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100 records · Page 6

Innovating the next generation of commercial smart building software

Nearly 30% of commercial building energy use is wasted due to equipment faults and HVAC controls problems. The result is increased emissions, compromised comfort and productivity, and less reliable coordination of building power needs with a clean grid. The energy impact alone represents $17 billion in potential savings. Today’s smart building software provides a robust solution to address these operational deficiencies. Energy management and information systems (EMIS) are saving up to 9% on average, with two-year paybacks. They are being incorporated into energy management processes, commissioning services, and utility programs. As effective as they are, two barriers prevent even deeper benefits; limited personnel to fix problems once they are identified, and the expense and time to manually implement changes in control systems. In partnership with the research community, the EMIS industry is developing new capabilities to overcome these barriers. Moving beyond siloed products for either fault detection and diagnostics, or optimal control, these new capabilities empower users to not only automatically identify faults, but also to push corrective action, and control improvements to their buildings. In this paper, several areas for enhancements are documented: ‘one-time’ correction of faults such as setpoints, schedules, and economizer lockouts; short-term active testing for automated proportional integral derivative (PID) loop tuning and functional testing; and continuous supervisory control for demand flexibility and year-round efficiency. Results are presented from a pair of partner implementations out of a dozen providers integrating these enhancements into their products, including field tests from across the country, and insights into operator acceptance and integration into operations and maintenance practices.

Casillas, Armando

RhizoNet segments plant roots to assess biomass and growth for enabling self-driving labs

Abstract Flatbed scanners are commonly used for root analysis, but typical manual segmentation methods are time-consuming and prone to errors, especially in large-scale, multi-plant studies. Furthermore, the complex nature of root structures combined with noisy backgrounds in images complicates automated analysis. Addressing these challenges, this article introduces RhizoNet, a deep learning-based workflow to semantically segment plant root scans. Utilizing a sophisticated Residual U-Net architecture, RhizoNet enhances prediction accuracy and employs a convex hull operation for delineation of the primary root component. Its main objective is to accurately segment root biomass and monitor its growth over time. RhizoNet processes color scans of plants grown in a hydroponic system known as EcoFAB, subjected to specific nutritional treatments. The root detection model using RhizoNet demonstrates strong generalization in the validation tests of all experiments despite variable treatments. The main contributions are the standardization of root segmentation and phenotyping, systematic and accelerated analysis of thousands of images, significantly aiding in the precise assessment of root growth dynamics under varying plant conditions, and offering a path toward self-driving labs.

59 BASIC BIOLOGICAL SCIENCES

Program Instrumentation and Trace Analysis

Several attempts have been made recently to apply techniques such as model checking and theorem proving to the analysis of programs. This shall be seen as a current trend to analyze real software systems instead of just their designs. This includes our own effort to develop a model checker for Java, the Java PathFinder 1, one of the very first of its kind in 1998. However, model checking cannot handle very large programs without some kind of abstraction of the program. This paper describes a complementary scalable technique to handle such large programs. Our interest is turned on the observation part of the equation: How much information can be extracted about a program from observing a single execution trace? It is our intention to develop a technology that can be applied automatically and to large full-size applications, with minimal modification to the code. We present a tool, Java PathExplorer (JPaX), for exploring execution traces of Java programs. The tool prioritizes scalability for completeness, and is directed towards detecting errors in programs, not to prove correctness. One core element in JPaX is an instrumentation package that allows to instrument Java byte code files to log various events when executed. The instrumentation is driven by a user provided script that specifies what information to log. Examples of instructions that such a script can contain are: 'report name and arguments of all called methods defined in class C, together with a timestamp'; 'report all updates to all variables'; and 'report all acquisitions and releases of locks'. In more complex instructions one can specify that certain expressions should be evaluated and even that certain code should be executed under various conditions. The instrumentation package can hence be seen as implementing Aspect Oriented Programming for Java in the sense that one can add functionality to a Java program without explicitly changing the code of the original program, but one rather writes an aspect and compiles it into the original program using the instrumentation. Another core element of JPaX is an observation package that supports the analysis of the generated event stream. Two kinds of analysis are currently supported. In temporal analysis the execution trace is evaluated against formulae written in temporal logic. We have implemented a temporal logic evaluator on finite traces using the Maude rewriting system from SRI International, USA. Temporal logic is defined in Maude by giving its syntax as a signature and its semantics as rewrite equations. The resulting semantics is extremely efficient and can handle event streams of hundreds of millions events in few minutes. Furthermore, the implementation is very succinct. The second form of even stream analysis supported is error pattern analysis where an execution trace is analyzed using various error detection algorithms that can identify error-prone programming practices that may potentially lead to errors in some different executions. Two such algorithms focusing on concurrency errors have been implemented in JPaX, one for deadlocks and the other for data races. It is important to note, that a deadlock or data race potential does not need to occur in order for its potential to be detected with these algorithms. This is what makes them very scalable in practice. The data race algorithm implemented is the Eraser algorithm from Compaq, however adopted to Java. The tool is currently being applied to a code base for controlling a spacecraft by the developers of that software in order to evaluate its applicability.

