PROPOSAL FOR A. Last Modified January 24, 2012

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1 N E W Y O R K C I T Y COLLEGE OF TECHNOLOGY THE CITY UNIVERSITY OF NEW YORK 300 JAY STREET BROOKLYN, NEW YORK Biological Sciences Department Room P305 Phone: (718) Fax: (718) PROPOSAL FOR A BACHELOR OF SCIENCE DEGREE IN BIOMEDICAL INFORMATICS Last Modified January 24, 2012 SPONSORED BY BIOLOGICAL SCIENCES DEPARTMENT SCHOOL OF ARTS AND SCIENCES NEW YORK CITY COLLEGE OF TECHNOLOGY THE CITY UNIVERSITY OF NEW YORK PROPOSED INITIATION: Fall 2012 DATE OF COLLEGE GOVERNANCE APPROVAL: --/--/-- 1

2 PROGRAM IDENTIFICATION COLLEGE PROGRAM TITLE DEGREE CONTACT PERSONS New York City College of Technology of The City University of New York Biomedical Informatics Bachelor of Science Prof. Karl Botchway, Ph.D. Interim Dean, School of Arts & Sciences Prof. Walied Samarrai, Ph.D. Chair, Biological Sciences Department 2

3 TABLE OF CONTENTS TOPIC PAGE Program Identification 2 Curriculum Modification Proposal 6 Introduction 8 1. Purpose and Goals 8 2. Need and Justification 2.1 Relationship to Other Programs at CUNY 2.2 Resources Available to Implement the Program Student Interest and Anticipated Enrollment Curriculum 4.1 Overview of Courses in the Proposed Curriculum 4.2 Anticipated Learning Outcomes of the Curriculum 4.3 Courses Required to Complete the Program 4.4 Typical Course Sequences for a 4-Year Timeframe 4.5 Course Descriptions for Six New Courses for the Program 5. Faculty Cost Assessment Acknowledgements References 22 New Course Proposal: Medical Informatics Fundamentals Chancellor s Report Form for New Courses Course Summary Catalog Course Description Extended Course Description Anticipated Learning Objectives Assessment of Specific Learning Outcomes Topical Lecture Outline Grading Procedure Research Project and Class Presentation Class Participation Library Resources Form New Course Proposal: Bioinformatics II Chancellor s Report Form for New Courses Course Summary Catalog Course Description Anticipated Learning Objectives Assessment of Specific Learning Outcomes

4 Topical Lecture and Laboratory Outline Grading Procedure Research Project and Class Presentation Class Participation Library Resources Form New Course Proposal: Molecular and Cell Biology Chancellor s Report Form for New Courses Course Summary Catalog Course Description Learning Objectives (Lecture) Assessment of Specific Learning Outcomes Topical Lecture Outline Grading Policy Class Participation Molecular and Cell Biology Laboratory Learning Objectives (Lab) Assessment of Student Learning Topical Laboratory Outline Library Resources Form New Course Proposal: Computational Genomics Chancellor s Report Form for New Courses Course Summary Catalog Course Description Extended Course Description Learning Objectives Assessment of Specific Learning Outcomes Topical Lecture Outline Grading Procedure Class Participation Library Resources Form New Course Proposal: Molecular Modeling in Biology Chancellor s Report Form for New Courses Course Summary Catalog Course Description Extended Course Description Anticipated Learning Objectives Assessment of Specific Learning Outcomes Topical Lecture Outline Grading Procedure Class Project

5 Participation Library Resources Form New Course Proposal: Internship/Research in Biomedical Informatics Chancellor s Report Form for New Courses Course Summary Catalog Course Description Extended Course Description Anticipated Learning Objectives General Course Structure Options for Internship and Research Grading Procedure Student Log/Journal Final Project and Oral Presentation Library Resources Form Letters of Support Dr. Karl Botchway, Dean of the School of Arts and Sciences American Medical Informatics Association (AMIA) New York City Economic Development Corporation (NYCEDC) Relevant Meeting Minutes Biological Sciences Department Curriculum Committee Minutes Biological Sciences Department Meeting Minutes

6 New York City College of Technology, CUNY CURRICULUM MODIFICATION PROPOSAL Please refer to the Curriculum Modification Guide before submitting a proposal. Title of Proposal NEW BACHELOR OF SCIENCE PROGRAM IN BIOMEDICAL INFORMATICS Department Chairperson / Coordinator PROF. WALIED SAMARRAI Date OCTOBER 12, 2011 Department/Program BIOLOGICAL SCIENCES DEPARTMENT Brief Description The Biological Sciences Department proposes a Bachelor of Science degree program in Biomedical Informatics, and six new courses in support of the program. The proposed program will prepare students for enriching careers in the growing field of Bioinformatics. The program will equip students with the technical skills and knowledge needed to navigate the mass of biological and biomedical data that is increasingly driving new developments in pharmacology and therapeutics, molecular biology, biomedical science, and healthcare. Upon completing this program, students will have a wide range of career options, from direct employment to continuation of studies in graduate and medical school. The program will be interdisciplinary, in that technology is used to connect expertise in computer science, medicine, biology, statistics, and healthcare. Indicate the specific change or changes desired. MAJOR: _X_new course(s) experimental courses Continuing Education courses for credit _X_ addition or elimination of programs or certificates changes in entrance requirements for matriculation or admission to a specific degree program a change which would affect the educational objective of a department and/or of the college MINOR: change in course number and/or title change in course description change in sequence of courses change in prerequisites or corequisites for individual course substitution of one course for another of similar hours and credits substitution of required course(s) for the degree course(s) withdrawn or reinstated Supporting Documents Checklist: MAJOR: MINOR: Complete description of MAJOR modifications and rationale All course proposals (see Course Proposal Document Checklist) Catalog course description specifying hours and credits for lecture and labs, prerequisites and/or Description of MINOR modifications and rationale Department minutes with record of the approval Memo or from the Dean approving the change Evidence of consultation with all affected departments Completed Curriculum Modification Questions 6

7 corequisites Relevant minutes from department meetings Completed Curriculum Modification Questions Documentation of needs assessment Documentation of student views Evidence of consultation with all affected departments Projected headcounts (fall/spring and day/evening) for each new or modified course. Memo or from the academic dean to the Curriculum Committee chairperson with a recommendation for or against adopting the proposed change(s) and reasons for the recommendation. Completed Library Resources and Information Literacy Form Comparative charts, specifying differences in class hours, lab hours and credits, including course titles and codes. Documentation indicating core curriculum requirements have been met for New Programs/Options or Program Changes. (if applicable) N/A Documentation of Advisory Commission views (if applicable) N/A A memorandum from the VP for Finance and Administration with written comments regarding additional and/or new facilities, renovations or construction (if applicable). N/A Plan and process for evaluation of Curricular Experiments (if applicable) N/A Established time limit for Curricular Experiments (if applicable) Submitted by PROF. WALIED SAMARRAI CHAIR BIOLOGICAL SCIENCES DEPARTMENT this form along with all supporting documents to the Chair of the College Council Curriculum Committee. Prof. Jill Bouratglou jbouratoglou@citytech.cuny.edu 7

8 BACHELOR OF SCIENCE PROGRAM IN BIOMEDICAL INFORMATICS Introduction The Biological Sciences Department at New York City College of Technology (City Tech) proposes a Bachelor of Science degree program in Biomedical Informatics. The Biomedical Informatics program will significantly increase opportunities for City Tech students interested in the healthcare and biomedical fields. The outlook is promising for enrollment in such a program. Graduates of the program will be positioned to take advantage of excellent opportunities for employment in the public and private sectors as well as for post-baccalaureate study. The program will also meet a regional need as part of the city s long-running campaign to become a capital for the biotechnology industry Purpose and Goals The proposed program in Biomedical Informatics will prepare students for enriching careers in the growing field of Bioinformatics. The program will equip students with the technical skills and knowledge needed to navigate the mass of biological and biomedical data that is increasingly driving new developments in pharmacology and therapeutics, molecular biology, biomedical science, and healthcare. The program will be truly interdisciplinary, in that technology is used to connect expertise in computer science, medicine, biology, statistics, and healthcare. Upon completing this program, students will have a wide range of career options, from direct employment to continuation of studies in graduate or medical school. In order to better prepare students for these options, the program has been designed with two tracks: the Healthcare Technology Track and the Pre-Med Track. The Healthcare Technology Track will equip students with knowledge and skills required for direct employment in a fast-growing market as well as for further studies in applied biomedical informatics, while the Pre-Med Track will serve students who may want to seek further studies in the medical and research fields. Both tracks share a common core of courses (at least 87 of a total of 120 credits), which covers the multidisciplinary competencies of the field of Biomedical Informatics, while differing mostly in the allocation of elective courses. In particular, the Pre-Med Track ensures that standard academic prerequisites of medical schools (lab courses in Inorganic and Organic Chemistry, and Physics) are met. A rigorous core of courses, common to both tracks of study, will provide students with a strong foundation from which to develop competencies in two interrelated component areas of Bioinformatics that form the focus of the program: Molecular Bioinformatics and Health Informatics. This dual focus gives students a broad understanding of the critical importance of informatics for a wide range of biomedical and health applications. While each subfield involves different proficiencies, they share fundamental informatics principles, directed at the transformation of large raw databases into useful biological and biomedical knowledge. Moreover, these two subfields are seeing an exciting integration in cutting edge medicine, as 8

