Computational Biology & Bioinformatics Minor
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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. -
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. -
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. -
Wildcat Baseball 20 Media Guide 16 2016 Wildcat Baseball
WAYNE STATE COLLEGE WSCWILDCATS.COM WILDCAT BASEBALL 20 MEDIA GUIDE 16 2016 WILDCAT BASEBALL ATHLETIC PHONE DIRECTORY TABLE OF CONTENTS All Area Codes (402) Administration Staff Directory/Table of Contents ............................. 1 Dr. Marysz Rames, President’s Offi ce .............375-7200 About Wayne State College ....................................2 Mike Powicki, Athletic Director ........................ 375-7520 WSC Athletic Administration ....................................3 Mike Barry, Associate Athletic Director / Sports & Rec Pete Chapman Baseball Complex...........................4 Facilities Director .............................................375-7521 Wayne State Facilities ..........................................5-6 Linda Anderson, Assistant Athletic Director Athletic Training Services ........................................7 for Internal Affi ars ............................................375-7308 Wildcat Head Coach Alex Koch ...............................8 Ryan Hix, Asst. AD/Business Management ..... 375-7183 Wildcat Coaching Staff ............................................9 Muffi n Morris, Senior Woman Administrator ....375-7310 2016 Season Preview....................................... 10-11 Shawn Pearcy, Faculty Athletic Representative ... 375-7078 2016 Wildcat Roster ..............................................12 Deb Harm, Athletic Administrative Assistant .... 375-7520 Wildcat Player Profi les......................................13-28 Athletic Department FAX .................................375-7120 -
Wsc Catalog 2012-2013
2012-2013 General Catalog www.wsc.edu 0 Wayne State College 2012-2013 General Catalog Mr. Curt Frye President Wayne State College Mission Statement Learning Excellence, Student Success, Regional Engagement Wayne State College is a comprehensive institution of higher education dedicated to freedom of inquiry, excellence in teaching and learning, and regional service and development. Offering affordable undergraduate and graduate programs, the College prepares students for careers, advanced study, and civic involvement. The College is committed to faculty-staff student interaction, public service, and diversity within a friendly and collegial campus community. www.wsc.edu 1 Wayne State College 2012-2013 General Catalog Wayne State College From the point of application to enrollment, the Office of Admissions has one goal in mind—your success! Office of Admissions Wayne State College 1111 Main Street Wayne, Nebraska 68787 Phone: 1-866-228-9972 or 402-375-7234 [email protected] www.wsc.edu/admission Academic Schools and Departments School of Arts & Humanities School of Education & Counseling Art & Design Counseling & Special Education Communication Arts Educational Foundations & Leadership Language & Literature Music School of Business & Technology School of Natural & Social Sciences Business & Economics Health, Human Performance & Sport Computer Technology & History, Politics & Geography Information Systems Life Sciences Technology & Applied Science Physical Sciences & Math Sociology, Psychology & Criminal Justice Call 1-800-228-9972 or -
Visual Programming: a Programming Tool for Increasing Mathematics Achivement
ARTICLES VISUAL PROGRAMMING: A PROGRAMMING TOOL FOR INCREASING MATHEMATICS ACHIVEMENT By CHERYL SWANIER * CHERYL D. SEALS ** ELODIE BILLIONNIERE *** * Associate Professor, Mathematics and Computer Science Department, Fort Valley State University ** Associate Professor, Computer Science and Software Engineering Department, Auburn University *** Doctoral Student, Computer Science and Engineering Department, Arizona State University ABSTRACT This paper aims to address the need of increasing student achievement in mathematics using a visual programming language such as Scratch. This visual programming language facilitates creating an environment where students in K-12 education can develop mathematical simulations while learning a visual programming language at the same time. Furthermore, the study of visual programming tools as a means to increase student achievement in mathematics could possibly generate interests within the computer-supported collaborative learning community. According to Jerome Bruner in Children Learn By Doing, "knowing how something is put together is worth a thousand facts about it. It permits you to go beyond it” (Bruner, 1984, p.183). Keywords : Achievement, Creativity, End User Programming, Mathematics Education, K-12, Learning, Scratch, Squeak, Visual Programming INTRODUCTION programming language as a tool to create Across the nation, math scores lag (Lewin, 2006). Students mathematical tutorials. Additionally, this paper provides a are performing lower than ever. Lewin reports, for “the modicum of information as it relates to the educational second time in a generation, education officials are value of visual programming to mathematical rethinking the teaching of math in American schools” achievement. Peppler and Kafai (2007) indicate “game (p.1). It is imperative that higher education, industry, and players program their own games and learn about K-12 collaborate to ascertain a viable solution to the software and interface design. -
Computational and Systems Biology
