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At least 487 records · Page 27

PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.

59 BASIC BIOLOGICAL SCIENCES↗

Architecture of a Data Portal for Publishing and Delivering Open Data for Atmospheric Measurement

Atmospheric data are collected by researchers every day. Campaigns such as GOAmazon 2014/2015 and the Amazon Tall Tower Observatory collect essential data on aerosols, gases, cloud properties, and meteorological parameters in the Brazilian Amazon basin. These data products provide insights and essential information for analyzing and predicting natural processes. However, in Brazil, it is estimated that more than 80% of the scientific data collected are not published due to the lack of web portals that collect and store these data. This makes it difficult, or even impossible, to access and integrate the data, which can result in the loss of significant amounts of information and significantly affect the understanding of the overall data. To address this problem, we propose a data portal architecture and open data deployment that enable Big Data processing, human interaction, and download-oriented approaches with tools that help users catalog, publish and visualize atmospheric data. Thus, we describe the architecture developed, based on the experience of the Atmospheric Radiation Measurement Data Center, which incorporates the principles of FAIR, the infrastructure and content management system for managing scientific data. The portal partial results were tested with environmental data from contaminated areas at the University of São Paulo. Overall, this data portal creates more shared knowledge about atmospheric processes by providing users with access to open environmental data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

JOBRUNNER

SF-23-071 Jobrunner is a command line tool to manage and deploy computing jobs, organize complex workloads, and enforce a directory based hierarchy to enable reuse of files and bash scripts within a project. Organization details of a directory tree are encoded in Jobfiles which serve as an index of files/scripts, and indicate their purpose when deploying or setting up a job. It is a flexible tool that allows users to design 16 their own directory structure, perserve their design, and maintain 17 consistency with increase in complexity of the project.

DHRUV, AKASH VIJAYKUMAR↗

Extraction and Analysis of Time Series Data from Building Automation Systems Using Large Language Models

Semantic schemas like Haystack 4, Brick and ASHRAE standard 223 enable the structured, standardized, and machine-readable representation of building data, facilitating interoperability, data integration, and advanced analytics. However, extracting information from these models requires specialized expertise in SPARQL and other programming languages, skills that are not commonly found among building professionals. Recent advancements in Large Language Models (LLMs), such as ChatGPT, enable the construction of queries using natural language, making it easier for individuals to interact with these systems in a manner that resembles everyday speech. However, these methods have not yet been tested on building semantic ontologies. This paper introduces a novel workflow and tool for enabling users to ask questions about a specific building's data, using natural language and receive answers automatically generated by GPT-4o. Our approach integrates semantic ontologies with advanced LLM capabilities to automate three critical steps: (1) generating SPARQL queries to retrieve time series references from ontological models, (2) extracting the corresponding time series data from the Building Automation System, and (3) performing computations and visualizations tailored to the user's query. The proposed method simplifies access to BAS data, allowing both domain experts and non-specialists to conduct sophisticated analyses without needing extensive technical knowledge of semantic web technologies. By demonstrating this pipeline, we facilitate more accessible and scalable data-driven decision-making in building operations and management.

Mulayim, Ozan Baris↗

RIMS: Resource Information Management System

An overview is given of the capabilities and functions of the resource management system (RIMS). It is a simple interactive DMS tool which allows users to build, modify, and maintain data management applications. The RIMS minimizes programmer support required to develop/maintain small data base applications. The RIMS also assists in bringing the United Information Services (UIS) budget system work inhouse. Information is also given on the relationship between the RIMS and the user community.

Symes, J.↗

Listing Relationships Among Subroutines

HIERARCHY program is tool that assists users in obtaining information about relationships among subroutines in computer program. HIERARCHY written in FORTRAN 77.

Guest, C.↗

Computer program for calculating flow parameters and power requirements for cryogenic wind tunnels

A computer program has been written that performs the flow parameter calculations for cryogenic wind tunnels which use nitrogen as a test gas. The flow parameters calculated include static pressure, static temperature, compressibility factor, ratio of specific heats, dynamic viscosity, total and static density, velocity, dynamic pressure, mass-flow rate, and Reynolds number. Simplifying assumptions have been made so that the calculations of Reynolds number, as well as the other flow parameters can be made on relatively small desktop digital computers. The program, which also includes various power calculations, has been developed to the point where it has become a very useful tool for the users and possible future designers of fan-driven continuous-flow cryogenic wind tunnels.