Havelund, Klaus

Misconceptions of Synthetic Biology: Lessons from an Interdisciplinary Summer School

In 2014, an international group of scholars from various fields analysed the "societal dimensions" of synthetic biology in an interdisciplinary summer school. Here, we report and discuss the biologists' observations on the general perception of synthetic biology by non-biologists who took part in this event. Most attendees mainly associated synthetic biology with contributions from the best-known public figures of the field, rarely mentioning other scientists. Media extrapolations of those contributions appeared to have created unrealistic expectations and irrelevant fears that were widely disconnected from the current research in synthetic biology. Another observation was that when debating developments in synthetic biology, semantics strongly mattered: depending on the terms used to present an application of synthetic biology, attendees reacted in radically different ways. For example, using the term "GMOs" (genetically modified organisms) rather than the term "genetic engineering" led to very different reactions. Stimulating debates also happened with participants having unanticipated points of view, for instance biocentrist ethicists who argued that engineered microbes should not be used for human purposes. Another communication challenge emerged from the connotations and inaccuracies surrounding the word "life", which impaired constructive debates, thus leading to misconceptions about the abilities of scientists to engineer or even create living organisms. Finally, it appeared that synthetic biologists tend to overestimate the knowledge of non-biologists, further affecting communication. The motivation and ability of synthetic biologists to communicate their work outside their research field needs to be fostered, notably towards policymakers who need a more accurate and technical understanding of the field to make informed decisions. Interdisciplinary events gathering scholars working in and around synthetic biology are an effective tool in addressing those issues.

synthetic biology

DOE Repository Metadata Profile (DRMP): A Metadata Framework for Advancing Interoperability and AI Readiness Across Scientific Repositories

