Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools
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Wormhole: A Powerful Data Mashup
The mobile platform is quickly becoming the standard way that users interact with online resources. The iOS operating system allows iPhone and iPad users to seamlessly access highly interactive web applications that until recently were only available via a desktop or laptop. Wormhole is an AJAX application implemented as a smart web widget that allows users to easily supplement web pages with data directly from the Instrument Operations Subsystems division (IOS) at JPL. It creates an interactive mashup using a website's core content enhanced by dynamically retrieved image and metadata supplied by IOS using the webification API. Currently, this technology is limited in scope to NASA data; however, it can easily be augmented to serve many other needs. This web widget can be delivered in various ways, including as a bookmarklet. The underlying technology that powers Wormhole also has applications to other divisions while they are running current missions.
maship↗
ISS Operations Cost Reductions Through Automation of Real-Time Planning Tasks
In 2008 the Johnson Space Center s Mission Operations Directorate (MOD) management team challenged their organization to find ways to reduce the costs of International Space station (ISS) console operations in the Mission Control Center (MCC). Each MOD organization was asked to identify projects that would help them attain a goal of a 30% reduction in operating costs by 2012. The MOD Operations and Planning organization responded to this challenge by launching several software automation projects that would allow them to greatly improve ISS console operations and reduce staffing and operating costs. These projects to date have allowed the MOD Operations organization to remove one full time (7 x 24 x 365) ISS console position in 2010; with the plan of eliminating two full time ISS console support positions by 2012. This will account for an overall 10 EP reduction in staffing for the Operations and Planning organization. These automation projects focused on utilizing software to automate many administrative and often repetitive tasks involved with processing ISS planning and daily operations information. This information was exchanged between the ground flight control teams in Houston and around the globe, as well as with the ISS astronaut crew. These tasks ranged from managing mission plan changes from around the globe, to uploading and downloading information to and from the ISS crew, to even more complex tasks that required multiple decision points to process the data, track approvals and deliver it to the correct recipient across network and security boundaries. The software solutions leveraged several different technologies including customized web applications and implementation of industry standard web services architecture between several planning tools; as well as a engaging a previously research level technology (TRL 2-3) developed by Ames Research Center (ARC) that utilized an intelligent agent based system to manage and automate file traffic flow, archiving f data, and generating console logs. This technology called OCAMS (OCA (Orbital Communication System) Management System), is now considered TRL level 9 and is in daily use in the Mission Control Center in support of ISS operations. These solutions have not only allowed for improved efficiency on console; but since many of the previously manual data transfers are now automated, many of the human error prone steps have been removed, and the quality of the planning products has improved tremendously. This has also allowed our Planning Flight Controllers more time to focus on the abstract areas of the job, (like the complexities of planning a mission for 6 international crew members with a global planning team), instead of being burdened with the administrative tasks that took significant time each console shift to process. The resulting automation solutions have allowed the Operations and Planning organization to realize significant cost savings for the ISS program through 2020 and many of these solutions could be a viable
Hall, Timothy A.↗
ISS Operations Cost Reductions Through Automation of Real-Time Planning Tasks
In 2007 the Johnson Space Center s Mission Operations Directorate (MOD) management team challenged their organizations to find ways to reduce the cost of operations for supporting the International Space Station (ISS) in the Mission Control Center (MCC). Each MOD organization was asked to define and execute projects that would help them attain cost reductions by 2012. The MOD Operations Division Flight Planning Branch responded to this challenge by launching several software automation projects that would allow them to greatly improve console operations and reduce ISS console staffing and intern reduce operating costs. These tasks ranged from improving the management and integration mission plan changes, to automating the uploading and downloading of information to and from the ISS and the associated ground complex tasks that required multiple decision points. The software solutions leveraged several different technologies including customized web applications and implementation of industry standard web services architecture; as well as engaging a previously TRL 4-5 technology developed by Ames Research Center (ARC) that utilized an intelligent agent-based system to manage and automate file traffic flow, archive data, and generate console logs. These projects to date have allowed the MOD Operations organization to remove one full time (7 x 24 x 365) ISS console position in 2010; with the goal of eliminating a second full time ISS console support position by 2012. The team will also reduce one long range planning console position by 2014. When complete, these Flight Planning Branch projects will account for the elimination of 3 console positions and a reduction in staffing of 11 engineering personnel (EP) for ISS.