Dress, D. A.↗

Queueing in networks of computers

The designers of networks of computers must assess the capacity of the network to complete work within reasonable times. The utilization law, Little's law, forced-flow law, and response time formula are simple tools that can be used to calculate throughput and response times of networks. Bottleneck analysis can be used to calculate simple lower bounds on response time in terms of individual server parameters and the load on network as a whole. These simple results are important tools for all users of scientific networks - back of the envelope calculations can quickly reveal the effects of distant servers on local throughput and response time.

Denning, Peter J.↗

A CLIPS/X-window interface

The design and implementation of an interface between the C Language Integrated Production System (CLIPS) expert system development environment and the graphic user interface development tools of the X-Window system are described. The underlying basis of the CLIPS/X-Window is a client-server model in which multiple clients can attach to a single server that interprets, executes, and returns operation results, in response to client action requests. Implemented in an AIX (UNIX) operating system environment, the interface has been successfully applied in the development of graphics interfaces for production rule cooperating agents in a knowledge-based computer aided design (CAD) system. Initial findings suggest that the client-server model is particularly well suited to a distributed parallel processing operational mode in a networked workstation environment.

Pohl, Kym Jason↗

Automating software design system DESTA

'DESTA' is the acronym for the Dialogue Evolutionary Synthesizer of Turnkey Algorithms by means of a natural language (Russian or English) functional specification of algorithms or software being developed. DESTA represents the computer-aided and/or automatic artificial intelligence 'forgiving' system which provides users with software tools support for algorithm and/or structured program development. The DESTA system is intended to provide support for the higher levels and earlier stages of engineering design of software in contrast to conventional Computer Aided Design (CAD) systems which provide low level tools for use at a stage when the major planning and structuring decisions have already been taken. DESTA is a knowledge-intensive system. The main features of the knowledge are procedures, functions, modules, operating system commands, batch files, their natural language specifications, and their interlinks. The specific domain for the DESTA system is a high level programming language like Turbo Pascal 6.0. The DESTA system is operational and runs on an IBM PC computer.

Lovitsky, Vladimir A.↗

Multiple-body simulation with emphasis on integrated Space Shuttle vehicle

The program to obtain intergrid communications - Pegasus - was enhanced to make better use of computing resources. Periodic block tridiagonal and penta-diagonal diagonal routines in OVERFLOW were modified to use a better algorithm to speed up the calculation for grids with periodic boundary conditions. Several programs were added to collar grid tools and a user friendly shell script was developed to help users generate collar grids. User interface for HYPGEN was modified to cope with the changes in HYPGEN. ET/SRB attach hardware grids were added to the computational model for the space shuttle and is currently incorporated into the refined shuttle model jointly developed at Johnson Space Center and Ames Research Center. Flow simulation for the integrated space shuttle vehicle at flight Reynolds number was carried out and compared with flight data as well as the earlier simulation for wind tunnel Reynolds number.

Chiu, Ing-Tsau↗

Jet Engine hot parts IR Analysis Procedure (J-EIRP)

A thermal radiation analysis method called Jet Engine IR Analysis Procedure (J-EIRP) was developed to evaluate jet engine cavity hot parts source radiation. The objectives behind J-EIRP were to achieve the greatest accuracy in model representation and solution, while minimizing computer resources and computational time. The computer programs that comprise J-EIRP were selected on the basis of their performance, accuracy, and flexibility to solve both simple and complex problems. These programs were intended for use on a personal computer, but include the ability to solve large problems on a mainframe or supercomputer. J-EIRP also provides the user with a tool for developing thermal design experience and engineering judgment through analysis experimentation, while using minimal computer resources. A sample jet engine cavity analysis demonstrates the procedure and capabilities within J-EIRP, and is compared to a simplified method for approximating cavity radiation. The goal is to introduce the terminology and solution process used in J-EIRP and to provide insight into the radiation heat transfer principles used in this procedure.

Baumeister, Joseph F.↗

Automatic structured grid generation using Gridgen (some restrictions apply)

The authors have noticed in the recent grid generation literature an emphasis on the automation of structured grid generation. The motivation behind such work is clear; grid generation is easily the most despised task in the grid-analyze-visualize triad of computational analysis (CA). However, because grid generation is closely coupled to both the design and analysis software and because quantitative measures of grid quality are lacking, 'push button' grid generation usually results in a compromise between speed, control, and quality. Overt emphasis on automation obscures the substantive issues of providing users with flexible tools for generating and modifying high quality grids in a design environment. In support of this paper's tongue-in-cheek title, many features of the Gridgen software are described. Gridgen is by no stretch of the imagination an automatic grid generator. Despite this fact, the code does utilize many automation techniques that permit interesting regenerative features.