The Department of Energy (DOE) funds a diverse and distributed ecosystem of repositories that steward scientific data, publications, and software across its research programs, user facilities, and national laboratories. While significant progress has been made in standardizing dataset-level metadata, the metadata describing repositories themselves (their identity, governance, access interfaces, policies, and technical capabilities) remains inconsistent and fragmented across DOE-funded systems. This variability limits discoverability, interoperability, automated validation, and AI-driven analysis, all of which are increasingly essential for modern scientific workflows. To address this gap, the DOE Data Curation Working Group (DCWG) developed the DOE Repository Metadata Profile (DRMP). The DRMP is a practical, community-driven framework that defines how repositories can describe themselves in a consistent, machine-actionable, and scalable manner. The DRMP is not a new metadata schema. Instead, it is a mapping profile and structured element set capturing the essential characteristics of DOE repositories. It harmonizes repository-level metadata across six widely adopted community schemas: RE3Data; DCAT-US v3; Schema.org; Dublin Core; DataCite 4.6; and PREMIS 3.0. This harmonization eliminates reinvention and enables interoperability within DOE and across the broader scientific ecosystem. A core objective of the DRMP is to reduce burden on repositories by allowing them to reuse their existing metadata through a Rosetta-style crosswalk rather than redesigning local implementations. The profile introduces a three-level conformance model that supports incremental adoption: • Level 1 – Minimum Viable Record (MVR): foundational identification elements required for workflows, project registration, and basic repository presence. • Level 2 – Interoperable: structured metadata enabling alignment with national and international discovery systems. • Level 3 – AI-Ready: enhanced provenance, policy transparency, fixity, semantic context, and capabilities that support automated reasoning, model training governance, and machine-assisted curation. To support implementation, the DRMP includes JSON Schema definitions, OpenAPI patterns, and MCP templates that allow repositories to publish machine-readable metadata directly within existing platforms. These resources are modular and lightweight, enabling adoption without major architectural change. Adopting the DRMP enables repositories to: • Enhance discoverability and interoperability by aligning identifiers, classifications, and descriptive elements across widely used schema standards. • Support federated discovery and cross-registration across DOE systems, Data.gov, and international catalogs. • Enable AI agents and workflow orchestration systems to interpret repository-level metadata within the American Science Cloud (AmSC) through Model Context Protocol (MCP)-based context publication. • Demonstrate alignment with DOE’s open science, stewardship, and FAIR data priorities. This guidance represents a community-driven step forward. Through voluntary adoption and continued feedback, the DRMP advances a cohesive, machine-actionable description of DOE repositories that supports FAIR data practices, preparing the infrastructure for AI-enabled research, and strengthening the discoverability and reuse of DOE’s scientific outputs.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION

NASA Tech Briefs, May 2009

Topics covered include: Valve-"Health"-Monitoring System; Microstrip Antenna for Remote Sensing of Soil Moisture and Sea Surface Salinity; Biomedical Wireless Ambulatory Crew Monitor; Wireless Avionics Packet to Support Fault Tolerance for Flight Applications; Aerobot Autonomy Architecture; Submillimeter Confocal Imaging Active Module; Traveling-Wave Maser for 32 GHz; System Synchronizes Recordings from Separated Video Cameras; Piecewise-Planar Parabolic Reflectarray Antenna; Reducing Interference in ATC Voice Communication; EOS MLS Level 1B Data Processing, Version 2.2; Auto-Generated Semantic Processing Services; Geospatial Authentication; Maneuver Automation Software; Event Driven Messaging with Role-Based Subscriptions; Estimating Relative Positions of Outer-Space Structures; Fabricating PFPE Membranes for Capillary Electrophoresis; Linear Actuator Has Long Stroke and High Resolution; Installing a Test Tap on a Metal Battery Case; Fabricating PFPE Membranes for Microfluidic Valves and Pumps; Room-Temperature-Cured Copolymers for Lithium Battery Gel Electrolytes; Catalysts for Efficient Production of Carbon Nanotubes; Amorphous Silk Fibroin Membranes for Separation of CO2; "Zero-Mass" Noninvasive Pressure Transducers; Radial-Electric-Field Piezoelectric Diaphragm Pumps; Ejector-Enhanced, Pulsed, Pressure-Gain Combustor; Suppressing Ghost Diffraction in E-Beam-Written Gratings; Target-Tracking Camera for a Metrology System; Polarimetric Imaging using Two Photoelastic Modulators; Miniature Wide-Angle Lens for Small-Pixel Electronic Camera; Modal Filters for Infrared Interferometry; Mo(3)Sb(7-x)Te(x) for Thermoelectric Power Generation; Two-Dimensional Quantum Model of a Nanotransistor; Scanning Miniature Microscopes without Lenses; Manipulating Neutral Atoms in Chip-Based Magnetic Traps; Expansion Compression Contacts for Thermoelectric Legs; Processing Electromyographic Signals to Recognize Words; Physical Principle for Generation of Randomness; DSN Beowulf Cluster-Based VLBI Correlator; Hybrid NN/SVM Computational System for Optimizing Designs; Criteria for Modeling in LES of Multicomponent Fuel Flow; Computerized Machine for Cutting Space Shuttle Thermal Tiles; Orbiting Depot and Reusable Lander for Lunar Transportation; FPGA-Based Networked Phasemeter for a Heterodyne Interferometer; Aquarius Digital Processing Unit; Three-Dimensional Optical Coherence Tomography; Benchtop Antigen Detection Technique using Nanofiltration and Fluorescent Dyes; Isolation of Precursor Cells from Waste Solid Fat Tissue; Identification of Bacteria and Determination of Biological Indicators; Further Development of Scaffolds for Regeneration of Nerves; Chemically Assisted Photocatalytic Oxidation System; Use of Atomic Oxygen for Increased Water Contact Angles of Various Polymers for Biomedical Applications; Crashworthy Seats Would Afford Superior Protection; Open-Access, Low-Magnetic-Field MRI System for Lung Research; Microfluidic Mixing Technology for a Universal Health Sensor; Microfluidic Extraction of Biomarkers using Water as Solvent; Microwell Arrays for Studying Many Individual Cells; Droplet-Based Production of Liposomes; and Identifying and Inactivating Bacterial Spores