9 genomic information is used increasingly in medical diagnosis and care. The dual focus of the program thus prepares students for a range of career options and to adapt to changing conditions in the field. The proposed common curriculum also consists of courses in general education, advanced biology, and computer systems. These courses not only provide a solid liberal arts education, but also a solid background in biological sciences and computer technology; which serve as prerequisites for interdisciplinary training in Biomedical Informatics; and prepare students to become creative thinkers able to meet emerging challenges in fields of study and in their careers. The Molecular Bioinformatics component of the curriculum will train students for careers in industry and academia that require skills for the effective manipulation and analysis of molecular databases of DNA, RNA and protein sequences and structures. Concerted efforts in the sequencing of complete genomes of organisms, including the Human Genome Project, have generated vast amounts of raw molecular data. Likewise, proteomic data is becoming increasingly vital in the development of molecular therapies in biotechnology and medicine. For such data to be useful for biomedical and pharmacological applications, extensive biological and computational analyses are required. As expected, we are witnessing an increasing demand for biotechnologists equipped with knowledge of biomedical databases and bioinformatic computer tools, as well as with skills in biostatistics and data mining. The Molecular Bioinformatics courses will prepare graduates of the Biomedical Informatics program for employment as bioinformatics specialists in pharmaceutical and biotech companies, research hospitals, academic institutions, and government-sponsored research institutes such as the National Institutes of Health (NIH) and the Centers for Disease Control (CDC). Alternatively, students will be well positioned to enter numerous master s and doctoral programs in Molecular Bioinformatics at research universities in the region and across the country. The Health Informatics component of the curriculum will prepare students for careers with responsibility for the secure storage, retrieval, and use of biomedical information. The Health Insurance Portability and Accountability Acts (HIPAA) of 1996 and 2004 (for small health plans) require national standards for electronic health care records to facilitate electronic processing of claims and other transactions. These laws also require privacy and security standards in order to protect health information. Hospitals and health care centers are eager to maintain an information system that is secure, efficient, timely, patient-centered, equitable, effective and compliant with HIPAA. Experts in the field report a growing demand for trained individuals to assume this responsibility. In addition, President Barack Obama has proposed a massive mobilization to modernize healthcare by making all health records standardized and electronic. The goal is to computerize all health records within five years. 2 While it is anticipated that this will result in improved quality of healthcare for all Americans, this initiative also requires skilled health informaticians for its successful implementation. The Health Informatics component of the program will therefore position graduates to seek employment as consultants, hospital record managers, data analysts in industry, librarians, and staff in state health departments and family medical centers. Both tracks of the program are designed to provide well-rounded, interdisciplinary training for a new generation of biomedical and healthcare workers prepared to meet the challenges of today 9

10 and of the future. Student knowledge acquired in the college classroom and laboratory will be reinforced by College-sponsored internships (for credit) at clinical and research locations in the region. Because Biomedical Informatics is a rapidly evolving field, it is also important that students benefit from City Tech s strong General Education requirements and courses, so that they will be able to adapt to changes in this field as creative thinkers and lifelong learners. The goal is not only to provide students with the training they need to enter this growing field in its current state, but also with the personal and intellectual resources to participate in and lead its inevitable advances and transformations. 2. Need and Justification City Tech s proposed Biomedical Informatics program addresses employment needs in both Health Informatics and Molecular Bioinformatics, two growing subfields of Bioinformatics. Fundamentally, these two areas share a common core of computational and informatics principles, differing only in the kinds of databases that require professional management and scientific analysis. The manner in which data is managed in the healthcare industry is being transformed. Medical Records and Health Information technicians are being supplemented or replaced by Health Informaticians. The need to strengthen the breadth and depth of the health informatics workforce is a critical component in this transformation. City Tech s program will ensure the education and training of a new generation of medical and health informaticians that will develop new ways to organize, manage, store, and use information to the benefit of the healthcare industry. They will find the means to communicate this information effectively among the professionals who need it and control the amount and type of information that is disseminated. The Bureau of Labor Statistics 3 reports that job opportunities in the field are expected to grow faster than average. Employment is expected to grow 20 percent between 2008 and Graduates of the program will be fully prepared to assume the responsibilities of a Health Informatician. Another career path for program graduates will be in Molecular Bioinformatics, as informatics specialists involved in managing and analyzing large biological databases arising from genomic and proteomic research. City Tech s program will aim to provide students with a solid bioinformatics foundation for careers in pharmaceutical and biotechnology companies. According to the US Department of Labor, 4 the projected growth in employment in this young field is higher than average, at 14 to 19 percent between 2008 and Alternatively, graduates will be able to continue study at the graduate level, which should lead to specialist jobs or research positions in both industry and academia. There are numerous graduate programs in computational biology and bioinformatics in the tri-state region that are looking for qualified applicants, and we are in a good position to establish mutually beneficial relationships with them. Among them, Hunter College has a Bioinformatics MA program; the Polytechnic Institute of NYU has a Bioinformatics MS program; SUNY Downstate Medical Center has a Medical Informatics masters program; and Columbia University has a Biomedical Informatics MA and PhD program. Some students may proceed to medical schools as well, since the 10

11 proposed curriculum provides an opportunity to complete many of the courses required to apply to medical school. The proposed program is among the few in the country to combine courses in medical informatics and molecular bioinformatics within an integrated undergraduate curriculum. The staggering growth in the amount of biological data being generated, including the sequencing of personal genomes which are becoming increasingly affordable, 5 has created a need for professionals who are adept at engaging such databases for diagnostic and therapeutic purposes. Graduates of the program are poised to be practitioners of the emerging trend called translational bioinformatics, whose purpose is to develop and implement medical applications based on a meaningful integration of clinical, genomic, and molecular data. Because of the multidisciplinary nature of the proposed curriculum, those graduates seeking to be at the forefront of this exciting field will find a seamless path to any advanced degree towards which they aspire Relationship to Other Programs at CUNY No other CUNY campus presently offers a BS in Biomedical Informatics. Borough of Manhattan Community College (BMCC) offers an AAS in Health Information Technology. The chair of the BMCC program has been contacted, and an articulation agreement is currently being developed. Graduates of a number of existing associates programs elsewhere may also be interested in pursuing higher education in the proposed program. Such programs include the AS in Biotechnology at Kingsborough Community College (KCC). The School of Professional Studies (SPS) offers an online BS in Health Information Management, which provides CAHIIMaccredited (Commission on Accreditation for Health Informatics and Information Management Education) training in health informatics but not in molecular bioinformatics Resources Available to Implement the Program City Tech presently offers both associate and bachelor s degrees in numerous health professions: Nursing (AAS and BS), Dental Hygiene (AAS), Health Services Administration (BS), Radiological Technology and Medical Imaging (AAS), Restorative Dentistry (AAS), and Vision Care Technology (AAS). In addition, technology degrees are offered in Computer Science (AS), Microcomputer Business Systems (AAS), Computer Information Systems (AAS), and Computer Systems (BTech). These programs are complemented by a full range of general education courses, some specifically tailored to the needs of health and technology students. Thus, most of the required courses in the proposed Biomedical Informatics program already exist, as well as the needed scientific and computer laboratory facilities. As a result, only six new courses need to be designed. Importantly, the College currently has faculty with the expertise necessary to develop and teach these new courses. The Biological Sciences Department has been working with the chair and faculty of the Computer Systems Technology Department to develop those courses involving computer technology. Additionally, 11

12 many of City Tech s programs in the health profession have faculty members who are familiar with the skill sets needed by medical informaticians and should be available for consultation. Most upper-level courses in the proposed program will be held in computer laboratories, with some held in traditional lecture rooms. A number of courses will be offered using partially online or fully online formats. New software will be installed in existing computer laboratories, limiting the cost of this part of the program initially to the cost of the software. 3. Student Interest and Anticipated Enrollment A large pool of students at City Tech aspires to careers in healthcare professions and the biological sciences. With the creation of the Biomedical Informatics program, these students will have another alternative to the College s highly competitive health programs, which have limited capacity. Additionally, students who have completed an AS degree in Liberal Arts and Sciences (LAS) can transfer into the program seamlessly and continue towards the bachelor s degree. Currently, over 1500 students are enrolled in the Liberal Arts programs (LAS and LAA). A survey of senior high school students was conducted at a recent City Tech Open House. Of the 104 students who responded, 64 expressed interest in Medical Technology and/or Medical Informatics, and 75 expected to attend college on a full-time basis. A survey of undergraduate students in 23 lecture and lab sections of General Biology I (BIO 1101) was conducted early in the spring of Of the 693 students surveyed, 122 students indicated that they would be interested in a program in Medical Informatics if it were offered by the College. The survey questions and results are summarized in the table below. SURVEY QUESTIONS For High School Students: How interested are you in enrolling in the Biological Sciences Department s new programs in Medical Informatics and Medical Technology? (n=104) For BIO 1101 Students: Would you be interested in enrolling in the Biological Sciences Department s new programs in Medical Informatics and Medical Technology? (n=693) very/somewhat interested: 61.5% yes 17.6% RESULTS not interested: 38.5% no 82.4% The following table is a projection of the number of students expected to enroll in the program. We extrapolated from the results of these surveys that about 70% of the students will enroll on a full-time basis, and we assumed 80% one-year retention, the typical rate for bachelor s degree students at City Tech, and a 15% graduation rate after four years of study for full-time first time freshmen. There will not be any special admissions requirements. Biomedical Informatics Projected Enrollment Year 1 Year 2 Year 3 Year 4 Year 5 Full-time Part-time Total

