Bioinformatics Is an Interdisciplinary Field That Incorporates Computer
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Artificial Intelligence in Health Care: the Hope, the Hype, the Promise, the Peril
Artificial Intelligence in Health Care: The Hope, the Hype, the Promise, the Peril Michael Matheny, Sonoo Thadaney Israni, Mahnoor Ahmed, and Danielle Whicher, Editors WASHINGTON, DC NAM.EDU PREPUBLICATION COPY - Uncorrected Proofs NATIONAL ACADEMY OF MEDICINE • 500 Fifth Street, NW • WASHINGTON, DC 20001 NOTICE: This publication has undergone peer review according to procedures established by the National Academy of Medicine (NAM). Publication by the NAM worthy of public attention, but does not constitute endorsement of conclusions and recommendationssignifies that it is the by productthe NAM. of The a carefully views presented considered in processthis publication and is a contributionare those of individual contributors and do not represent formal consensus positions of the authors’ organizations; the NAM; or the National Academies of Sciences, Engineering, and Medicine. Library of Congress Cataloging-in-Publication Data to Come Copyright 2019 by the National Academy of Sciences. All rights reserved. Printed in the United States of America. Suggested citation: Matheny, M., S. Thadaney Israni, M. Ahmed, and D. Whicher, Editors. 2019. Artificial Intelligence in Health Care: The Hope, the Hype, the Promise, the Peril. NAM Special Publication. Washington, DC: National Academy of Medicine. PREPUBLICATION COPY - Uncorrected Proofs “Knowing is not enough; we must apply. Willing is not enough; we must do.” --GOETHE PREPUBLICATION COPY - Uncorrected Proofs ABOUT THE NATIONAL ACADEMY OF MEDICINE The National Academy of Medicine is one of three Academies constituting the Nation- al Academies of Sciences, Engineering, and Medicine (the National Academies). The Na- tional Academies provide independent, objective analysis and advice to the nation and conduct other activities to solve complex problems and inform public policy decisions. -
Software Development Career Pathway
Career Exploration Guide Software Development Career Pathway Information Technology Career Cluster For more information about NYC Career and Technical Education, visit: www.cte.nyc Summer 2018 Getting Started What is software? What Types of Software Can You Develop? Computers and other smart devices are made up of Software includes operating systems—like Windows, Web applications are websites that allow users to contact management system, and PeopleSoft, a hardware and software. Hardware includes all of the Apple, and Google Android—and the applications check email, share documents, and shop online, human resources information system. physical parts of a device, like the power supply, that run on them— like word processors and games. among other things. Users access them with a Mobile applications are programs that can be data storage, and microprocessors. Software contains Software applications can be run directly from a connection to the Internet through a web browser accessed directly through mobile devices like smart instructions that are stored and run by the hardware. device or through a connection to the Internet. like Firefox, Chrome, or Safari. Web browsers are phones and tablets. Many mobile applications have Other names for software are programs or applications. the platforms people use to find, retrieve, and web-based counterparts. display information online. Web browsers are applications too. Desktop applications are programs that are stored on and accessed from a computer or laptop, like Enterprise software are off-the-shelf applications What is Software Development? word processors and spreadsheets. that are customized to the needs of businesses. Popular examples include Salesforce, a customer Software development is the design and creation of Quality Testers test the application to make sure software and is usually done by a team of people. -
Annual Report 2018–2019 Our Vision
