speckle-tracking: a software suite for ptychographic X-ray speckle tracking
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99 GENERAL AND MISCELLANEOUS↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes
While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.
59 BASIC BIOLOGICAL SCIENCES↗
Modular Security Apparatus for Managing Distributed Cryptography for Command-and-Control Messages on Operational Technology Networks (Module-OT)
Module-OT is a bump- in- the- wire solution acting as a secure conduit for data between devices or systems across a network. Using the latest in open-source cryptographic libraries, all defined communications undergo authentication, authorization, and encryption. The core system can be easily installed through industry standard processes, and the use of popular open-source packages allows for it to be customizable customized by the developer community or deployed in unique embedded environments.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Supervisory genset control in range-extended electric vehicle
A controls system for a range-extended electric vehicle comprising an overall system control unit, an engine control module configured to control a range extender of the range-extended electric vehicle, power electronics configured to control a generator of the range-extended electric vehicle, and a supervisory control module coupled between the overall system control unit and the engine control module and the power electronics, the supervisory control module configured to receive information from the overall system control unit and provide commands to the engine control module and the power electronics.
Li, Ke↗
Massively parallel hierarchical control system and method
An electronic control system is disclosed for controlling individually controllable elements of an external component. In one embodiment the system may include a state translator subsystem for receiving a state command from an external subsystem. The state translator subsystem may have at least one module for processing the state command and generating operational commands for controlling the elements to achieve a desired state or condition. A programmable calibration command translation layer (PCCTL) subsystem may be included which receives and uses the operational commands to generate granular level commands for controlling the elements. A feedback control layer subsystem may be included which applies the granular level commands to the elements, and further modifies the granular level commands as needed to control the elements in closed loop fashion.
Panas, Robert Matthew↗
Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict
The reconstruction of complete microbial metabolic pathways using ‘omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.
59 BASIC BIOLOGICAL SCIENCES↗
ROBOT: A Tool for Automating Ontology Workflows
BACKGROUND:Ontologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms. For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool. RESULTS:ROBOT (a recursive acronym for "ROBOT is an OBO Tool") is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems. CONCLUSIONS:ROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Path-synchronous performance monitoring of interconnection networks based on source code attribution
Examples disclosed herein relate to path-synchronous performance monitoring of an interconnection network based on source code attribution. A processing node in the interconnection network has a profiler module to select a network transaction to be monitored, determine a source code attribution associated with the network transaction to be monitored, and issue a network command to execute the network transaction to be monitored. A logger module creates, in a buffer, a node temporal log associated with the network transaction and the network command. A drainer module periodically captures the node temporal log. The processing node has a network interface controller to receive the network command and mark a packet generated for the network command to be temporally tracked and attributed back to the source code attribution at each hop of the interconnection network traversed by the marked packet.
Chabbi, Milind M.↗
Design, Optimization, and Validation of GaN-Based DAB Converter for Active Cell Balancing in BTMS Applications
This paper focuses on the design of a bidirectional dual active bridge (DAB) DC/DC converter that utilizes Gallium Nitride (GaN) switches as active components. In the existing literature, MOSFET-based DAB for active cell balancing is available, but GaN-based DAB converter for active cell balancing is still new. The proposed modular isolated GaN-based DAB converter is designed as an individual module of active cell balancing for behind-the-meter storage (BTMS) applications, targeting high-power charging stations. Modular isolated converters are connected to each cell (low voltage bus), and each cell is connected in series to build up a battery module. According to the reference current command of supervisory control, each DAB converter can transfer power back and forth through the high voltage (HV) bus to balance the State of Charge (SoC) between the cells. Each module DAB converter is designed at a 50 W power rating. Switch power and transformer losses are analyzed for different switching frequencies, showing the optimum switching frequency for minimum losses. Furthermore, the procedure to select the required gate driver and the PCB layout optimization are discussed. Finally, the DAB performance analysis of GaN-based DAB and Si-based DAB is provided for a battery module operating with a LiFeMnPO4 prismatic cell with 3.2V 20Ah rated values.
active cell balancing↗
Design, Optimization, and Validation of GaN-Based DAB Converter for Active Cell Balancing in BTMS Applications: Preprint
This paper focuses on the design of a bidirectional dual active bridge (DAB) DC/DC converter that utilizes Gallium Nitride (GaN) switches as active components. In the existing literature, MOSFET-based DAB for active cell balancing is available, but GaN-based DAB converter for active cell balancing is still new. The proposed modular isolated GaN-based DAB converter is designed as an individual module of active cell balancing for behind-the-meter storage (BTMS) applications, targeting high-power charging stations. Modular isolated converters are connected to each cell (low voltage bus), and each cell is connected in series to build up a battery module. According to the reference current command of supervisory control, each DAB converter can transfer power back and forth through the high voltage (HV) bus to balance the State of Charge (SoC) between the cells. Each module DAB converter is designed at a 50W power rating. Switch power and transformer losses are analyzed for different switching frequencies, showing the optimum switching frequency for minimum losses. Furthermore, the procedure to select the required gate driver and the PCB layout optimization are discussed. Finally, the DAB performance analysis of GaNbased DAB and Si-based DAB is provided for a battery module operating with a LiFeMnPO4 prismatic cell with 3.2V 20Ah rated values.