13 4. Curriculum City Tech is proposing a bachelor s degree program in Biomedical Informatics to meet the human resource needs of the growing health and biomedical fields. Biomedical Informatics is the discipline formed by the intersection of computing, healthcare, and biological science. It incorporates the advances arising from the computing revolution and the exponential growth of biological data. City Tech s proposed Biomedical Informatics program is an interdisciplinary major, designed to educate individuals to process seemingly disparate information and integrate into useful knowledge. In addition, the program will produce specialists with practical skills required in the acquisition, maintenance, security, and analysis of health and biomolecular data. Students in the program will choose between two tracks: the Healthcare Technology Track and the Pre-Med Track. At least 87 of a total of 120 credits are shared between the two tracks; they differ mostly in the allocation of elective courses to satisfy academic prerequisites of medical schools and some doctoral programs. The Healthcare Technology Track is designed to equip students with knowledge and skills required for both direct employment in a fast-growing market and for further studies in applied biomedical informatics. Students who are interested in advanced post-baccalaureate studies in the medical and research fields, including medical and doctoral degrees, will be strongly advised to choose the Pre-Med Track. 4.1 Overview of Courses in the Proposed Curriculum Students will acquire the required competencies through a curriculum designed to include: 1. A strong foundation in the biological sciences, including Anatomy and Physiology and Pathophysiology, combined with the opportunity to take fundamental mathematics and science courses such as calculus, general chemistry, organic chemistry, and calculusbased physics, for those interested in pursuing admission to medical or other professional graduate schools. 2. Significant requirements in computer systems including Programming Fundamentals, JAVA or C++ Programming, Healthcare Databases and Information Systems, as well as in mathematics, including Probability & Statistics. 3. Specially-designed courses in Health Informatics combined with existing courses in Health Services Administration, in order to provide the required background in medicine, medical terminology, healthcare data management, and healthcare organizations. These competencies will link with the student s skills and knowledge in mathematics, science, and general education to produce competent Health Informaticians. 4. Specially-designed courses in Molecular Bioinformatics, including two semesters of Bioinformatics and one each of Computational Genomics and Molecular Modeling. These courses provide the foundation for competencies in understanding and analyzing genetic, genomic, and proteomic data for cutting-edge healthcare applications and biomedical research. 5. General education core requirements which can be satisfied with existing courses designed for students in the college s health career programs, and which will enrich the educational experience of Biomedical Informatics students. These include: The 13

14 Literature of Illness and Care (ENG 3404), Health Care Ethics (PHIL 2203), and Specialized Communication for Technology Students (ENG 1133). Up to 80 credits required for this new program in Biomedical Informatics overlap with the Biological Sciences Department s proposed BS degree program in Medical Technology, which has been approved by the College Council in Specialty courses in both programs are offered mostly in the third and fourth years, providing students with the opportunity to switch between them and complete their course work with minimal delay Anticipated Learning Outcomes of the Curriculum The proposed program is consistent with the mission of the College to provide students with both a command of skills necessary in their respective career areas, and the educational foundation for lifelong learning. General Education courses, central to this effort, include a year of English composition, and courses in speech, behavioral and social science, literature and ethics. These courses should provide students with a strong foundation in oral and written communication skills and a well-rounded understanding of human nature and culture. The program curriculum is designed to meet the following learning goals: 1. A broad general education which lays the ground work for lifelong learning, and prepares for future education at the graduate level. 2. Ability to communicate effectively with other members of the healthcare and information technology professions and research fields. 3. Competencies in general biological sciences and in the fundamentals of computer technology and computer programming. 4. In-depth knowledge and skills in: a. Computational and mathematical basis of molecular biology and molecular bioinformatics; b. Biomolecular sequence and structure databases of DNA, RNA, and proteins, as well as the use of standard bioinformatics software for the retrieval and analysis of information from such databases for biomedical applications; c. Healthcare information systems analysis and design, including healthcare database structures, data security, privacy, confidentiality, and associated legal and ethical issues. d. The growing application of molecular bioinformatics in cutting edge medical diagnosis and treatment Courses Required to Complete the Program The proposed curriculum of the Biomedical Informatics Program, which meets the College s general education core requirement, is outlined below. The two tracks, the Healthcare Technology Track and the Pre-Med Track, share the same General Education courses (except the MAT Core), Biomedical and Molecular Bioinformatics courses, Computer and Healthcare 14

15 Informatics courses, and the Internship course. The two tracks differ in the Track-Specific courses (Part V) as well as the number of free elective credits (Part VI). Students who are interested in moving on to medical school or graduate research studies will be advised to complete the Pre-Med Track. I. General Education Courses (42/43 credits) General Biology I, BIO 1101/1101L (SCI Core) 4 General Biology II, BIO 1201/1201L (SCI Core) 4 English Composition I, ENG 1101 (ENG Core) 3 The Literature of Illness and Care, ENG 3404 (LIT Core) 3 Health Care Ethics, PHIL 2203 (PHIL Core) 3 Literature/Aesthetics Core Course (LAP Core) 3 Introduction to Psychology, PSY 1101 (BS Core) 3 Behavioral Science Core Course (BS Core) 3 Behavioral/Social Science Core Course (BS/SS Core) 3 Specialized Communications for Technology Students, ENG 1133 (COMM Core) 3 Speech Communication Elective (COMM Core) 3 Calculus I, MAT 1475 (Pre-Med Track) or Precalculus, MAT 1375 (Healthcare Technology Track) 4 Probability and Math. Statistics I, MAT 2572 (Pre-Med Track) or Statistics with Probability, MAT 1372 (Healthcare Technology Track) 3/4 II. Biomedical and Molecular Bioinformatics Courses (29 credits) Anatomy and Physiology I, BIO 2311/2311L 4 Anatomy and Physiology II, BIO 2312/2312L 4 Pathophysiology, BIO Molecular and Cell Biology, BIO Bioinformatics I, BIO 3350/3350L 4 Bioinformatics II, BIO 3352/3352L 4 Computational Genomics, BIO Molecular Modeling in Biology, BIO III. Computer and Healthcare Informatics Courses (18 credits) Problem Solving with Computer Programming, CST Programming Fundamentals, CST 1201 or Introductory C++ Programming Language, CST Medical Informatics Fundamentals, MED Healthcare Databases, MED Healthcare Information Systems, HSA Legal Aspects of Health Care, HSA

16 IV. Internship/Research Course (5 credits) Internship/Research in Biomedical Informatics, MED V. Track-Specific Courses 1. Pre-Med Track (21 credits) General Chemistry I, CHEM General Chemistry II, CHEM Organic Chemistry I, CHEM Physics 1.3, PHYS Physics 2.3, PHYS Healthcare Technology Track (12 credits) Health Services Management, HSA CST Electives: choice of three courses from the following courses: 9 Database Systems Fundamentals, CST 1204 Web Programming I, CST 2309 C++ Programming Part II, CST 3503 Computer Security, CST 3510 Database Systems and Programming, MST 1204 Microcomputer Systems, MST 1205 Local Area Networks, MST 2307 Microcomputer Operating Systems, MST 2405 VI. Free Electives Total number of credits for free electives is 4 for the Pre-Med Track, and 14 for the Healthcare Technology Track. Choose from the following courses: All courses listed in the Track-Specific Courses section above, plus the following: Biochemistry, BIO credits Organic Chemistry II, CHEM Calculus II, MAT Differential Equations, MAT Discrete Structures and Algorithms I and II, MAT 2440 & credits each Intro. to Linear Algebra, MAT Stochastic Models, MAT Operating Systems Fundamentals, CST Networking Fundamentals, CST Web Programming II, CST Object Oriented Programming in Java, CST Object Oriented Programming, CST Health Services Management II, HSA Health Care Finance and Accounting Management, HSA

17 Summary of Credits Pre-Med Track General Education Courses 43 Specialized Biology and Molecular Biology Courses 29 Computer and Healthcare Systems Courses 18 Internship/Research 5 Track-Specific Courses 21 Electives 4 Total Credits 120 Healthcare Technology Track General Education Courses 42 Specialized Biology and Molecular Biology Courses 29 Computer and Healthcare Systems Courses 18 Internship/Research 5 Track-Specific Courses 12 Electives 14 Total Credits Typical Course Sequences for a 4-Year Timeframe Two semester-by-semester sequences of courses for students in the two tracks of study are outlined below. Healthcare Technology Track First Year First Semester BIO 1101/1101L General Biology I 4 ENG 1101 English Composition 3 MAT 1375 Precalculus 4 CST 1101 Problem Solving with Computer Programming 3 Total 14 Second Semester BIO 1201/1201L General Biology II 4 COMM Speech Communication Elective 3 CST 1201 Programming Fundamentals 3 PSY 1101 Introduction to Psychology 3 MAT 1372 Statistics with Probability 3 Total 16 First Semester Second Year 17