Source record

The Role of Ontologies in Schema-based Program Synthesis

Program synthesis is the process of automatically deriving executable code from (non-executable) high-level specifications. It is more flexible and powerful than conventional code generation techniques that simply translate algorithmic specifications into lower-level code or only create code skeletons from structural specifications (such as UML class diagrams). Key to building a successful synthesis system is specializing to an appropriate application domain. The AUTOBAYES and AUTOFILTER systems, under development at NASA Ames, operate in the two domains of data analysis and state estimation, respectively. The central concept of both systems is the schema, a representation of reusable computational knowledge. This can take various forms, including high-level algorithm templates, code optimizations, datatype refinements, or architectural information. A schema also contains applicability conditions that are used to determine when it can be applied safely. These conditions can refer to the initial specification, to intermediate results, or to elements of the partially-instantiated code. Schema-based synthesis uses AI technology to recursively apply schemas to gradually refine a specification into executable code. This process proceeds in two main phases. A front-end gradually transforms the problem specification into a program represented in an abstract intermediate code. A backend then compiles this further down into a concrete target programming language of choice. A core engine applies schemas on the initial problem specification, then uses the output of those schemas as the input for other schemas, until the full implementation is generated. Since there might be different schemas that implement different solutions to the same problem this process can generate an entire solution tree. AUTOBAYES and AUTOFILTER have reached the level of maturity where they enable users to solve interesting application problems, e.g., the analysis of Hubble Space Telescope images. They are large (in total around 100kLoC Prolog), knowledge intensive systems that employ complex symbolic reasoning to generate a wide range of non-trivial programs for complex application do- mains. Their schemas can have complex interactions, which make it hard to change them in isolation or even understand what an existing schema actually does. Adding more capabilities by increasing the number of schemas will only worsen this situation, ultimately leading to the entropy death of the synthesis system. The root came of this problem is that the domain knowledge is scattered throughout the entire system and only represented implicitly in the schema implementations. In our current work, we are addressing this problem by making explicit the knowledge from Merent parts of the synthesis system. Here; we discuss how Gruber's definition of an ontology as an explicit specification of a conceptualization matches our efforts in identifying and explicating the domain-specific concepts. We outline the dual role ontologies play in schema-based synthesis and argue that they address different audiences and serve different purposes. Their first role is descriptive: they serve as explicit documentation, and help to understand the internal structure of the system. Their second role is prescriptive: they provide the formal basis against which the other parts of the system (e.g., schemas) can be checked. Their final role is referential: ontologies also provide semantically meaningful "hooks" which allow schemas and tools to access the internal state of the program derivation process (e.g., fragments of the generated code) in domain-specific rather than language-specific terms, and thus to modify it in a controlled fashion. For discussion purposes we use AUTOLINEAR, a small synthesis system we are currently experimenting with, which can generate code for solving a system of linear equations, Az = b.