ANNUAL REPORT 2018–2019 OUR VISION We shape tomorrow. We confront problems and create solutions. We expand information’s impact and technology’s potential. Together, our faculty, staff, students, and alumni make the world a better place—day by day, project by project, leap by leap. LEADERSHIP Raj Acharya Since its establishment in 2000, the Luddy School of Informatics, Computing, and Dean Engineering has built a reputation as one of the broadest of its kind. Our more than 3,000 students come from Indiana and around the world, and our unique blend Mathew Palakal of programs in informatics, computer science, intelligent systems engineering, Senior Executive Associate information and library science, data science, and more create an interdisciplinary, Dean collaborative environment where ideas thrive. Erik Stolterman Bergqvist Our forward-looking school is a mélange, a salad bowl of disparate but related Senior Executive Associate disciplines. That salad bowl provides us with a holistic taste of creativity and Dean innovation while preserving and enhancing the taste of the individual components. Esfandiar Haghverdi As we have grown exponentially through our first two decades, we have maintained Executive Associate Dean for our core values with an open-minded view of tomorrow, one that has allowed us to Undergraduate Education stay on the cutting edge of technology while anticipating what the future holds. David Leake We accomplished much during the 2018-19 school year. Our information and library Executive Associate Dean science program was ranked second in the world behind only Harvard by the 2018 Academic Ranking of World Universities. Researchers at our school garnered Kay Connelly $16.1 million in grants from the National Science Foundation, the National Institute Associate Dean for Research of Health, the National Cancer Institute, the Department of Defense, and other prestigious organizations, and our school ranks 12th in computer and information Karl F. -
Bioinformatics 1
Bioinformatics 1 Bioinformatics School School of Science, Engineering and Technology (http://www.stmarytx.edu/set/) School Dean Ian P. Martines, Ph.D. ([email protected]) Department Biological Science (https://www.stmarytx.edu/academics/set/undergraduate/biological-sciences/) Bioinformatics is an interdisciplinary and growing field in science for solving biological, biomedical and biochemical problems with the help of computer science, mathematics and information technology. Bioinformaticians are in high demand not only in research, but also in academia because few people have the education and skills to fill available positions. The Bioinformatics program at St. Mary’s University prepares students for graduate school, medical school or entry into the field. Bioinformatics is highly applicable to all branches of life sciences and also to fields like personalized medicine and pharmacogenomics — the study of how genes affect a person’s response to drugs. The Bachelor of Science in Bioinformatics offers three tracks that students can choose. • Bachelor of Science in Bioinformatics with a minor in Biology: 120 credit hours • Bachelor of Science in Bioinformatics with a minor in Computer Science: 120 credit hours • Bachelor of Science in Bioinformatics with a minor in Applied Mathematics: 120 credit hours Students will take 23 credit hours of core Bioinformatics classes, which included three credit hours of internship or research and three credit hours of a Bioinformatics Capstone course. BS Bioinformatics Tracks • Bachelor of Science -
Biophysics, Structural and Computational Biology (BSCB) Faculty Administers the Ph.D
UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY Graduate Studies in BIOPHYSICS, STRUCTURAL AND COMPUTATIONAL BIOLOGY Student Handbook August 2019 David Mathews, Program Director Joseph Wedekind, Education Committee Chair Melissa Vera, Graduate Studies Coordinator PREFACE The Biophysics, Structural and Computational Biology (BSCB) Faculty administers the Ph.D. degree program in Biophysics for the Department of Biochemistry and Biophysics. This handbook is intended to outline the major features and policies of the program. The general features of the graduate experience at the University of Rochester are summarized in the Graduate Bulletin, which is updated every two years. Students and advisors will need to consult both sources, though it is our intent to provide the salient features here. Policy, of course, continues to evolve in response to the changing needs of the graduate programs and the students in them. Thus, it is wise to verify any crucial decisions with the Graduate Studies Coordinator. i TABLE OF CONTENTS Page I. DEFINITIONS 1 II. BIOPHYSICS CURRICULUM 2 A. Courses 2 1. Core Curriculum 2. Elective Courses 3 B. Suggested Progress Toward the Ph.D. in Biophysics 4 C. Other Educational Opportunities 4 1. Departmental Seminars 4 2. BSCB Program Retreat 5 3. Bioinformatics Cluster 5 D. Exemptions from Course Requirements 5 E. Minimum Course Performance 5 F. M.D./Ph.D. Students 6 III. ADDITIONAL DETAILS OF PROCEDURES AND REQUIREMENTS 7 A. Faculty Advisors for Entering Students 7 B. Student Laboratory Rotations 7 C. Radiation Certificate 8 D. Student Research Seminar 8 E. First Year Preliminary Examination and Evaluation 9 F. Teaching Assistantship 12 G. -