Hall, Timothy A.↗
The Next Generation of NASA Rapid Response: Worldview Snapshots
The NASA Rapid Response system started in 2001 by serving static subsets of Near Real Time MODIS (Moderate Resolution Imaging Spectroradiometer) imagery acquired from the Terra satellite. Over this time, Rapid Response has been used to support near real time applications such as wildfire and sea ice mapping for hundreds of thousands of users. In 2011, the toolset expanded to include GIBS, the Global Imagery Browse Services, which provides a web map tiling service of over 700 imagery products, and Worldview (https://worldview.earthdata.nasa.gov/), an interactive web application that showcases the products available in GIBS. This year a new application, Worldview Snapshots, has been added to complete the toolset by providing a flexible, low bandwidth method to download personalized subsets for those who do not need or cannot use a fully featured web mapping application. The original Rapid Response subset tool has been retired and we thank it for its seventeen years of service. Stop by to learn more about the next generation of NASA Rapid Response.
Rapid response system↗
Crowdsourcing quality control for Dark Energy Survey images
We have developed a crowdsourcing web application for image quality control employed by the Dark Energy Survey. Dubbed the "DES exposure checker", it renders science-grade images directly to a web browser and allows users to mark problematic features from a set of predefined classes. Users can also generate custom labels and thus help identify previously unknown problem classes. User reports are fed back to hardware and software experts to help mitigate and eliminate recognized issues. We report on the implementation of the application and our experience with its over 100 users, the majority of which are professional or prospective astronomers but not data management experts. We discuss aspects of user training and engagement, and demonstrate how problem reports have been pivotal to rapidly correct artifacts which would likely have been too subtle or infrequent to be recognized otherwise. We conclude with a number of important lessons learned, suggest possible improvements, and recommend this collective exploratory approach for future astronomical surveys or other extensive data sets with a sufficiently large user base. We also release open-source code of the web application and host an online demo versionat http://des-exp-checker.pmelchior.net
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes
Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.
59 BASIC BIOLOGICAL SCIENCES↗
Centralized and Decentralized Distributed Energy Resource Access Control Implementation Considerations.
A global transition to power grids with high penetrations of renewable energy generation is being driven in part by rapid installations of distributed energy resources (DER). New DER equipment includes standardized IEEE 1547-2018 communication interfaces and proprietary communications capabilities. Interoperable DER provides new monitoring and control capabilities. The existence of multiple entities with different roles and responsibilities within the DER ecosystem makes the Access Control (AC) mechanism necessary. In this paper, we introduce and compare two novel architectures, which provide a Role-Based Access Control (RBAC) service to the DER ecosystem’s entities. Selecting an appropriate RBAC technology is important for the RBAC administrator and users who request DER access authorization. The first architecture is centralized, based on the OpenLDAP, an open source implementation of the Lightweight Directory Access Protocol (LDAP). The second approach is decentralized, based on a private Ethereum blockchain test network, where the RBAC model is stored and efficiently retrieved via the utilization of a single Smart Contract. We have implemented two end-to-end Proofs-of-Concept (PoC), respectively, to offer the RBAC service to the DER entities as web applications. Finally, an evaluation of the two approaches is presented, highlighting the key speed, cost, usability, and security features.
42 ENGINEERING↗
Creating Web-Based Scientific Applications Using Java Servlets
There are many advantages to developing web-based scientific applications. Any number of people can access the application concurrently. The application can be accessed from a remote location. The application becomes essentially platform-independent because it can be run from any machine that has internet access and can run a web browser. Maintenance and upgrades to the application are simplified since only one copy of the application exists in a centralized location. This paper details the creation of web-based applications using Java servlets. Java is a powerful, versatile programming language that is well suited to developing web-based programs. A Java servlet provides the interface between the central server and the remote client machines. The servlet accepts input data from the client, runs the application on the server, and sends the output back to the client machine. The type of servlet that supports the HTTP protocol will be discussed in depth. Among the topics the paper will discuss are how to write an http servlet, how the servlet can run applications written in Java and other languages, and how to set up a Java web server. The entire process will be demonstrated by building a web-based application to compute stagnation point heat transfer.
Palmer, Grant↗
Let Our Powers Combine! Harnessing NASA's Earth Observatory Natural Event Tracker (EONET) in Worldview
Constellations of NASA Earth Observing System (EOS) satellites orbit the earth to collect images and data about the planet in near real-time. Within hours of satellite overpass, you can discover where the latest wildfires, severe storms, volcanic eruptions, and dust and haze events are occurring using NASA's Worldview web application. By harnessing a repository of curated natural event metadata from NASA Earth Observatory's Natural Event Tracker (EONET), Worldview has moved natural event discovery to the forefront and allows users to select events-of-interest from a curated list, zooms to the area, and adds the most relevant imagery layers for that type of natural event. This poster will highlight NASA Worldviews new natural event feed functionality.