18 BIO 2311/2311L Anatomy and Physiology I 4 CST/MST CST Elective I 3 PHIL 2203 Health Care Ethics 3 BS/SS Core Behavioral/Social Science Core Course 3 Elective 3 Total 16 Second Semester BIO 2312/2312L Anatomy and Physiology II 4 BIO 3620/3620L Molecular and Cell Biology 4 MED 2400 Medical Informatics Fundamentals 3 Elective 4 Total 15 Third Year First Semester BIO 3350/3350L Bioinformatics I 4 MED 4229 Healthcare Databases 3 ENG 1133 Specialized Communications for Tech Students 3 HSA 3510 Health Services Management 3 Total 13 Second Semester BIO 3352/3352L Bioinformatics II 4 BIO 3526 Pathophysiology 3 LAP Core Literature/Aesthetics Core Course 3 HSA 3620 Healthcare Information Systems 3 Elective 3 Total 16 Fourth Year First Semester BIO 3354 Computational Genomics 3 CST 3510 CST Elective II 3 ENG 3404 The Literature of Illness and Care 3 HSA 3560 Legal Aspects of Healthcare 3 Elective 4 Total 16 Second Semester BIO 3356 Molecular Modeling in Biology 3 MED 3910 Internship/Research in Biomedical Informatics 5 BS Core Behavioral Science Core Course 3 MST 2307 CST Elective III 3 Total 14 18

19 Pre-Med Track First Year First Semester BIO 1101/1101L General Biology I 4 ENG 1101 English Composition 3 MAT 1475 Calculus I 4 CST 1101 Problem Solving with Computer Programming 3 Total 14 Second Semester BIO 1201/1201L General Biology II 4 COMM Speech Communication Elective 3 CST 1201 Programming Fundamentals 3 PSY 1101 Introduction to Psychology 3 CHEM 1110 General Chemistry I 4 Total 17 Second Year First Semester BIO 2311/2311L Anatomy and Physiology I 4 MAT 2572 Probability and Math. Statistics I 4 CHEM 1210 General Chemistry II 4 PHIL 2203 Health Care Ethics 3 Total 15 Second Semester BIO 2312/2312L Anatomy and Physiology II 4 BIO 3620/3620L Molecular and Cell Biology 4 MED 2400 Medical Informatics Fundamentals 3 CHEM 2223 Organic Chemistry I 5 Total 16 Third Year First Semester BIO 3350/3350L Bioinformatics I 4 MED 4229 Healthcare Databases 3 ENG 1133 Specialized Communications for Tech Students 3 PHYS 1441 Physics Total 14 Second Semester BIO 3352/3352L Bioinformatics II 4 LAP Core Literature/Aesthetics Core Course 3 HSA 3620 Healthcare Information Systems 3 PHYS 1442 Physics Total 14 19

20 Fourth Year First Semester BIO 3354 Computational Genomics 3 BIO 3526 Pathophysiology 3 ENG 3404 The Literature of Illness and Care 3 HSA 3560 Legal Aspects of Healthcare 3 Elective 4 Total 16 Second Semester BIO 3356 Molecular Modeling in Biology 3 MED 3910 Internship/Research in Biomedical Informatics 5 BS Core Behavioral Science Core Course 3 BS/SS Core Behavioral/Social Science Core Course 3 Total 14 In summary, both tracks of the proposed BS program in Biomedical Informatics will provide rigorous and specialized technical training within an interdisciplinary curriculum, to fulfill the growing need for information specialists, researchers, and educators who can perform in roles requiring healthcare and medical competencies as well as technological and computational proficiency Catalog Course Descriptions of the Six Courses to be Established for the Program Molecular and Cell Biology, BIO cl hrs, 3 lab hrs, 4 cr An overview of eukaryotic cells including the molecular basis for its structure and functions. Topics introduce key principles of Cell Biology, including cellular energetics and biochemistry, roles of cell membranes and the detailed functions of organelles. Molecular structure of DNA, RNA and Proteins will be discussed as well as Transcription, Translation and Post-translational modifications. Cell signaling pathways, cell cycle and cell death will be discussed, with the detailed reference to its regulations. The laboratory component provides in-depth experimentation with the techniques and tools utilized in the study of molecular and cell biology. Bioinformatics II, BIO cl hrs, 4 lab hrs, 4 cr A continuation of Bioinformatics I. Advanced topics in structural bioinformatics, functional genomics, and evolutionary processes. The course covers molecular evolution and phylogenetics; protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; protein-nucleic acid interactions; RNA bioinformatics, microarray and expression data; and systems biology. The lab component of the course introduces computational tools used to implement analysis of sequence, structural, and functional data. 20

21 Computational Genomics, BIO cl hrs, 3 cr Covers selected advanced topics in computational genomics. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods. Molecular Modeling in Biology, BIO cl hrs, 3 cr This course covers the applications of computer modeling and simulation to problems involving biological macromolecules. The targeted areas are in protein structure modeling, structure-based drug design, drug screening, cheminformatics, and intermolecular interactions and binding. Students will learn the theory and algorithms underlying a variety of simulation techniques. Medical Informatics Fundamentals, MED cl hrs, 3 cr An introduction to the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Internship/Research in Biomedical Informatics, MED field hrs total, 5 cr An internship/research course that exposes majors to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. 5. Faculty The Biological Sciences Department has 20 tenured or tenure-track faculty, of which ninety percent hold a Ph.D. degree. More than 40 adjunct faculty members are hired each semester. A large pool of adjunct faculty, many with PhDs is also available. The current faculty are qualified to teach all of the courses that will be hosted by the Department for the proposed program. Three faculty members have expertise in bioinformatics, and are active in bioinformatics and computational biology research. The Health Services Administration Program consists of three faculty members with field experience. The Computer Systems Technology (CST) Department has 19 faculty members, of whom two-thirds hold a PhD degree. Dr. Candido Cabo, professor of CST, specializes in research on computer modeling of biological systems. 21

22 6. Cost Assessment The program will draw substantially on existing curricula, academic structures, and faculty resources within City Tech. Additional computer classrooms may be needed as the program grows, but are not required at the start of the program. While most software programs are freely available in the public domain, some specialty software will have to be acquired. The cost will be provided through normal college channels and available technology funds. 7. Acknowledgements This proposal has benefited from expert review and feedback from Prof. Robert A. Chamberlain, professor of the Medical Informatics Program at SUNY Downstate Medical Center, in meetings with the Chair of the Biological Sciences Department; and from Prof. Lynda Carlson, program director of the Health Information Technology program in Borough of Manhattan Community College (BMCC), in meetings with faculty from the Biological Sciences Department. As of December 2011, letters of support for the proposed program has been received from the following: American Medical Informatics Association (AMIA) and New York City Economic Development Corporation (NYCEDC). 8. References 1. accessed 12 September accessed 06 June accessed 06 June accessed 06 June accessed 12 September,

23 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: MED 2400 Title: MEDICAL INFORMATICS FUNDAMENTALS Hours: 3 class hours/week Credits: 3 credits Prerequisite: BIO 2311 Corequisites: none Course Description: An introduction to the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Rationale: This course provides a comprehensive introduction to the field of Medical/Health Informatics, one of two critical components of the proposed BS program in Biomedical Informatics. (The other component is Molecular Bioinformatics.) Topics covered in the course comprise the foundational knowledge needed in upper level courses (i.e., Healthcare Databases and Internship/Research in Biomedical Informatics) required by the major. No other course currently being offered at City Tech covers the topics described in the course syllabus key knowledge that program students are expected to acquire to a sufficient focus and depth. 23

24 NEW COURSE PROPOSAL MEDICAL INFORMATICS FUNDAMENTALS Prepared By: Prof. Armando D. SOLIS NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Biological Sciences Department Course title: Course code: MED 2400 Credit Hours: Course Information Medical Informatics Fundamentals 3 credit hours Prerequisite: BIO 2311 Text: Course Summary: Additional Suggested Reading: Exams: 50% Quizzes: 15% Online Assignments: 15% Research Project: 15% Participation: 5 % Name: 3 hours lecture per week Biomedical Informatics: Computer Applications in Health Care and Biomedicine, 3 rd Edition (2006) by Edward H. Shortliffe (Editor), James J. Cimino (Associate Editor). (A new edition is forthcoming.) An introduction to the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Lecture notes, journal articles, and other reading materials provided by the instructor. Grading Procedure Proposer Information Armando D. Solis, Ph.D. Phone: (718) asolis@citytech.cuny.edu 24

25 MEDICAL INFORMATICS FUNDAMENTALS CATALOG COURSE DESCRIPTION An introduction to the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Prerequisite: BIO 2311 EXTENDED COURSE DESCRIPTION This course provides a full introduction to the issues involved in the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Through timely examples and real-life case studies, students will understand medical informatics as a critical component of the practice of medical care and public health. Topics covered in the semester include acquisition, storage, use and representation of medical data; medical terminology and associated databases; health information management and retrieval methods; privacy and security of health data; electronic health records (EHR); evidence-based medicine; and a survey of ethical, legal, and political issues at play in the technological shifts in the field of medical informatics. ANTICIPATED LEARNING OBJECTIVES Upon satisfactory completion of the course, the student will be able to: 1. describe how the healthcare information infrastructure is used to collect, process, maintain, exchange, and disseminate data. 2. demonstrate familiarity with information systems that employ communication and computer technology to collect, maintain, access, evaluate, and interpret healthcare/public health data. 3. demonstrate understanding of the use of informatics methods and resources as strategic tools to improve healthcare delivery and public health. 4. articulate the importance of collaboration among medical, public health, communication, and informatics specialists in the process of design, implementation, and evaluation of healthcare/public health programs. 5. articulate legal and ethical principles fundamental to the use of information technology and 25