13 Genomics and Bioinformatics
Enderle / Introduction to Biomedical Engineering 2nd ed. Final Proof 5.2.2005 11:58am page 799 13 GENOMICS AND BIOINFORMATICS Spencer Muse, PhD Chapter Contents 13.1 Introduction 13.1.1 The Central Dogma: DNA to RNA to Protein 13.2 Core Laboratory Technologies 13.2.1 Gene Sequencing 13.2.2 Whole Genome Sequencing 13.2.3 Gene Expression 13.2.4 Polymorphisms 13.3 Core Bioinformatics Technologies 13.3.1 Genomics Databases 13.3.2 Sequence Alignment 13.3.3 Database Searching 13.3.4 Hidden Markov Models 13.3.5 Gene Prediction 13.3.6 Functional Annotation 13.3.7 Identifying Differentially Expressed Genes 13.3.8 Clustering Genes with Shared Expression Patterns 13.4 Conclusion Exercises Suggested Reading At the conclusion of this chapter, the reader will be able to: & Discuss the basic principles of molecular biology regarding genome science. & Describe the major types of data involved in genome projects, including technologies for collecting them. 799 Enderle / Introduction to Biomedical Engineering 2nd ed. Final Proof 5.2.2005 11:58am page 800 800 CHAPTER 13 GENOMICS AND BIOINFORMATICS & Describe practical applications and uses of genomic data. & Understand the major topics in the field of bioinformatics and DNA sequence analysis. & Use key bioinformatics databases and web resources. 13.1 INTRODUCTION In April 2003, sequencing of all three billion nucleotides in the human genome was declared complete. This landmark of modern science brought with it high hopes for the understanding and treatment of human genetic disorders. There is plenty of evidence to suggest that the hopes will become reality—1631 human genetic diseases are now associated with known DNA sequences, compared to the less than 100 that were known at the initiation of the Human Genome Project (HGP) in 1990. -
Chapter 1 Introduction to Computers, Programs, and Java
Chapter 1 Introduction to Computers, Programs, and Java 1.1 Introduction • The central theme of this book is to learn how to solve problems by writing a program . • This book teaches you how to create programs by using the Java programming languages . • Java is the Internet program language • Why Java? The answer is that Java enables user to deploy applications on the Internet for servers , desktop computers , and small hand-held devices . 1.2 What is a Computer? • A computer is an electronic device that stores and processes data. • A computer includes both hardware and software. o Hardware is the physical aspect of the computer that can be seen. o Software is the invisible instructions that control the hardware and make it work. • Computer programming consists of writing instructions for computers to perform. • A computer consists of the following hardware components o CPU (Central Processing Unit) o Memory (Main memory) o Storage Devices (hard disk, floppy disk, CDs) o Input/Output devices (monitor, printer, keyboard, mouse) o Communication devices (Modem, NIC (Network Interface Card)). Bus Storage Communication Input Output Memory CPU Devices Devices Devices Devices e.g., Disk, CD, e.g., Modem, e.g., Keyboard, e.g., Monitor, and Tape and NIC Mouse Printer FIGURE 1.1 A computer consists of a CPU, memory, Hard disk, floppy disk, monitor, printer, and communication devices. CMPS161 Class Notes (Chap 01) Page 1 / 15 Kuo-pao Yang 1.2.1 Central Processing Unit (CPU) • The central processing unit (CPU) is the brain of a computer. • It retrieves instructions from memory and executes them. -
A Sample Workload for Bioinformatics and Computational Biology for Optimizing Next-Generation High-Performance Computer Systems