earth science↗
The Behavior, Constraint, and Scenario (BeCoS) Tool: A Web-Based Software Application for Modeling Behaviors and Scenarios
The Behavior, Constraint, and Scenario (BeCoS) tool has been developed to allow engineers to specify system and component behaviors. The tool is a web application that is developed in JavaScript and uses the React framework for the user interface and Redux for maintaining application state. The foundation of the tool is its underlying ontology, which expands upon a previously-defined behavior ontology with a scenario ontology. The behavior ontology includes elements like behaving elements, state variables, parameters, and constraints, while the scenario ontology includes core constructs like activities, temporal constraints, and timepoints. BeCoS allows users to easily create behaving elements and to specify their state variables, parameters, state machines, and constraints. BeCoS also allows users to develop temporal constraint networks that specify constraints on component states over time. BeCoS is a prototype tool that has been deployed and tested by systems engineers on the Europa Clipper project, which generated several use cases and helped steer its current developmental effort. By enabling systems engineers to specify behavior in a semantically-rigorous manner, BeCoS is an enabling technology for analyses that previously could not be performed, and when exporting its model to other tools, allows for consistent behavior models to be used.
Ingham, Michel D.↗
The Behavior, Constraint, and Scenario (BeCoS) Tool: A Web-Based Software Application for Modeling Behaviors and Scenarios
The Behavior, Constraint, and Scenario (BeCoS) tool has been developed to allow engineers to specify system and component behaviors. The tool is a web application that is developed in JavaScript and uses the React framework for the user interface and Redux for maintaining application state. The foundation of the tool is its underlying ontology, which expands upon a previously-defined behavior ontology with a scenario ontology. The behavior ontology includes elements like behaving elements, state variables, parameters, and constraints, while the scenario ontology includes core constructs like activities, temporal constraints, and timepoints. BeCoS allows users to easily create behaving elements and to specify their state variables, parameters, state machines, and constraints. BeCoS also allows users to develop temporal constraint networks that specify constraints on component states over time. BeCoS is a prototype tool that has been deployed and tested by systems engineers on the Europa Clipper project, which generated several use cases and helped steer its current developmental effort. By enabling systems engineers to specify behavior in a semantically-rigorous manner, BeCoS is an enabling technology for analyses that previously could not be performed, and when exporting its model to other tools, allows for consistent behavior models to be used.
Inghams, Michel D.↗
Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung
Systems biology uses computational approaches to integrate diverse data types to understand cell and organ behavior. Data derived from complementary technologies, for example transcriptomic and proteomic analyses, are providing new insights into development and disease. We compared mRNA and protein profiles from purified endothelial, epithelial, immune, and mesenchymal cells from normal human lung tissue. Signatures for each cell type were identified and compared at both mRNA and protein levels. Cell specific biological processes and pathways were predicted by analysis of concordant and discordant RNA-protein pairs. Cell clustering and gene set enrichment comparisons identified shared versus unique processes associated with transcriptomic and/or proteomic data. Clear cell-cell correlations between mRNA and protein data were obtained from each cell type. Approximately 40% of RNA-protein pairs were coherently expressed. While the correlation between RNA and their protein products was relatively low (approximately 0.4), cell specific signature genes involved in functional processes characteristic of each cell type, were more highly correlated with their protein products. Consistency of cell specific RNA-protein signatures indicated an essential framework for the function of each cell type. Visualization and reutilization of the protein and RNA profiles are supported by a new web application, "LungProteomics," which is incorporated into the LGEA web portal and freely accessible at (https://research.cchmc.org/pbge/lunggens/lungProteomics/human_sorted_profiles.html).
human lung, sorted cells, integrated omics, Transc↗
CropManage Application for Vineyard Irrigation Decision-Support
CropManage is a free web-application developed by U.C. Cooperative Extension to support evapotranspiration based irrigation scheduling and nutrient management for major specialty crops. Prescribed phenology curves are used to develop daily estimates of canopy cover within a given field, based on days since planting (annual crops) or budbreak (trees, vines). These curves are modulated by a MaxCan parameter representing seasonal maximum canopy cover. Crop development observations can be used to adjust for such factors as weather anomalies or non-standard agronomic practice, as needed. Canopy cover is converted to crop coefficient and combined with reference evapotranspiration to derive daily water consumption. Guidance on crop water requirement is then conveyed to users in terms of system runtime issued on-demand for a given date, largely based on total evapotranspiration since last irrigation event. In this study, CropManage was adapted to vineyards by adding modules accounting for early-season soil moisture depletion and cover crop presence. A crop stress parameter was added to accommodate deficit irrigation practice, allowing the user to specify percentage departure from full water requirement along with start/stop dates. An initial verification exercise was performed on three winegrape vineyards located in California’s Central Coast (2020), North Coast (2020) and Central Valley (2019). Daily crop evapotranspiration was monitored by eddy-covariance fluxtowers. MaxCan was measured by ground and satellite observation. Stress regime was specified by grower practice where available, otherwise stress levels were inferred from applied water records. Mean absolute error and mean bias error of modeled cumulative evapotranspiration were computed with respect to the eddy covariance measurements collected throughout the growing season. Results indicate the modified CropManage water management module performs reasonably well for winegrape. Additional effort is planned to modify the nutrient module for vineyard use.