Bures, Tomas

Aggregation Tool to Create Curated Data albums to Support Disaster Recovery and Response

Despite advances in science and technology of prediction and simulation of natural hazards, losses incurred due to natural disasters keep growing every year. Natural disasters cause more economic losses as compared to anthropogenic disasters. Economic losses due to natural hazards are estimated to be around $6-$10 billion dollars annually for the U.S. and this number keeps increasing every year. This increase has been attributed to population growth and migration to more hazard prone locations such as coasts. As this trend continues, in concert with shifts in weather patterns caused by climate change, it is anticipated that losses associated with natural disasters will keep growing substantially. One of challenges disaster response and recovery analysts face is to quickly find, access and utilize a vast variety of relevant geospatial data collected by different federal agencies such as DoD, NASA, NOAA, EPA, USGS etc. Some examples of these data sets include high spatio-temporal resolution multi/hyperspectral satellite imagery, model prediction outputs from weather models, latest radar scans, measurements from an array of sensor networks such as Integrated Ocean Observing System etc. More often analysts may be familiar with limited, but specific datasets and are often unaware of or unfamiliar with a large quantity of other useful resources. Finding airborne or satellite data useful to a natural disaster event often requires a time consuming search through web pages and data archives. Additional information related to damages, deaths, and injuries requires extensive online searches for news reports and official report summaries. An analyst must also sift through vast amounts of potentially useful digital information captured by the general public such as geo-tagged photos, videos and real time damage updates within twitter feeds. Collecting and aggregating these information fragments can provide useful information in assessing damage in real time and help direct recovery efforts. The search process for the analyst could be made much more efficient and productive if a tool could go beyond a typical search engine and provide not just links to web sites but actual links to specific data relevant to the natural disaster, parse unstructured reports for useful information nuggets, as well as gather other related reports, summaries, news stories, and images. This presentation will describe a semantic aggregation tool developed to address similar problem for Earth Science researchers. This tool provides automated curation, and creates "Data Albums" to support case studies. The generated "Data Albums" are compiled collections of information related to a specific science topic or event, containing links to relevant data files (granules) from different instruments; tools and services for visualization and analysis; information about the event contained in news reports, and images or videos to supplement research analysis. An ontology-based relevancy-ranking algorithm drives the curation of relevant data sets for a given event. This tool is now being used to generate a catalog of Hurricane Case Studies at Global Hydrology Resource Center (GHRC), one of NASA's Distribute Active Archive Centers. Another instance of the Data Albums tool is currently being created in collaboration with NASA/MSFC's SPoRT Center, which conducts research on unique NASA products and capabilities that can be transitioned to the operational community to solve forecast problems. This new instance focuses on severe weather to support SPoRT researchers in their model evaluation studies

Ramachandran, Rahul

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES

Mondo: integrating disease terminology across communities

Precision medicine aims to enhance diagnosis, treatment, and prognosis by integrating multimodal data at the point of care. However, challenges arise due to the vast number of diseases, differing methods of classification, and conflicting terminological coding systems and practices used to represent molecular definitions of disease. This lack of interoperability artificially constrains the potential for diagnosis, clinical decision support, care outcome analysis, as well as data linkage across research domains to support the development or repurposing of therapeutics. There is a clear and pressing need for a unified system for managing disease entities⁠—including identifiers, synonyms, and definitions. To address these issues, we created the Mondo disease ontology—a community-driven, open-source, unified disease classification system that harmonizes diverse terminologies into a consistent, computable framework. Mondo integrates key medical and biomedical terminologies, including Online Mendelian Inheritance in Man (OMIM), Orphanet, Medical Subject Headings (MeSH), National Cancer Institute Thesaurus (NCIt), and more, to provide a comprehensive and accurate representation of disease concepts with fully provenanced and attributed links back to the sources. Mondo can be used as the handle for curation of gene–disease associations utilized in diagnostic applications, research applications such as computational phenotyping, and in clinical coding systems in clinical decision support by pointing the clinician to the numerous knowledge resources linked to the Mondo identifier. Mondo's community-centric approach, stewarded by the Monarch Initiative's expertise in ontologies, ensures that the ontology remains adaptable to the evolving needs of biomedical research and clinical communities, as well as the knowledge providers.

biomedical informatics