructure, network science, net.science« less
  4. Global airline networks play a key role in the global importation of emerging infectious diseases. Detailed information on air traffic between international airports has been demonstrated to be useful in retrospectively validating and prospectively predicting case emergence in other countries. In this paper, we use a well-established metric known as effective distance on the global air traffic data from IATA to quantify risk of emergence for different countries as a consequence of direct importation from China, and compare it against arrival times for the first 24 countries. Using this model trained on official first reports from WHO, we estimate timemore »of arrival (ToA) for all other countries. We then incorporate data on airline suspensions to recompute the effective distance and assess the effect of such cancellations in delaying the estimated arrival time for all other countries. Finally we use the infectious disease vulnerability indices to explain some of the estimated reporting delays.« less