Chawner, John R.↗

Level Indicator On A Tubular Inside Micrometer

Leveling helps to ensure accurate measurements. Attachment helpful because in some situations that involve measurement of large, tight-tolerance inside dimensions, inside micrometers not held level between contact point give inaccurate readings. User adjusts position and orientation of micrometer and verifies level by observing bubble in level indicator. Upon feeling correct drag between micrometer tips and workpiece, user confident that tool used correctly and accurate measurement obtained.

Malinzak, R. Michael↗

Computing Instability In Combustion Of Liquid Propellants

Computational fluid dynamics (CFD) code developed for use in design analyses of flow instabilities associated with combustion of sprayed liquid propellants in rocket engines. Code also contributes to design of improved commercial sprayed-fuel combustors in furnaces and jet engines. Proves robust, user-friendly software tool with comprehensive analysis capability. Enables characterization of stability or instability of engine in terms of such physically meaningful parameters as initial conditions of spray, spatial distribution of ratio between concentrations of fuel and oxidizer at injector faces, geometry of combustor, and configurations of baffles.

Chen, Yen-Sen↗

Equivalent plate modeling for conceptual design of aircraft wing structures

This paper describes an analysis method that generates conceptual-level design data for aircraft wing structures. A key requirement is that this data must be produced in a timely manner so that is can be used effectively by multidisciplinary synthesis codes for performing systems studies. Such a capability is being developed by enhancing an equivalent plate structural analysis computer code to provide a more comprehensive, robust and user-friendly analysis tool. The paper focuses on recent enhancements to the Equivalent Laminated Plate Solution (ELAPS) analysis code that significantly expands the modeling capability and improves the accuracy of results. Modeling additions include use of out-of-plane plate segments for representing winglets and advanced wing concepts such as C-wings along with a new capability for modeling the internal rib and spar structure. The accuracy of calculated results is improved by including transverse shear effects in the formulation and by using multiple sets of assumed displacement functions in the analysis. Typical results are presented to demonstrate these new features. Example configurations include a C-wing transport aircraft, a representative fighter wing and a blended-wing-body transport. These applications are intended to demonstrate and quantify the benefits of using equivalent plate modeling of wing structures during conceptual design.

Giles, Gary L.↗

Visualization of IACG data

The common data format (CDF), adopted by the international solar terrestrial physics (ISTP) program and the Interagency Consultative Group (IACG), is considered. Extensive data sharing and data analysis are needed to ensure the success of the ISTP/IACG program. The CDF user guidelines and tools for creation, visualization and manipulation are underlined. Computer software applications based on CDF data sets and designed using ISTP/IACG guidelines are shown.

Kessel, Ramona L.↗

The 1997 HST Calibration Workshop with a New Generation of Instruments

The Second Servicing mission in early 1997 has brought major changes to the Hubble Space Telescope (HST). Two of the original instruments, Faint Object Spectrograph (FOS) and Goddard High Resolution Spectrograph (GHRS), were taken out, and replaced by completely new instruments, the Space Telescope Imaging Spectrograph (STIS) and the Near Infrared Camera Multi-Object Spectrograph (NICMOS). Two new types of detectors were installed, and for the first time, HST gained infrared capabilities. A new Fine Guidance Sensor (FGS) was installed, with an alignment mechanism that could improve substantially both guiding and astrometric capabilities. With all these changes come new challenges. The characterization of the new instruments has required a major effort, both by their respective Investigation Definition Teams and at the Space Telescope Science Institute. All necessary final calibrations for the retired spectrographs needed to be carried out, and their properties definitively characterized. At the same time, work has continued to improve our understanding of the instruments that have remained on board. The results of these activities were discussed in the 1997 HST (Hubble Space Telescope) Calibration Workshop. The main focus of the Workshop was to provide users with the tools and the understanding they need to use HST's instruments and archival data to the best of their possibilities. This book contains the written record of the Workshop. As such, it should provide a valuable tool to all interested in using existing HST data or in proposing for new observations.

Casertano, S.↗