BioSPLASH: A sample workload for bioinformatics and computational biology for optimizing next-generation high-performance computer systems David A. Bader∗ Vipin Sachdeva Department of Electrical and Computer Engineering University of New Mexico, Albuquerque, NM 87131 Virat Agarwal Gaurav Goel Abhishek N. Singh Indian Institute of Technology, New Delhi May 1, 2005 Abstract BioSPLASH is a suite of representative applications that we have assembled from the com- putational biology community, where the codes are carefully selected to span a breadth of algorithms and performance characteristics. The main results of this paper are the assembly of a scalable bioinformatics workload with impact to the DARPA High Produc- tivity Computing Systems Program to develop revolutionarily-new economically- viable high-performance computing systems,andanalyses of the performance of these codes for computationally demanding instances using the cycle-accurate IBM MAMBO simulator and real performance monitoring on an Apple G5 system. Hence, our work is novel in that it is one of the first efforts to incorporate life science application per- formance for optimizing high-end computer system architectures. 1 Algorithms in Computational Biology In the 50 years since the discovery of the structure of DNA, and with new techniques for sequencing the entire genome of organisms, biology is rapidly moving towards a data-intensive, computational science. Biologists are in search of biomolecular sequence data, for its comparison with other genomes, and because its structure determines function and leads to the understanding of bio- chemical pathways, disease prevention and cure, and the mechanisms of life itself. Computational biology has been aided by recent advances in both technology and algorithms; for instance, the ability to sequence short contiguous strings of DNA and from these reconstruct the whole genome (e.g., see [34, 2, 33]) and the proliferation of high-speed micro array, gene, and protein chips (e.g., see [27]) for the study of gene expression and function determination. -
FUNDAMENTALS of COMPUTING (2019-20) COURSE CODE: 5023 502800CH (Grade 7 for ½ High School Credit) 502900CH (Grade 8 for ½ High School Credit)
EXPLORING COMPUTER SCIENCE NEW NAME: FUNDAMENTALS OF COMPUTING (2019-20) COURSE CODE: 5023 502800CH (grade 7 for ½ high school credit) 502900CH (grade 8 for ½ high school credit) COURSE DESCRIPTION: Fundamentals of Computing is designed to introduce students to the field of computer science through an exploration of engaging and accessible topics. Through creativity and innovation, students will use critical thinking and problem solving skills to implement projects that are relevant to students’ lives. They will create a variety of computing artifacts while collaborating in teams. Students will gain a fundamental understanding of the history and operation of computers, programming, and web design. Students will also be introduced to computing careers and will examine societal and ethical issues of computing. OBJECTIVE: Given the necessary equipment, software, supplies, and facilities, the student will be able to successfully complete the following core standards for courses that grant one unit of credit. RECOMMENDED GRADE LEVELS: 9-12 (Preference 9-10) COURSE CREDIT: 1 unit (120 hours) COMPUTER REQUIREMENTS: One computer per student with Internet access RESOURCES: See attached Resource List A. SAFETY Effective professionals know the academic subject matter, including safety as required for proficiency within their area. They will use this knowledge as needed in their role. The following accountability criteria are considered essential for students in any program of study. 1. Review school safety policies and procedures. 2. Review classroom safety rules and procedures. 3. Review safety procedures for using equipment in the classroom. 4. Identify major causes of work-related accidents in office environments. 5. Demonstrate safety skills in an office/work environment. -
Biology (BA) Biology (BA)
Biology (BA) Biology (BA) This program is offered by the College of Arts & Sciences/ • CHEM 1110 General Chemistry II (3 hours) Biological Sciences Department and is only available at the St. and CHEM 1111 General Chemistry II: Lab (1 hour) Louis home campus. • CHEM 2100 Organic Chemistry I (3 hours) and CHEM 2101 Organic Chemistry I: Lab (1 hour) Program Description • MATH 1430 College Algebra (3 hours) • MATH 2200 Statistics (3 hours) The bachelor of arts degree is designed for students who seek or STAT 3100 Inferential Statistics (3 hours) a broad education in biology. This degree is suitable preparation or PSYC 2750 Introduction to Measurement and Statistics (3 for a diverse range of careers including health science, science hours) education and ecology-related fields. • PHYS 1710 College