26 resources in healthcare/public health settings. 6. explain issues of privacy, confidentiality, and security of medical data in the context of an electronic information infrastructure. 7. demonstrate effective written and oral skills for communicating with different audiences in the context of professional healthcare/public health activities. ASSESSMENT OF SPECIFIC LEARNING OUTCOMES LEARNING OUTCOMES Use proper terminology related to information systems used to collect, maintain, and access medical data. Articulate the need for standard and controlled terminology in the digitization of clinical and biomedical data. Describe information systems in current use in medical and public health centers and how they are used in practice. Discuss the history and development of the Electronic Health Record (EHR), the parts of the EHR, and its current and intended use in healthcare settings. Articulate the need for, as well as issues relating to, EHR in the delivery and quality of healthcare. Compare health information systems in different clinical settings (i.e., hospital, clinic, laboratory, radiology, and pharmacy), and describe the common and unique features of each. Discuss the ways in which health information systems contribute to the improvement of public health. Describe the processes involved in health finance and insurance systems, and discuss the issues involved in health insurance. Explain how bioinformatics and biomedical informatics can assist in biomedical research. Identify ways in which data mining of biological and health record databases can improve healthcare. ASSESSMENT Quizzes and exams that are given throughout the semester. Quizzes and exams that are given throughout the semester. Multiple-choice and short-answer quizzes; essay-type answer exams. Short-answer quizzes and essay-type answer exams. Quizzes and exams that are given throughout the semester. Multiple-choice and short-answer quizzes; essay-type answer exams. Short-answer quizzes and essay-type answer exams. Short-answer quizzes and essay-type answer exams. Short-answer quizzes and essay-type answer exams. Multiple-choice and short-answer quizzes; essay-type answer exams. 26

27 Describe the impact of health informatics technologies on clinical decision making. Participate in an informed discussion and debate about the ethical issues relating to the EHR and other public health information technologies. Discuss the legal ramifications of the use of EHR and associated data in healthcare delivery. Explain the political issues (both domestic and international) at play in mandating EHR use. Identify new and emerging informatic technologies that could transform healthcare in the future. Design a project report plan and formulate appropriate scientific questions to be addressed in the project. Efficiently use online and library resources to gather appropriate information sources, and incorporate these in a coherent written report. Be able to express complex scientific ideas and social issues orally, in a clear and critical manner. Incorporate many health informatics and bioinformatics topics covered in class into a coherent final project. Short-answer quizzes and essay-type answer exams. Short-answer quizzes and essay-type answer exams; evaluation of online Discussion Board forum participation; class participation. Short-answer quizzes and essay-type answer exams; evaluation of Discussion Board forum participation; class participation. Short-answer quizzes and essay-type answer exams; evaluation of Discussion Board forum participation; class participation. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of Research Project Worksheets to track progress of research work. Evaluation of Research Project Worksheets to track progress of research work; evaluation of semester-long research project. Evaluation of oral report of the class project; instructor evaluation of class participation. Evaluation of Research Project Worksheets to track progress of research work; evaluation of semester-long research project. TOPICAL LECTURE OUTLINE WEEK TOPIC PART 1: Themes in Medical Informatics UNIT I: What is Medical Informatics? The Goals of Medical Informatics 1 A Brief History of Medical Informatics The Organization of Medicine and Healthcare Systems Design Considerations for the Clinical User 2 UNIT II: Controlled Medical Terminology 27

28 A Taxonomy of Medical Informatics Standards in medical informatics MeSH (Medical Subject Headings) UMLS(Universal Medical Language System) Specific systems including ICD9, SNOMED, LOINC Adverse Drug Reaction Terminology, RxNORM and OMIM Case Studies UNIT III: The Electronic Health Record (EHR) The Organization of Health Information (CCHIT, HL7, HIMSS, DICOM, CCR, XML) The Paper-based Medical Record Current Use of EHR in Healthcare Settings VistA (VA EHR System) EXAM 1 Issues with EHR History, Organization Case Studies Current Projects and Latest Technologies Impact on Quality of Care Part II: Medical Informatics and Health Information Systems UNIT IV: Health Information Systems in Clinical Settings Hospital Information Systems Clinic Information Systems Laboratory Information Systems Radiology Information Systems Pharmacy Information Systems UNIT V: Health Information Systems in Public Health Disease Surveillance (NEDSS) Chronic Disease Management Disease Registries Epidemiology Health Indicators (BioSense, Health Information Exchange) Statistical Reporting International Health (in the Developed and Developing World) International Health Agencies Disaster Informatics EXAM 2 UNIT V: Systems for Health Finance and Health Insurance Methods of Payment Payer-side systems Provider-side systems 28

29 Managed Care and Managed Costs Case Studies Part III: Applications of Medical Informatics and Related Issues UNIT VI: Informatics Issues in Virtual Healthcare, Telemedicine, and Expert Systems ehealth Virtual Healthcare Delivery System Issues in Telemedicine: Real-time, Store-and-forward Artificial Intelligence in Medicine Expert Systems in Medicine UNIT VII: Medical Informatics and Clinical Decision Making Measuring Quality and Outcomes Standards and Quality Improvement Evidence-Based Medicine Case Studies EXAM 3 UNIT VIII: Ethical, Legal, and Political Issues (HIPAA) Accessibility vs. Confidentiality Health as a Human Right Laws Relating to Healthcare Ethical Use of Medical Data for Public Health Research Case Studies UNIT IX: Future Technologies Integrating the Personal Health Record with Mobile Technology Personalized Medicine Genome-based Medical Care Various readings from current literature on future trends Project Presentations FINAL EXAMINATION GRADING PROCEDURE Student scores from quizzes (15%), take-home (online) assignments (15%), final class project and presentation (15%) (see details below), class participation (both in-class and online) (5%), and four exams (50%), including one comprehensive final exam, will constitute the final grade. RESEARCH PROJECT AND CLASS PRESENTATION The research project, which accounts for 15% of the final grade, involves: (1) a formal write-up of at least 5 pages (not including the cover page), using 1.5 line spacing (not double spaced); 29

30 and (2) a 8-10 minute oral presentation in class. Class presentations will be held on the last week of the semester, and the written reports will be due on the last class meeting. A list of suggested topics of current interest in medical informatics will be provided. However, students are encouraged to explore other topics outside the list. Students will discuss their research topic with the instructor by Week 10 of the course. During the succeeding weeks, students will be expected to accomplish 3 Research Project Worksheets, designed to guide them through the many steps of organizing a comprehensive research project and oral presentation. CLASS PARTICIPATION Participation is key to making everyone s experience pleasant and productive. Participation means not only that the student be present in class (or online), but also that the student should: review all course sections and complete all weekly assignments on a timely basis; fully cooperate and collaborate with classmates in group work assignments and exercises. actively and interactively participate in each lecture s discussion in the classroom and online. This requirement applies to students whether they are taking the course online (fully or partially online) or face to face. 30

31 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal MEDICAL INFORMATICS FUNDAMENTALS Department Chairperson/Coordinator Prof. Walied Samarrai Proposed by Prof. Armando D. Solis (718) Department/Program Biological Sciences Department, Program in Biomedical Informatics Expected date course(s) will be offered Spring of 2013 # of students 24 Date 09/07/11 #2 Brief description of course(s) and/or program An introduction to the current practice of medical informatics. Major course topics address challenges related to the implementation of electronic health records and other medical and healthcare databases in patient care settings, and their effective use in managing and improving personal and public health. Prerequisite: BIO 2311 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. New books on bioinformatics should be obtained. In particular: 31

32 1. Biomedical Informatics: Computer Applications in Health Care and Biomedicine, 3 rd Edition (2006) by Edward H. Shortliffe (Editor), James J. Cimino (Associate Editor). 2. Medical Informatics: Knowledge Management and Data Mining in Biomedicine (Integrated Series in Information Systems) (2010) by Hsinchun Chen (Editor), Sherrilynne S. Fuller (Editor), Carol Friedman (Editor), William Hersh (Editor). #4 Are additional resources needed for course assignments? No #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Completion of the course involves a semester-long final research project, which will utilize online resources such as online journals, newspapers, magazines, and e-books. Involvement of library faculty will ensure the success of our students in the efficient use of library resources, as well as the effective and ethical use of information. #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Introduction to Medical Informatics and the related library resources have been reviewed. The requested books for this new course will be acquired by the library. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop for this new course. Date: January 20,

