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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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RATIONALE FOR AN ADA SOFTWARE engineering ENVIRONMENT FOR NAVY MISSION CRITICAL APPLICATIONS

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NAVAL ENGINEERS JOURNAL 1984年第4期96卷 133-145页

作者： PAIGE, KK CONVERSE, RA USN LCdr. Kathleen K. Paige USN:graduated with a BA from the University of New Hampshire in 1970. She received her commission from Officer Candidate School in April 1971 and performed her first tour of duty with VFP-63 NAS Miramar. LCdr. Paige then received her MS from the Naval Post Graduate School in June 1976 and returned to San Diego to serve as Head Support Software Division at the Fleet Combat Direction System Support Activity. In May 1981 she reported to NA VSEA (PMS-408) where she served initially as Chairman of the NAVMAT Software Engineering Environment Working Group. She has been assigned as Deputy AN/UYK-43 Acquisition Manager since October 1981. LCdr. Paige was designated a fully qualified Engineering Duty Officer in December 1983. Robert A. Converse:is presently the Acquisition Manager for the Ada Language System/Navy (ALS/N) for the Naval Sea Systems Command Tactical Embedded Computer Resources Project. As such he is responsible for the definition and development of the ALS/N to be provided as a Navy standard computer programming system for Navy mission critical applications. Mr. Converse received a Bachelor of Science degree in Physics from Wheaton College Wheaton II. He spent fourteen years with the Naval Underwater Systems Center Newport Rhode Island during which time he designed and developed the Fortran compiler for the Navy Standard AN/UYK-7 computer. Also during that period he received a Master of Science degree in Computer Science from the University of Rhode Island. His thesis for that degree was entitled “Optimization Techniques for the NUSC Fortran Cross-Compiler”. Mr. Converse started his involvement with the Ada program in 1975 with the initial “Strawman” requirements review. Subsequently he was named as the Navy Ada Distinguished Reviewer and was intimately involved in the selection and refinement of the Ada language as it evolved to become ANSI/MIL-STD-1815A.

The U.S. Navy introduced the use of digital computers in mission critical applications over a quarter of a century ago. Today, virtually every system in the current and planned Navy inventory makes extensive use of computer technology. computers embedded in mission critical Navy systems are integral to our strategic and tactical defense capabilities. Thus, the military power of the U.S. Navy is inextricably tied to the use of programmable digital computers. The computer program is the essential element that embodies the system “intelligence”. In addition, it provides the flexibility to respond to changing threats and requirements. However, this very flexibility and capability poses a host of difficulties hindering full realization of the advantages. This paper describes the lessons learned about computer program development over the past twenty five years and discusses a software engineering process that addresses these lessons. It then describes how Ada and its related Ada programming Support and Run-Time Environments foster this software engineering process to improve computer program productivity and achieve greater system reliability and adaptibility. Finally, the paper discusses how the use of Ada and its environments can enhance the interoperability and transferability of computer programs among Navy projects and significantly reduce overall life cycle costs for Navy mission critical computer programs.

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The Jimmie Hamilton Award

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Naval Engineers Journal 1971年第3期83卷 36-38页

作者： NACHTSHEIM, JOHN J. BALLOU, L. DENNIS John J. Nachtsheim:is currently the Deputy Assistant Administrator for Research & Development for the Maritime Administration. His duties are the planning coordinating organizing evaluating and directing of the R&D activities of MarAd. His past experiences include: Naval Architect for the Naval Ship Engineering Center 1959 Deputy Chief Design Engineer for the Puget Sound Naval Shipyard 1958 to 1959 and Naval Architect the former Bureau of Ships 1948 to 1958. His education is comprised of a B.S. degree from the Webb Institute of Naval Architecture an L.L.B. degree from the George Washington University Law School completion of the Advanced Management Program at Harvard University and current study of Transportation at the American University. He is a Registered Professional Engineer in the District of Columbia and a Member of the Bar in the District of Columbia and the State of Maryland. In addition to ASNE his other professional memberships include the Society of Naval Architects and Marine Engineers the Society of Aeronautical Weight Engineers and the Association of Senior Engineers of the Naval Ships Systems Command (Honorary). USN Commander L. Dennis Ballou: USN is the Head of the Engineering Service Office Naval Ship Engineering Center. He is involved in computer hardware and software services to support engineering design automatic data processing systems design work study and quality assurance. Prior to NavSec duty Commander Ballou served in various billets afloat and ashore: tours on the USS Skagit and Tang supervision of the USS Skipjack's first overhul construction of the USS Nathanael Greene and helping to establish the Polaris overhaul program. He is a graduate of the U.S. Naval Academy Officers' Submarine School and the Webb Institute of Naval Architecture. He holds BS and MS degrees in marine engineering and naval architecture respectively. He has also completed many graduate