Physics I (3 hours) Students can earn the BA in biology alone, or with one of four and PHYS 1711 College Physics I: Lab (1 hour) emphases: biodiversity, computational biology, education or • PHYS 1720 College Physics II (3 hours) health science. and PHYS 1721 College Physics II: Lab (1 hour) Learning Outcomes BA in Biology (66 hours) Students who complete any of the bachelor of arts in biology will The general degree offers the greatest flexibility, allowing students be able to: to select 12 hours of electives from any of our 2000+ level BIOL, CHEM or PHYS courses in addition to the 54 credits of core • Describe biological, chemical and physical principles as they coursework in biology listed above. (Up to 3 credit hours of BIOL relate to the natural world in writings and presentations to a 4700/CHEM 4700/PHYS 4700 can be used toward these 12 credit diverse audience. -
Use of Bioinformatics Resources and Tools by Users of Bioinformatics Centers in India Meera Yadav University of Delhi, [email protected]
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Library Philosophy and Practice (e-journal) Libraries at University of Nebraska-Lincoln 2015 Use of Bioinformatics Resources and Tools by Users of Bioinformatics Centers in India meera yadav University of Delhi, [email protected] Manlunching Tawmbing Saha Institute of Nuclear Physisc, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/libphilprac Part of the Library and Information Science Commons yadav, meera and Tawmbing, Manlunching, "Use of Bioinformatics Resources and Tools by Users of Bioinformatics Centers in India" (2015). Library Philosophy and Practice (e-journal). 1254. http://digitalcommons.unl.edu/libphilprac/1254 Use of Bioinformatics Resources and Tools by Users of Bioinformatics Centers in India Dr Meera, Manlunching Department of Library and Information Science, University of Delhi, India [email protected], [email protected] Abstract Information plays a vital role in Bioinformatics to achieve the existing Bioinformatics information technologies. Librarians have to identify the information needs, uses and problems faced to meet the needs and requirements of the Bioinformatics users. The paper analyses the response of 315 Bioinformatics users of 15 Bioinformatics centers in India. The papers analyze the data with respect to use of different Bioinformatics databases and tools used by scholars and scientists, areas of major research in Bioinformatics, Major research project, thrust areas of research and use of different resources by the user. The study identifies the various Bioinformatics services and resources used by the Bioinformatics researchers. Keywords: Informaion services, Users, Inforamtion needs, Bioinformatics resources 1. Introduction ‘Needs’ refer to lack of self-sufficiency and also represent gaps in the present knowledge of the users. -
Challenges in Bioinformatics
Yuri Quintana, PhD, delivered a webinar in AllerGen’s Webinars for Research Success series on February 27, 2018, discussing different approaches to biomedical informatics and innovations in big-data platforms for biomedical research. His main messages and a hyperlinked index to his presentation follow. WHAT IS BIOINFORMATICS? Bioinformatics is an interdisciplinary field that develops analytical methods and software tools for understanding clinical and biological data. It combines elements from many fields, including basic sciences, biology, computer science, mathematics and engineering, among others. WHY DO WE NEED BIOINFORMATICS? Chronic diseases are rapidly expanding all over the world, and associated healthcare costs are increasing at an astronomical rate. We need to develop personalized treatments tailored to the genetics of increasingly diverse patient populations, to clinical and family histories, and to environmental factors. This requires collecting vast amounts of data, integrating it, and making it accessible and usable. CHALLENGES IN BIOINFORMATICS Data collection, coordination and archiving: These technologies have evolved to the point Many sources of biomedical data—hospitals, that we can now analyze not only at the DNA research centres and universities—do not have level, but down to the level of proteins. DNA complete data for any particular disease, due in sequencers, DNA microarrays, and mass part to patient numbers, but also to the difficulties spectrometers are generating tremendous of data collection, inter-operability