active cell balancing↗
Module-OT: A Turnkey Solution for Securing Energy Systems
The Modular Security Apparatus for Managing Distributed Cryptography for Command-and-Control Messages on Operational Technology Networks (Module-OT) is a flexible and lightweight solution for grid-edge devices focusing on end-to-end security. It is a bump- in- the-wire solution acting as a secure conduit for data between devices or systems across a network. It improves the cybersecurity posture of DER systems by providing authentication, authorization, and data integrity to secure DER communications. Additionally, it performs key management, provides data security through whitelisting Internet Protocol addresses and ports, blocks unauthorized connections, controls user access, and allows serial or Ethernet connections for added flexibility. The core software is portable to various Linux-based operating systems and is developed to be customized by the developer and researcher communities. Module-OT has been validated in the lab, has been demonstrated at a 500-KW PV-plus-storage site, and has been proven ready to secure operational technology devices. Its core functionality meets current standards, including validation procedures of the NIST Cryptographic Algorithm Validation Program (CAVP) and the Federal Information Processing Standard (FIPS 140-2). Because of its capability to provide an accessible and affordable option for stepping up security across modern energy systems, Module-OT can serve as an effective technological option to standardize cybersecurity moving forward.
cryptography↗
A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.
59 BASIC BIOLOGICAL SCIENCES↗
Normality of I-V Measurements Using ML
There is an increased interest in instrument-computing ecosystems (ICEs) that support science workflows empowered by AI-automated experiments and computations in diverse areas. In particular, electrochemistry ICEs are promising for accelerating the design and discovery of electrochemical systems for energy storage and conversion, by automating significant parts of workflows that combine synthesis and characterization experiments with computations. They require the integration of flow controllers, solvent containers, pumps, fraction collectors, and potentiostats, all connected to an electrochemical cell, as illustrated in Fig. 1. These are specialized instruments with custom software that is not originally designed for network integration. We developed network and software solutions for electrochemical workflows that adapt system and instrument settings in real-time for multiple rounds of experiments. In particular, we developed Python wrappers for Application Programming Interfaces (APIs) of instrument commands and Pyro client-server modules that enable them to be executed from remote computers. The entire workflow is orchestrated by a Jupyter notebook running on a remote computer.
Al Najjar, Anees↗
Multilane Automated Driving With Optimal Control and Mixed-Integer Programming
Road vehicle lane changes often initiate traffic disturbances and can therefore impact road networks’ energy and time efficiency. Furthermore, unexpected changes in traffic conditions may also render lane changes counterproductive for the lane-changing vehicle. Vehicle-to-vehicle connectivity combined with anticipative control could address these challenges via improved lane change decisions by automated vehicles. In a move toward this objective, receding horizon control cast as a mixed-integer quadratic program is used to plan lane changing and acceleration in a coupled optimization. A long-term pacing module, based on Pontryagin’s minimum principle from optimal control theory, sets terminal and input references for receding horizon control to target a user’s expected travel time. To remove nonlinear vehicle dynamics from the receding horizon controller, lane change commands are passed to a pure pursuit steering module whose response is approximated by a second-order linear model. Here, comparison against a rule-based reactive algorithm in arterial and highway scenarios shows an 8.9%–13.7% reduction in energy consumption and a 5.2%–10.3% reduction in the travel time, along with navigational improvements.
33 ADVANCED PROPULSION SYSTEMS↗
Cyber Framework for Steering and Measurements Collection Over Instrument-Computing Ecosystems
We propose a framework to develop cyber solutions to support the remote steering of science instruments and measurements collection over instrument-computing ecosystems. It is based on provisioning separate data and control connections at the network level, and developing software modules consisting of Python wrappers for instrument commands and Pyro server-client codes that make them available across the ecosystem network. We demonstrate automated measurement transfers and remote steering operations in a microscopy use case for materials research over an ecosystem of Nion microscopes and computing platforms connected over site networks. The proposed framework is currently under further refinement and being adopted to science workflows with automated remote experiments steering for autonomous chemistry laboratories and smart energy grid simulations.
Al Najjar, Anees↗
CMEC driver
CMEC driver is a command line tool that runs earth system evaluation modules.
Ordonez, AnaC.↗
SIERRA/Aero User Manual - Version 5.8
SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services also allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.
42 ENGINEERING↗
Generalizable, fast, and accurate DeepQSPR with fastprop
Abstract Quantitative Structure–Property Relationship studies (QSPR), often referred to interchangeably as QSAR, seek to establish a mapping between molecular structure and an arbitrary target property. Historically this was done on a target-by-target basis with new descriptors being devised to specifically map to a given target. Today software packages exist that calculate thousands of these descriptors, enabling general modeling typically with classical and machine learning methods. Also present today are learned representation methods in which deep learning models generate a target-specific representation during training. The former requires less training data and offers improved speed and interpretability while the latter offers excellent generality, while the intersection of the two remains under-explored. This paper introduces , a software package and general Deep-QSPR framework that combines a cogent set of molecular descriptors with deep learning to achieve state-of-the-art performance on datasets ranging from tens to tens of thousands of molecules. provides both a user-friendly Command Line Interface and highly interoperable set of Python modules for the training and deployment of feedforward neural networks for property prediction. This approach yields improvements in speed and interpretability over existing methods while statistically equaling or exceeding their performance across most of the tested benchmarks. is designed with Research Software Engineering best practices and is free and open source, hosted at github.com/jacksonburns/fastprop.
Burns, Jackson W. (ORCID:0000000206579426)↗