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Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics

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BMC Bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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Multimodal Whole Slide Foundation Model for Pathology

arXiv

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arXiv 2024年

作者： Ding, Tong Wagner, Sophia J. Song, Andrew H. Chen, Richard J. Lu, Ming Y. Zhang, Andrew Vaidya, Anurag J. Jaume, Guillaume Shaban, Muhammad Kim, Ahrong Williamson, Drew F.K. Chen, Bowen Almagro-Perez, Cristina Doucet, Paul Sahai, Sharifa Chen, Chengkuan Komura, Daisuke Kawabe, Akihiro Ishikawa, Shumpei Gerber, Georg Peng, Tingying Le, Long Phi Mahmood, Faisal Department of Pathology Mass General Brigham Harvard Medical School BostonMA United States Data Science Program Dana-Farber Cancer Institute BostonMA United States Cancer Program Broad Institute of Harvard and MIT CambridgeMA United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA United States Helmholtz Munich German Research Center for Environment and Health Munich Germany School of Computation Information and Technology Technical University of Munich Munich Germany Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA United States Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology CambridgeMA United States Department of Pathology Pusan National University Busan Korea Republic of Department of Pathology and Laboratory Medicine Emory University School of Medicine AtlantaGA United States Harvard Data Science Initiative Harvard University CambridgeMA United States Department of Systems Biology Harvard Medical School BostonMA United States Department of Preventive Medicine Graduate School of Medicine The University of Tokyo Tokyo Japan Division of Pathology National Cancer Center Exploratory Oncology Research & Clinical Trial Center Chiba Japan

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation. The model is publicly accessible at https://***/mahmoodlab/TITAN © 2024, CC BY-NC-ND.

关键词： Self-supervised learning

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TECHNOLOGICAL ADVANCES IN AIRCRAFT CARRIER DESIGN

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NAVAL ENGINEERS JOURNAL 1980年第5期92卷 71-85页

作者： REIN, RJ RYAN, JC USN (RET.) Cdr. Robert J. Rein USN (Ret.)currently is the Director of Naval Support Systems for the Columbia Research Corporation Washington D. C. At the time this paper was presented he was on active duty in the U.S. Navy serving as the Ship Design Manager for the CVV Naval Sea Systems Command. Prior to that his duty assignments included Deputy Program Manager for the Sea Control Ship Assistant Ship Material Officer. Staff of Commander Naval Air Force U.S. Pacific Fleet and Type Desk Officer for Cruisers/Destroyers and New Construction (CG 30) at the former Hunter's Point Naval Shipyard. He is a graduate of General Motors Institute an accredited private college sponsored by the General Motors Corporation: the U.S. Naval Postgraduate School Monterey. Calif.: and the Defense Systems Management College. Fort Belvoir. Va. Additionally. he has had extensive postgraduate study in Systems Management at The George Washington University. Cdr. Rein is extremely active in his support of professional engineering societies and as a member of ASNE since 1964 has been responsible for the founding of ASNE Local Sections on the west coast and presently is serving as the Society's National Assistant Secretary-Treasurer. In addition he also was the creator and coordinator for the highly successful. Society sponsored Symposium “Aircraft Carriers — Present and Future.”which was held in October 1976 at the U.S. Grant Hotel. San Diego. Calif. and was the first such Symposium jointly sponsored by an Operating Fleet command and a professional society. Mr. J. Christopher Ryanreceived his B.S. degree in Naval Architecture and Marine Engineering from Webb Institute of Naval Architecture in 1967 and his M.S. degree in Naval Architecture from Massachusetts Institute of Technology in 1969. His initial work experience was at Litton Ship Systems where he was associated primarily with the general arrangements development of the DD 963 Class design. Subsequently. he was employed at the former Naval Ship Engineering Center with work as