33 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: BIO 3352 Title: BIOINFORMATICS II Hours: 2 lecture hours/week and 4 lab hours/week Credits: 4 credits Prerequisites: BIO 3350 Corequisites: none Course Description: A continuation of Bioinformatics I. Advanced topics in structural bioinformatics, functional genomics, and evolutionary processes. The course covers molecular evolution and phylogenetics; protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; protein-nucleic acid interactions; RNA bioinformatics, microarray and expression data; and systems biology. The lab component of the course introduces computational tools used to implement analysis of sequence, structural, and functional data. Rationale: Currently, City Tech has a one-semester course in Bioinformatics, a Laboratory Science elective. However, a BS program in Biomedical Informatics, proposed herewith, requires a more comprehensive treatment of the canonical topics of Molecular Bioinformatics; therefore, a second semester course is necessary to provide full coverage. BIO 3350 (Bioinformatics I) and this proposed course, BIO 3352 (Bioinformatics II), constitute a full-year Bioinformatics sequence (with laboratory), which should provide majors with a broad knowledge of the basic theoretical underpinnings and current applications of all common computational tools of bioinformatics used by molecular biologists and geneticists, competencies that are expected of biomedical informaticians. 33

34 NEW COURSE PROPOSAL BIOINFORMATICS II Prepared By: Prof. Armando D. SOLIS NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Biological Sciences Department Course title: Course code: BIO 3352 Credit Hours: Course Information Bioinformatics II (Lecture and Laboratory) 4 credit hours Prerequisite: BIO 3350 Text: Course Summary: Additional Suggested Reading: Lecture Exams: 40% Lab Quizzes: 15% Lab Exercises: 25% Research Project: 15% Class Participation: 5 % Name: 2 hours LECTURE and 4 LAB hours per week Understanding Bioinformatics by Marketa Zvelebil & Jeremy O. Baum, Garland Science, New York (2008). A continuation of Bioinformatics I, covering advanced topics in structural bioinformatics, functional genomics, and evolutionary processes. The lab component of the course introduces computational tools used to implement analysis of sequence, structural, and functional data. Lecture notes and web resources provided by instructor, and supplementary materials including scientific journal articles and other scholarly literature. Grading Procedure Proposer Information Armando D. Solis, Ph.D. Phone: (718) asolis@citytech.cuny.edu 34

35 BIOINFORMATICS II CATALOG COURSE DESCRIPTION A continuation of Bioinformatics I. Advanced topics in structural bioinformatics, functional genomics, and evolutionary processes. The course covers molecular evolution and phylogenetics; protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; protein-nucleic acid interactions; RNA bioinformatics, microarray and expression data; and systems biology. The lab component of the course introduces computational tools used to implement analysis of sequence, structural, and functional data. Prerequisite: BIO 3350 ANTICIPATED LEARNING OBJECTIVES Upon satisfactory completion of the course, the student will: 1. understand fundamental principles behind key molecular biology concepts such as molecular evolution, phylogeny, gene structure, and protein structure and folding. 2. understand the mathematical basis of statistical tools and computational algorithms and their role in processing large databases to discover new biological insight. 3. be proficient in utilizing online resources such as the National Center for Biotechnology Information (NCBI) to locate data relevant to any particular biological question or problem. 4. be able to use commonly used bioinformatics programs available online to analyze DNA sequence data for gene detection; amino acid sequence data for protein structure prediction; and microarray expression data for expression analysis and classification. 5. be aware of the importance of structural and functional analysis in biological and biomedical research. 6. be able to synthesize complex bioinformatics and biological knowledge, and use appropriate bioinformatic tools to address a particular research question. 7. demonstrate effective written and oral skills in discussing bioinformatics concepts and issues. ASSESSMENT OF SPECIFIC LEARNING OUTCOMES LEARNING OUTCOMES Explain the molecular basis of evolution, and describe how bioinformatics can uncover phylogenetic relationships. ASSESSMENT Multiple-choice and short-answer quizzes; essay-type answer exams. 35

36 Use distance measures to construct phylogenetic trees. Identify appropriate phylogenetic models for various cases, and recognize the variety of phylogenetic models in use. Navigate the NCBI website, and locate the database(s) appropriate to the given problem. Describe the structure and features of both prokaryotic and eukaryotic genomes, and explain how these can be exploited in gene detection and prediction. Explain the theory behind the algorithms used for intron/exon and splice site prediction. Use commonly available software for gene detection and prediction, as well as intron/exon and splice site prediction. Recognize the need for gene ontology and genome annotation. Use accuracy measures to assess prediction algorithms. Discuss the methodologies behind commonly used secondary structure prediction algorithms, and use them to analyze protein sequences. Conduct searches in the Protein Data Bank (PDB) and the NCBI for protein sequences, and visualize molecular structure using visualization programs. Explain how score functions and potential energy functions are derived from databases, and demonstrate the mechanics using real data. Discuss the problem of protein folding and protein structure prediction, and explain the importance of these in biological and medical research and understanding. Conduct tertiary structure prediction using popular web-based computational tools. Explain the role of statistical tools in bioinformatics research. Utilize computer programs for protein function prediction. Evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams; evaluation of lab module report and problem solving exercises. Evaluation of lab module report; evaluation of semester-long research project. Multiple-choice and short-answer quizzes; essay-type answer exams. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams; evaluation of lab module report and problem solving exercises. Evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams; evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of lab module report and problem solving exercises. 36

37 Discuss the computational basis of large expression data (for both genes and proteins), and use programs to undertake expression analysis with real data. Discuss fundamental aspects of molecular interaction networks, metabolomics, functional genomics. Design a project report plan and formulate appropriate scientific questions to be addressed in the project. Efficiently use online and library resources to gather appropriate information sources, and incorporate these in a coherent written report. Be able to express complex scientific ideas orally, in a clear and critical manner. Incorporate many bioinformatics topics covered in class into a coherent final project. Multiple-choice and short-answer quizzes; essay-type answer exams; evaluation of lab module report and problem solving exercises. Multiple-choice and short-answer quizzes; essay-type answer exams. Evaluation of Research Project Worksheets to track progress of research work. Evaluation of Research Project Worksheets to track progress of research work; evaluation of semester-long research project. Evaluation of oral report of the class project; instructor evaluation of class participation. Evaluation of Research Project Worksheets to track progress of research work; evaluation of semester-long research project. TOPICAL LECTURE AND LABORATORY OUTLINE WEEK 1 TOPICS COVERED LECTURE: Evolutionary Processes I Molecular Evolution and Evolutionary Models Evolutionary Distance Calculations and Phylogenetic Trees LAB 1: Structure and Interpretation of Phylogenetic Trees 2 LECTURE: Evolutionary Processes II Generating Single Phylogenetic Trees Generating Multiple Tree Topologies Evaluation of Tree Topologies and Tree Comparison LAB 2: Phylogenetic Tree Reconstruction 3 LECTURE: Genomics I Structure of Prokaryotic and Eukaryotic Genomes Gene Features for Gene Prediction in Prokaryotes and Eukaryotes 37

38 LAB 3: Exploring Whole Genome Databases in NCBI 4 LECTURE: Genomics II Splice Site and Exon/Intron Structure Prediction Gene Signals and Features Used in Gene Detection Markov Chain Methods in Sequence and Genomic Analysis LAB 4: Computational Tools for Prokaryotic Gene Prediction 5 6 EXAM I LAB 5: Computer Programs for Eukaryotic Gene Prediction and Splice Site Detection LECTURE: Genomics III Large Genome Comparisons Gene Ontology and Genome Annotation Confirmation of Gene Predictions and Accuracy Measures LAB 6: Practical Genome Annotation 7 8 LECTURE: Protein Structure I Problem of Protein Structure Prediction from Amino Acid Sequence Secondary Structure and Secondary Structure Prediction Algorithms Assessing the Accuracy of Prediction Programs LAB 7: Exploring the Protein Data Bank (PDB) and Molecular Structure Visualization Programs LECTURE: Protein Structure II Statistical and Knowledge-Based Methods for Structure Prediction Role of Scoring Functions (Potential Energy Functions) Work in Structure Prediction Neural Network Methods and Hidden Markov Models in Structure Prediction LAB 8: Secondary Structure Prediction using PREDATOR and PSIPRED 9 LECTURE: Protein Structure III Protein Folding (Experimental and Theoretical) Force Fields 38

39 Tertiary Structure Prediction Principles and Steps in Homology Modeling and Threading LAB 9: Homology Modeling, MODELLER, and Threading EXAM II LAB 10: Protein Function Prediction LECTURE: Protein Structure IV Protein Function Functional Conservation, Finding Binding and Active Sites, docking Methods Quaternary Structure and Protein-Nucleic Acid Interaction LAB 11: Scientific Literature, PubMed, and Effective Research Practice 12 LECTURE: Systems Biology I Proteomics Large-Scale Gene and Protein Expression Analysis LAB 12: Microarray Data Analysis 13 LECTURE: Systems Biology II Molecular Interaction Networks, Functional Genomics, and Metabolomics Cluster Analysis Network Analysis Statistical Tools for Classification based on Gene and Protein Expression Data LAB 13: Cluster Analysis in Expression Data for Classification 14 LECTURE: Special Topics Advances in the Bioinformatics of the Human Genome and their Applications in Medicine and Healthcare Computational Drug Design Medical Informatics: The Use of Patient Health Records in Biomedical Research 39