COMPUTATIONAL AND SYSTEMS BIOLOGY COMPUTATIONAL AND SYSTEMS BIOLOGY quantitative imaging; regulatory genomics and proteomics; single cell manipulations and measurement; stem cell and developmental systems biology; and synthetic biology and biological design. The eld of computational and systems biology represents a synthesis of ideas and approaches from the life sciences, physical The CSB PhD program is an Institute-wide program that has been sciences, computer science, and engineering. Recent advances jointly developed by the Departments of Biology, Biological in biology, including the human genome project and massively Engineering, and Electrical Engineering and Computer Science. parallel approaches to probing biological samples, have created new The program integrates biology, engineering, and computation to opportunities to understand biological problems from a systems address complex problems in biological systems, and CSB PhD perspective. Systems modeling and design are well established students have the opportunity to work with CSBi faculty from across in engineering disciplines but are newer in biology. Advances in the Institute. The curriculum has a strong emphasis on foundational computational and systems biology require multidisciplinary teams material to encourage students to become creators of future tools with skill in applying principles and tools from engineering and and technologies, rather than merely practitioners of current computer science to solve problems in biology and medicine. To approaches. Applicants must have an undergraduate degree in provide education in this emerging eld, the Computational and biology (or a related eld), bioinformatics, chemistry, computer Systems Biology (CSB) program integrates MIT's world-renowned science, mathematics, statistics, physics, or an engineering disciplines in biology, engineering, mathematics, and computer discipline, with dual-emphasis degrees encouraged. -
Comparing SSD Forensics with HDD Forensics
St. Cloud State University theRepository at St. Cloud State Culminating Projects in Information Assurance Department of Information Systems 5-2020 Comparing SSD Forensics with HDD Forensics Varun Reddy Kondam [email protected] Follow this and additional works at: https://repository.stcloudstate.edu/msia_etds Recommended Citation Kondam, Varun Reddy, "Comparing SSD Forensics with HDD Forensics" (2020). Culminating Projects in Information Assurance. 105. https://repository.stcloudstate.edu/msia_etds/105 This Starred Paper is brought to you for free and open access by the Department of Information Systems at theRepository at St. Cloud State. It has been accepted for inclusion in Culminating Projects in Information Assurance by an authorized administrator of theRepository at St. Cloud State. For more information, please contact [email protected]. Comparing SSD Forensics with HDD Forensics By Varun Reddy Kondam A Starred Paper Submitted to the Graduate Faculty of St. Cloud State University in Partial Fulfillment of the Requirements for the Degree Master of Science in Information Assurance May 2020 Starred Paper Committee: Mark Schmidt, Chairperson Lynn Collen Sneh Kalia 2 Abstract The technological industry is growing at an unprecedented rate; to adequately evaluate this shift in the fast-paced industry, one would first need to deliberate on the differences between the Hard Disk Drive (HDD) and Solid-State Drive (SSD). HDD is a hard disk drive that was conventionally used to store data, whereas SSD is a more modern and compact substitute; SSDs comprises of flash memory technology, which is the modern-day method of storing data. Though the inception of data storage began with HDD, they proved to be less accessible and stored less data as compared to the present-day SSDs, which can easily store up to 1 Terabyte in a minuscule chip-size frame. -
Spring 2019 Commencement Program
Spring Commencement May 4, 2019 Graduate Commencement - 9:30 a.m. Baccalaureate Commencement - 1:00 p.m. Spring Graduate Commencement May 4, 2019 • 9:30 a.m. *Processional: “Pomp and Circumstance” ............................................................................................. Edward Elgar A Touch of Brass Welcome ....................................................................................................................................... Dr. Marysz Rames President *“The Star Spangled Banner” ...................................................................................................... John Stafford Smith Dr. Sarah Farr, Assistant Professor of Music (The audience is invited to sing) Invocation ............................................................................................................................Mr. Trevor William Longe Master of Science in Education – Curriculum & Instruction-Instructional Leadership Greetings from the Board ................................................................................................................ Mr. John Chaney Trustee, Nebraska State College System Remarks ............................................................................................................................ Ms. Allison Danyel Backer Master of Business Administration Musical Selection: “Pie Jesu” from Requiem ........................................................................................Gabriel Fauré A Touch of Brass Presentation of Candidates for Degree ............................................................................................Mr. -
2020 — College — Volleyball