Since the signing of the Contract Design Plane for the CVN 68 (the U.S. Navy's latest Class of Aircraft Carriers) In 1963, considerable technological advances have been made in Naval Ship Design. This paper provides specific examples of how new technology has affected traditional Carrier design practices and techniques, and also indicates areas where future advanced technology will be needed. It is divided into four sections: 1) computer Design Application; 2) Total Ship Energy Conservation Analysis; 3) Advances in Structural Design; and 4) Impact of V/STOL Aircraft. The increased use of the computer to define ship characteristics in the initial stage of ship design is discussed, followed by a report on efforts to include energy conservation as an integral part of the design process. The energy conservation approach uses traditional analytical techniques to develop innovative design configurations that will achieve energy savings. Of the many advances in Carrier structural design, two specific examples are given: 1) Elimination of the infamous “knee-knockers” (high sills in passageway openings) common to Gallery Deck structure, and 2) Successful attempts at reducing the thickness of aircraft elevator platforms. The paper concludes by pointing out some possible challenges facing the ship designer and some of the technology already created by the expected introduction of advanced design Vertical/Short Takeoff and Landing (V/STOL) aircraft.

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AN EXPANDED GENETICALLY ENCODED VOLTAGE INDICATOR TOOLBOX FOR DEEP, RAPID, AND PROLONGED VOLTAGE RECORDINGS IN VIVO

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IBRO Neuroscience Reports 2023年 15卷 S264-S265页

作者： Shuyuan Yang Xiaoyu Lu Michelle Land Zhuohe Liu Alex Mcdonald Yueyang Gou Yunmiao Wang Elsayed Zaabout Xiaoyu Dong Shujuan Lai Dieter Jaeger Jacob Reimer François St-Pierre Rice University Department Of Chemical And Biomolecular Engineering Houston United States of America Rice University Systems Synthetic And Physical Biology Program Houston United States of America Baylor College of Medicine Department Of Neuroscience Houston United States of America Emory University Department Of Biology Atlanta United States of America Emory University Neuroscience Graduate Program Atlanta United States of America Baylor College of Medicine Center For Neuroscience And Artificial Intelligence Houston United States of America Rice University Department Of Electrical And Computer Engineering Houston United States of America Baylor College of Medicine Department Of Biochemistry And Molecular Biology Houston United States of America

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computer AIDS FOR SHIP DESIGN, INTEGRATION AND CONTROL

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NAVAL ENGINEERS JOURNAL 1980年第2期92卷 73-87页

作者： CARLSON, CM JOHNSON, RA HELMING, FW Mr. Craig M. Carlson received his B.S. degree in Naval Architecture and Marine Engineering from the University of Michigan in 1970 and began his career with the Department of the Navy at the Naval Ship Engineering Center (NAVSEC). In 1972. he returned to the University of Michigan under the NAVSEC Long Term Training Program and received his M.S. degree in Naval Architecture and Marine Engineering. After returning to the Ship Arrangements Branch at NAVSEC. he was assigned as Task Leader for General Arrangements for the PGG PCG PHM. and MCM ship designs and was awarded Outstanding Performance Awards in 1974 and 1975. In addition he was Manager of the Arrangement Subsystem of the Navy's Computer-Aided Ship Design and Construction Program (CASDAC). In October 1979. he became Manager of the CASDAC Hull Design System. Currently. he also is enrolled in the M.S. of Computer Science Program at Johns Hopkins University. Mr. Carlson previously has presented technical papers at ASNE Day 1974 and 1978 as well as at the 1979 DOD Manufacturing Technology Advisory Group Conference. Besides ASNE. which he joined in 1972. he is a member of SNAME. ASE. and the U.S. Naval Institute. Mr. Robert A. Johnson is a Naval Architect in Surface Combatants Design (SEA 03D3). Ship Design Integration Directorate Naval Sea Systems Command. He received an Associate in Engineering degree in Drafting and Design Technology in 1959. his B.S. degree in Aerospace Engineering in 1965. and his M.S. degree in Engineering Mechanics in 1970. all from the Pennsylvania State University. In 1973. he was selected for the NA VSEC Hull Division s Long Term Training Program at the University of Michigan subsequently receiving his M.S.E. degree in Naval Architecture in 1974. Mr. Johnson began his career with the Ordnance Research Laboratory at Pennsylvania State University in 1959 where he worked. on the design of hydroelastic submarine models and conducted research in the area of flow induced structural vibrations. In 1967 he joined HRB-Singer at State Colle