40 LAB 14: Preparation for Class Presentations and Research Reports 15 EXAM III (FINAL EXAM) LAB 15: Class Presentations of Research Projects GRADING PROCEDURE LECTURE: The lecture grade accounts for 40% of the final grade. Three exams, including one comprehensive final exam, will comprise the lecture grade. LABORATORY: The laboratory grade accounts for 60% of the final grade. This portion of the final grade is subdivided into the following components: bi-weekly quizzes (15%), weekly lab exercise reports (25%), final research project written report and oral presentation (15%) (see details below), and class participation, both in-class and online (5%). RESEARCH PROJECT AND CLASS PRESENTATION The research project, which accounts for 15% of the final grade, involves: (1) a formal write-up of at least 5 pages (not including the cover page), using 1.5 line spacing (not double spaced); and (2) a 8-10 minute oral presentation in class. Class presentations will be held on the last day of lab, and the written reports will be due on the lecture meeting time prior to the last lab. A list of suggested topics of current interest in structural and functional bioinformatics will be provided. However, students are encouraged to explore other topics outside the list. Students will discuss their research topic with the instructor by Week 10 of the course. During the succeeding weeks, students will be expected to accomplish 3 Research Project Worksheets, designed to guide them through the many steps of organizing a comprehensive research project and oral presentation. CLASS PARTICIPATION Participation is key to making everyone s experience pleasant and productive. Participation means not only that the student be present in class (or online), but also that the student should: review all course sections and complete all weekly assignments on a timely basis; fully cooperate and collaborate with classmates in group work assignments and lab 40

41 exercises. actively and interactively participate in each lecture s discussion in the classroom and online. This requirement applies to students whether they are taking the course online (fully or partially online) or face to face. 41

42 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal BIOINFORMATICS II Department Chairperson/Coordinator Prof. Walied Samarrai Proposed by Prof. Armando D. Solis (718) Department/Program Biological Sciences Department Program in Biomedical Informatics Expected date course(s) will be offered Spring of 2013 # of students 20 Date 09/07/11 #2 Brief description of course(s) and/or program A continuation of Bioinformatics I. Advanced topics in structural bioinformatics, functional genomics, and evolutionary processes. The course covers molecular evolution and phylogenetics; protein structure and stability, protein folding, and computational structure prediction of proteins; proteomics; protein-nucleic acid interactions; RNA bioinformatics, microarray and expression data; and systems biology. The lab component of the course introduces computational tools used to implement analysis of sequence, structural, and functional data Prerequisite: BIO

43 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. New books on bioinformatics should be obtained. In particular: Understanding Bioinformatics by Marketa Zvelebil & Jeremy O. Baum, Garland Science, New York (2008). Other textbooks in bioinformatics may be needed to provide further reading on the advanced topics covered in the course. #4 Are additional resources needed for course assignments? No #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Completion of the course involves a semester-long final research project, which will utilize online resources such as online journals, newspapers, magazines, and e-books. Involvement of library faculty will ensure the success of our students in the efficient use of library resources, as well as the effective and ethical use of information. #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Bioinformatics II and the related library resources have been reviewed. The requested books for this new course will be acquired by the library. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop for this new course. Date: January 20,

44 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: BIO 3620 Title: MOLECULAR AND CELL BIOLOGY Hours: 3 lecture hours/week and 3 lab hours/week Credits: 4 credits Prerequisite: BIO 1101 and ENG 1101 Corequisites: none Course Description: An overview of eukaryotic cells including the molecular basis for its structure and functions. Topics introduce key principles of Cell Biology, including cellular energetics and biochemistry, roles of cell membranes and the detailed functions of organelles. Molecular structure of DNA, RNA and Proteins will be discussed as well as Transcription, Translation and Post-translational modifications. Cell signaling pathways, cell cycle and cell death will be discussed, with the detailed reference to its regulations. The laboratory component provides in-depth experimentation with the techniques and tools utilized in the study of molecular and cell biology.. Rationale: Molecular and Cell Biology is a foundational course required for students to understand new genomic technologies. The massive amounts of data provided by these genomic technologies have created the need for fields like Biomedical Informatics for analyzing, modeling and visualizing biological and medical information. This course will provide students in the proposed program with the necessary foundation in the fundamental biomolecular and cellular topics will be used in advanced courses in Molecular Bioinformatics (i.e., Bioinformatics I and II, Computational Genomics, and Molecular Modeling in Biology). 44

45 PROPOSAL FOR NEW COURSE MOLECULAR AND CELL BIOLOGY by Prof. Sanjoy CHAKRABORTY and Prof. Laina KARTHIKEYAN NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Department of Biological Sciences Course title: Course code: BIO 3620 Credit Hours: Molecular and Cell Biology 4 credit hours Course Information 3 lecture class hours/week, 3 laboratory class hours/week Prerequisites: BIO 1101 and ENG 1101 Text: Course Summary: Additional Reading: Lecture Exams 60% Lab Quizzes 20 % Lab Assignments 5% Lab Research Paper 10% Class Participation 5% Name: 1. Molecular Biology of the Cell, 4 th Edition, by Alberts B. et.al. (Published by Garland Science, 2002) 2. Laboratory Manual: Laboratory Manual for Cell And Molecular Biology, 6th Edition (Published by Burgess Publishing Co., 2000) This is a one-semester course that will include three hours of lecture and three hours of laboratory procedures (4 credits). It is designed to provide students with an overview of eukaryotic cell biology, including the molecular basis of cell structure and functions. The laboratory component of this course will familiarize the student with basic concepts and expose students to the most common research methods in the field of cell and molecular biology. Lecture handouts will be provided Grading Procedure (for details see grading policies) Proposer Information Dr. Sanjoy Chakraborty and Dr. Laina Karthikeyan Phone: (718) ; (718) schakraborty@citytech.cuny.edu; lkarthikeyan@citytech.cuny.edu 45

46 MOLECULAR AND CELL BIOLOGY CATALOG COURSE DESCRIPTION An overview of eukaryotic cells including the molecular basis for its structure and functions. Topics introduce key principles of Cell Biology, including cellular energetics and biochemistry, roles of cell membranes and the detailed functions of organelles. Molecular structure of DNA, RNA and Proteins will be discussed as well as Transcription, Translation and Post-translational modifications. Cell signaling pathways, cell cycle and cell death will be discussed, with the detailed reference to its regulations. The laboratory component provides in-depth experimentation with the techniques and tools utilized in the study of molecular and cell biology. Prerequisites: BIO 1101 and ENG LEARNING OBJECTIVES To understand the structure and function of eukaryotic cells. To understand the key principles of cellular metabolism, cell-cell recognition, role of membranes and cell signaling pathways. To develop a detailed understanding of the central dogma of biology, DNA to RNA to Protein mechanisms at the molecular level. To understand the cell cycle and programmed cell death, and its regulations. To understand the molecular biology of cancer and its future. ASSESSMENT OF SPECIFIC LEARNING OUTCOMES LEARNING OUTCOMES ASSESSMENT Understand how to succeed in this course Complete pre-course quiz on the first day of the class. Understand the reading materials: information Group discussion of research paper; short from text book or research paper answer quizzes, and exam questions. Critically evaluate the biological process and Short answer quizzes, assignments, and exam be able to interpret the results. questions Understanding the molecular mechanism of Short answer quizzes and exams. Evaluation of the signalling pathway of the cell project and a short research paper Critical understanding of molecular structure Short answer quizzes, assignments and exams. of DNA, RNA and Proteins Identify the molecular processes namely, Short answer quizzes, assignments and exams. replication, transcription, translation. Discuss scientific materials and any ideas in a Observation of instructor. Participation in 46

47 logical and accurate manner Survey recent reports through extensive literature search in order to collect materials for research paper (library or internet-based analysis). Design and write a research paper using appropriate references, experimental data, correct scientific language, spelling and grammar; written in a formal scientific journal format. group-discussion in the class. Observation of instructor. Evaluation of the assignments and paper using rubric. Evaluation of assignments and semester long research paper based on the provided rubric. TOPICAL LECTURE OUTLINE Week Lecture Introduction to eukaryotic cells and genetic information in eukaryotes: Cytoskeleton: Self-assembly and dynamic structure of cytoskeletal filaments Regulation of cytoskeletal filaments Molecular motors Cell Chemistry: The chemical components of cells; Catalysis and the use of energy by the cell The shape and structure of Proteins: Folding patterns: Alpha helix and beta sheet Sequence homology search: Identify close relatives Multiple subunits; self-assembly The functions of Proteins: Protein conformation Binding sites Enzymes: catalysis; substrate binding The catalytic activities of enzymes are regulated Allosteric enzyme Exam 1 Structure of cell membrane: Fluidity of Lipid bilayer; Lipid rafts enriched in Sphingolipids, Cholesterol, and some membrane proteins Transmembrane protein channels: Alpha helical conformation and Beta barrels Membrane structure and transport: Principles of membrane transport 47

48 Carrier proteins; ion channels and electrical properties of membranes Intracellular compartments and protein sorting: The compartmentalization of the cell The transport of molecules between the nucleus and the cytosol The transport of protein into mitochondria Endoplasmic reticulum: Signal Recognition Particle (SRP) Intacellular vesicular traffic- the molecular mechanisms: Molecular mechanisms of membrane transport and the maintenance of compartmental diversity: Coated vesicles, SNARE proteins and targeting GTPases Vesicle Docking: Rab proteins Transport from ER to Golgi apparatus Transport from Trans Golgi to Lysosomes Exam 2 Energy conversion- mitochondria: Electron transport chains and their proton pumps Electrochemical proton gradient across the inner membrane Chemiosmotic process: Oxidation energy into ATP The genetic systems of Mitochondria DNA and chromosomes: Replication, repair and recombination DNA structure; Chromosomal DNA and its packaging DNA Replication mechanism: RNA primer, replication origins, direction, replication fork, proofreading DNA repair General Recombination and Site specific Recombination How cells read the genome - DNA to Protein: DNA to RNA: RNA polymerase and other transcription factors RNA capping, RNA splicing RNA to Protein Genetic switches and posttranslational controls Exam 3 Cell communication: Signaling through G-protein Signaling through enzyme linked cell surface receptors Signaling pathways that depend on regulated proteolysis The cell cycle and programmed cell death: Overview of the cell cycle Components of cell cycle control system Intracellular control of cell cycle events Programmed cell death: Apoptosis Extracellular control of cell division, cell growth, and Apoptosis Cancer: molecular basis of cancer: Finding the cancer-critical genes 48