CropManage↗
Leveraging Single-Page Applications for Seamless Scientific Workflows: DevSecOps Considerations
Single-page applications (SPAs) have become indispensable in modern frontend development, with widespread adoption in scientific applications. The process of creating a single-page web application development environment which accurately reflects the production environment isn’t always straightforward. Most SPA build systems assume configuration at build time, while DevSecOps engineers prefer runtime configuration. This paper suggests a framework-agnostic approach to address issues that encompass both development and deployment, but are difficult to tackle without knowledge in both domains.
Drane, Lance↗
Before the Battlefield: Competition Spurs Warfighter Innovations
In an effort funded by the Defense Threat Reduction Agency’s (DTRA) Joint Science and Technology Office, Pacific Northwest National Laboratory’s Dr. Lauren Charles and Mr. Michael Henry run an Intern-based Biosurveillance Ecosystem (BSVE) Web Application Development Contest. The competition topics target specific gaps in data collection, integration, analysis, and visualization of essential information needed for situational awareness of chemical and biological threats. The 10-week long summer internship program leverages the creativity and talent of graduate students as well as exposes bright, young professionals to the field of biosurveillance. For this past summer’s competition, Dr. Charles decided to try something different. She devised a new way to inspire innovation and gain higher quality results for the development of novel applications to aid in chemical and biological situational awareness. To this end, Dr. Charles developed and instantiated an Innovation Bootcamp Program aimed at training the student interns how to work effectively in interdisciplinary teams and quickly tackle new challenging problems while still producing top quality products. This new program was founded on three main components for success: people, tools, and application.
Innovation, Innovation, Biosurveillance, Intern Co↗
Optimizing Travel Time to Outpatient Interventional Radiology Procedures in a Multi-Site Hospital System Using a Google Maps Application
The purpose of this study is to determine whether a custom Google Maps application can optimize site selection when scheduling outpatient interventional radiology (IR) procedures within a multi-site hospital system. The Google Maps for Business Application Programming Interface (API) was used to develop an internal web application that uses real-time traffic data to determine estimated travel time (ETT; minutes) and estimated travel distance (ETD; miles) from a patient’s home to each a nearby IR facility in our hospital system. Hypothetical patient home addresses based on the 33 cities comprising our institution’s catchment area were used to determine the optimal IR site for hypothetical patients traveling from each city based on real-time traffic conditions. For 10/33 (30%) cities, there was discordance between the optimal IR site based on ETT and the optimal IR site based on ETD at non-rush hour time or rush hour time. By choosing to travel to an IR site based on ETT rather than ETD, patients from discordant cities were predicted to save an average of 7.29 min during non-rush hour (p = 0.03), and 28.80 min during rush hour (p < 0.001). Using a custom Google Maps application to schedule outpatients for IR procedures can effectively reduce patient travel time when more than one location providing IR procedures is available within the same hospital system.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Redesign of the Timeline Generator at Fermilab using a web-based Flutter Application, GraphQL API and an IOC
Redesign of the Timeline Generator at Fermilab using a web-based Flutter application, GraphQL API and an IOC ABSTRACT = The control system at Fermilab is undergoing an evolution with a shift towards web-based applications with connections to the EPICS infrastructure. The Timeline Generator (TLG) is an application that serves to coordinate events across the lab using different timing links. These links include the Tevatron clock (TCLK), a 10 MHz serial link with events encoded at 20Hz and Ma-chine Data (MDAT), a communication link with states encoded at 720Hz. This paper covers the redesign of the major components of the TLG. This includes a web-based Flutter application for building timelines. A placement service is in use that has a GraphQL interface and uses a timeline input to compute a schedule of events and states. The Flutter application sends this computed schedule to the TLG IOC via a GraphQL interface to the Data Pool Manager (DPM). The TLG IOC runs on an Arria FPGA, the Accelerator Clock Generator (ACLK-GEN), which is responsible for writing the events and states on to the different timing links.
Carmichael, Linden [Fermilab]↗