This paper presents an integrated approach to computer-Aided Ship Design for U.S. Navy preliminary and contract design. An integrated Hull Design System (HDS), currently under development by the Hull Group of the Naval Sea systems Command (NAVSEA 32). is the vehicle for the discussion. This paper is directed toward practicing ship design professionals and the managers of the ship design process. Primary emphasis of this paper, and of the development effort currently under way, is on aiding ship design professionals in their work. Focus is on integration and management control of the extremely complex set of processes which make up naval ship design. The terminology of the Ship Designer and Design Manager is used. The reader needs no familiarity with the technologies of computer science.

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Development and evaluation of a hospital-wide healthcare-associated surgical site infection detection algorithm

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Journal of Microbiology, Immunology and Infection 2015年第2期48卷 S43-S43页

作者： Yi-Ju Tseng Bo-Chiang Huang Hui-Chi Lin Ming-Yuan Chen Rung-Ji Shang Wang-Huei Sheng Yee-Chun Chen Feipei Lai Shan-Chwen Chang Children's Hospital Informatics Program Boston Children's Hospital Boston MA USA Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taiwan Center for Infection Control National Taiwan University Hospital (NTUH) Taiwan Information Systems Office NTUH Taipei Taiwan Department of Internal Medicine NTUH and College of Medicine Taiwan National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan Department of Computer Science and Information Engineering National Taiwan University Taiwan

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CENTML CONTROL SYSTEM TRAINING THROUGH STA TIC AND DYNAMIC SIMULATION

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Naval Engineers Journal 1980年第2期92卷 196-206页

作者： HALL, EDWIN E. MOSS, DONALD G. NORRIS, CLIFFORD S. PETERSON, HAROLD D. Mr. Edwin E. Hall received his Bachelor's degree in Electronics from Oklahoma City University. He also is a certified College-Level Instructor in the state of Florida and has done graduate work in Computer Science at the University of Florida. As the Technical Publications and Training Manager Simulation and Control Systems Department. General Electric Company Daytona Beach Fla. he currently is responsible for the costing. planning performance scheduling and timely completion of the Department's Technical Manuals and Technical Training Programs. These Training and Manual contracts cover Ship Systems Programs. Simulation Programs. and Communications Programs for the Armed Services and commercial customers. Mr. Hall has over twenty-years experience as a Technical Writer and Instructor and for the past seventeen years has been at the General Electric Company's Daytona Beach Facility. His experience ranges from teaching Basic Electronics and Radar Circuitry as a civilian instructor for the U.S. Army to writing Manuals Proposals Reports Specifications and Brochures for General Electric's product lines. Mr. Donald G. MOSS is a graduate of Kansas State University from which he received both his B.S. degree in Business Administration and his M.S. degree in Electrical Engineering. He is presently a Senior Systems Engineer for Control Systems in the Simulation and Control Systems Department at the General Electric Company's Daytona Beach Facility. He has been employed by General Electric for 23 years — the first seven as an Engineer and Program Manager on the Fire Control Systems for the Fleet Ballistics Missile Program the next six managing the design of control and checkout equipment on the APOLLO Program and the last ten years working on control equipment for the machinery plants of new Navy ships. Over the span of years at General Electric he has worked on propulsion control for the DD-963 propulsion electric plant and auxiliary control for the FFG-7: propulsion boiler burner electric auxiliary and car

Dynamic Simulation is defined as the hardware and software required to present to the student operator visual and audible cues and responses that are the same as those encountered when operating the Control Consoles aborad ship. This type of simulation is considered essential to the development of operator skills for critical tasks. Less critical tasks can be practiced using static simulation devices. This paper discusses the utilization of these types of training devices to train Navy crews. An overview of the Machinery Control systems of the FFG 7 and AO 177 Class ships is discussed to provide an understanding of state‐of‐the‐art equipment development. The training programs for these two ship Classes are then reviewed to show how simulation devices are currently used by the Training Community, and this is followed by a brief discussion of the additional benefits that also are derived. © 1980 by the American Society of Naval Engineers, Inc.

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