2020 — COLLEGE — VOLLEYBALL APPALACHIAN STATE UNIVERSITY AUGUSTANA UNIVERSITY Emma Longley Mearah Miedema Outside Hitter Middle Blocker Senior Junior Emma is one of the most talented athletes I have every Mearah’s intense love for lifting and competition has had the pleasure of working with. Great on the court, in made her a pleasure to work with. She holds team the weight room and in the class room. A true leader records in the vertical jump and approach jump. Mearah with a winning attitude and great work ethic. 135 Power was named to the NSIC All-Academic Team in 2018 and Clean, 125 Bench Press, 185 Squat and 31.5" approach 2019. Mearah’s affinity for lifting will undoubtedly fuel vertical jump. ~Anthony Glass her future endeavors. ~Andy Stocks ARCADIA UNIVERSITY BLACK HILLS STATE UNIVERSITY Angelo Giuffrida Peyton Bodemann OPPOSITE HITTER/OUTSIDE HITTER Middle Hitter Senior Sophomore Angelo is a member of the Men’s Volleyball Team and a Peyton is one of the strongest female athletes' across the Business Administration Major with a 3.2 cumulative board. She always comes in with a great attitude and is GPA. He is a part of the first MAC Commonwealth ready to work. Peyton has learned how to push herself Championship team. Angelo has reached Iron Knight 3 past her comfort zone to become a better player. times, and has twice received the Male Strength & ~Aaron Siekmann Conditioning Athlete of the Year award. Angelo has been an integral part our strength and conditioning program. BUFFALO STATE COLLEGE Some of his accomplishments in the weight room this Eimile O'brien year include, 34 inch Vertical Jump, Bench Press 225x6, Outside Hitter and Deadlift 515 x3. -
Spontaneous Generation & Origin of Life Concepts from Antiquity to The
SIMB News News magazine of the Society for Industrial Microbiology and Biotechnology April/May/June 2019 V.69 N.2 • www.simbhq.org Spontaneous Generation & Origin of Life Concepts from Antiquity to the Present :ŽƵƌŶĂůŽĨ/ŶĚƵƐƚƌŝĂůDŝĐƌŽďŝŽůŽŐLJΘŝŽƚĞĐŚŶŽůŽŐLJ Impact Factor 3.103 The Journal of Industrial Microbiology and Biotechnology is an international journal which publishes papers in metabolic engineering & synthetic biology; biocatalysis; fermentation & cell culture; natural products discovery & biosynthesis; bioenergy/biofuels/biochemicals; environmental microbiology; biotechnology methods; applied genomics & systems biotechnology; and food biotechnology & probiotics Editor-in-Chief Ramon Gonzalez, University of South Florida, Tampa FL, USA Editors Special Issue ^LJŶƚŚĞƚŝĐŝŽůŽŐLJ; July 2018 S. Bagley, Michigan Tech, Houghton, MI, USA R. H. Baltz, CognoGen Biotech. Consult., Sarasota, FL, USA Impact Factor 3.500 T. W. Jeffries, University of Wisconsin, Madison, WI, USA 3.000 T. D. Leathers, USDA ARS, Peoria, IL, USA 2.500 M. J. López López, University of Almeria, Almeria, Spain C. D. Maranas, Pennsylvania State Univ., Univ. Park, PA, USA 2.000 2.505 2.439 2.745 2.810 3.103 S. Park, UNIST, Ulsan, Korea 1.500 J. L. Revuelta, University of Salamanca, Salamanca, Spain 1.000 B. Shen, Scripps Research Institute, Jupiter, FL, USA 500 D. K. Solaiman, USDA ARS, Wyndmoor, PA, USA Y. Tang, University of California, Los Angeles, CA, USA E. J. Vandamme, Ghent University, Ghent, Belgium H. Zhao, University of Illinois, Urbana, IL, USA 10 Most Cited Articles Published in 2016 (Data from Web of Science: October 15, 2018) Senior Author(s) Title Citations L. Katz, R. Baltz Natural product discovery: past, present, and future 103 Genetic manipulation of secondary metabolite biosynthesis for improved production in Streptomyces and R. -
2019 State of Computer Science Education Equity and Diversity
2019 State of Computer Science Education Equity and Diversity About the Code.org About the CSTA About the ECEP Alliance Advocacy Coalition Advocacy Coalition The Computer Science Teachers The Expanding Computing Bringing together more than 70 Association (CSTA) is a membership Education Pathways (ECEP) Alliance industry, non-profit, and advocacy organization that supports and is an NSF-funded Broadening organizations, the Code.org promotes the teaching of computer Participation in Computing Alliance Advocacy Coalition is growing science. CSTA provides opportunities (NSF-CNS-1822011). As an alliance the movement to make computer for K–12 teachers and their students to of 22 states and Puerto Rico, ECEP science a fundamental part of better understand computer science seeks to increase the number and K–12 education. and to more successfully prepare diversity of students in computing themselves to teach and learn. and computing-intensive degrees Advocacy through advocacy and policy reform. Coalition About the Code.org About the Expanding Computing Advocacy Coalition Education Pathways Alliance Advocacy Coalition Bringing together more than 70 industry, non-profit, The Expanding Computing Education Pathways and advocacy organizations, the Code.org Advocacy (ECEP) Alliance is an NSF-funded Broadening Coalition is growing the movement to make computer Participation in Computing Alliance (NSF-CNS-1822011). science a fundamental part of K–12 education. ECEP seeks to increase the number and diversity of students in computing and computing-intensive About the CSTA degrees by promoting state-level computer science education reform. Working with the collective impact model, ECEP supports an alliance of 22 states and Puerto Rico to identify and develop effective The Computer Science Teachers Association (CSTA) educational interventions, and expand state-level is a membership organization that supports and infrastructure to drive educational policy change.