49 The preventable causes of cancer Treatment: present and future 15 Exam 4 (Final Exam) Participation: Classroom participation is not only the key for success but it also creates a pleasant and friendly environment, which support enhanced learning. However, participation does not merely indicate the presence of a student in the classroom, but it is the active involvement. Students should: Prior to attending any classes review all course materials and complete all assignments and any homework given by the instructor on a timely basis. Ask thought-provoking questions about the topics and evaluate the topic presentations. Get involved in any group-discussions actively in the classroom and/or online. This is a requirement, and applies to students whether they are taking the course online or face-toface. MOLECULAR AND CELL BIOLOGY LABORATORY Molecular and Cell Biology Laboratory (3 laboratory hours) Current techniques that are utilized in a modern Molecular and Cell Biology research laboratory. Practical skills taught include fundamental microscopy, monitoring bacterial growth, plasmid isolation, restriction digest analysis, DNA cloning, and DNA fingerprinting using the polymerase chain reaction (PCR). Advanced techniques include DNA transfection and protein quantitation. In this course safety policies and instructions will be reviewed in the first laboratory; students will be directed to read lab safety regulations. In addition, general laboratory practices and specific Molecular and Cell Biology procedures and techniques will be discussed. LEARNING OBJECTIVES (Gen Ed): Upon completion of the lab, the students will be able: 1. To learn to be observant and to develop and sharpen those observational and critical thinking skills through inquiry. 2. To discipline yourself to develop good record-keeping skills, required to be successful in any career you plan to pursue. a. To learn to think analytically about the observations you have made to be able to: b. analyze a problem and focus on a hypothesis to be tested. 3. Determine the best way of testing the hypothesis, and using creativity to solve problems, including interpretation of data. 4. To communicate your findings about the processes studied and results obtained in ways appropriate to the biological sciences, both in written and oral formats. 5. To work on collaborative projects and also in teams. 49

50 ASSESSMENT OF STUDENT LEARNING (Laboratory Grading Policy) 1. The Notebook and Report (15 % of the lab grades) Students are required to have a laboratory notebook, where they will record all observations, measurements, and other experimental details during the lab period. The notebook will be checked periodically by the instructor. 2. Scientific Report (10 % of the lab grade) A typed report, written in the style of a scientific paper, is due no later than two weeks before the end of the semester. The standard format for writing a scientific research article will be provided, in which the author has to present the research in an orderly and logical manner. 3. Project Presentation (15 % of the lab grades) Group of 4-5 students will work on a project and present their project at the end of the semester. By the third week of the course groups will be formed and each group would be assigned a project. 4. Quizzes (60% of the lab grade) 4 quizzes (15 % each quiz). TOPICAL LABORATORY OUTLINE Week Laboratory Introduction to Techniques -Data collection in laboratory environment -Discussion of group projects -Principles for safety in the laboratory -Review of basic molecular genetic techniques including micro-pipetting, electrophoresis etc. Study of Eukaryotic Cells -Microscopy - Students will be paired off and given the Cell Scavenger Hunt Handout, which they will complete by utilizing the Internet. Quantitative Determination of Proteins - Determination of protein concentration by the Lowry method Quiz 1 Protein Purification - Purification of protein - Enzyme assays Protein Characterization "SDS Poly Acrylamide Gel Electrophoresis (PAGE) 6. Isolation of Plasmid DNA 7. Characterization of Plasmid DNA Quiz 2 50

51 8. Restriction Mapping of Lambda DNA 9. Restriction Mapping of Lambda DNA continued 10. DNA Recombination and Transformation DNA Recombination and Transformation continued Quiz 3 Polymerase Chain Reaction (PCR) Analysis of PCR products and discussion of RT-PCR Cell Cycle -Introduction to Modeling the Cell Cycle 15. Student Presentations Quiz 4 51

52 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal MOLECULAR AND CELL BIOLOGY Department Chairperson/Coordinator Dr. Walied Samarrai Proposed by Sanjoy Chakraborty and Laina Karthikeyan (718) (718) Department/Program Department of Biological Sciences Expected date course(s) will be offered Fall of 2012 # of students 24 Date 09/27/11 #2 Brief description of course(s) and/or program An overview of eukaryotic cells including the molecular basis for its structure and functions. Topics introduce key principles of Cell Biology, including cellular energetics and biochemistry, roles of cell membranes and the detailed functions of organelles. Molecular structure of DNA, RNA and Proteins will be discussed as well as Transcription, Translation and Post-translational modifications. Cell signaling pathways, cell cycle and cell death will be discussed, with the detailed reference to its regulations. The laboratory component provides in-depth experimentation with the techniques and tools utilized in the study of molecular and cell biology. Prerequisites: BIO 1101 and ENG

53 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. New books on healthcare database should be obtained 1. Molecular Biology of the Cell, 4 th Edition, by Alberts B. et.al. Published by Garland Science, Molecular Cell Biology, 6 th Edition, by Lodish et.al. Published by W.H. Freeman &Co., 2007 #4 Are additional resources needed for course assignments? No Books / journals Electronic books Databases and other electronic resources Multimedia (DVDs, CDs, CD-ROMs, etc.) Other #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Yes Writing the research paper would require extensive literature and internet public library search (such as NIH Pubmed). #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Molecular and Cell Biology and the related library resources have been reviewed. The requested books for this new course will be acquired by the library. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop, such as conducting research with PubMed database, for this new course. Date: January 20,

54 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: BIO 3354 Title: COMPUTATIONAL GENOMICS Hours: 3 lecture hours per week Credits: 3 credits Prerequisite: BIO 3350 Corequisites: none Course Description: Covers selected advanced topics in computational genomics. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods.. Rationale: One of the most important current interests in biology is the mechanism of gene regulation and the production of the main functional building blocks of proteins and cells. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. This course will open wide range of venues for students and enable them to work in interdisciplinary teams of biologists, biochemists, medical researchers, geneticists, and computer engineers. Furthermore it will prepare students for their advanced level research and studies, should a student decide to pursue their graduate studies. 54

55 PROPOSAL FOR NEW COURSE COMPUTATIONAL GENOMICS by Prof. Walied SAMARRAI NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Department of Biological Sciences Course title: Course code: BIO 3354 Credit Hours: Computational Genomics 3 credit hours Prerequisite: BIO 3350 Text: Course Summary: Additional Reading: Exams: 60% Assignments: 10 % Project: 20% Participation: 10 % Name: Course Information 3 hours lecture per week for 15 weeks Next Generation Microarray Bioinformatics by Wang, Junbai; Tan, Aik Choon; Tian, Tianhai (Eds.) 2012 (Humana Press) This is a one semester course where the emphasis will be on studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods. Advanced analysis of gene expression microarray data, by Aidong Zhang, World Scientific 2006, ISBN Analysis of Biological Networks, by Junker, Bjorn & Schreiber, Falk, Wiley- Interscience, 2008, ISBN: In addition, materials from recent scientific literature will also be used. Grading Procedure (for details see grading policies) Dr. Walied Samarrai Phone: (718) wsamarrai@citytech.cuny.edu Proposer Information 55

56 COMPUTATIONAL GENOMICS CATALOG COURSE DESCRIPTION Covers selected advanced topics in computational genomics. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods. Prerequisite: BIO 3350 EXTENDED COURSE DESCRIPTION Recent developments in biotechnology have enabled large-scale DNA sequencing and highthroughput measurement of several cellular phenomena such as gene expression, protein-protein interactions and protein localization. These technologies have generated an unprecedented amount of data that contains rich information about gene function and systems-level organization of the cell. The tremendous amount of data presents an exciting opportunity for researchers to use tools for interpreting and integrating the data to make inferences about cellular function. This course gives an introduction to various types of functional genomic data available and current computational and statistical methods used for analyzing the data to answer questions in functional genomics and systems biology. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational method. We will cover the analysis of gene expression data, proteomic data, and interaction data, with a special focus on how they can be used to understand and infer networks. The objective of this class is to prepare students for undertaking bioinformatics research that is biologically driven and develop their skills for critical evaluation of computational biology literature. The specific goals for students include: 1. To acquire a solid background in fundamental concepts of functional genomics and systems biology. 2. To learn current computational methods for biological data analysis. 3. To develop a general understanding of the current state of the functional genomics field, and learn how to formulate and solve current biological questions with computational methods. 56

57 Upon completion of this course students will: LEARNING OBJECTIVES 1. Gain an understanding of computational tools needed for a wide range of genomics problems. 2. Be able to work in interdisciplinary teams of biologists, biochemists, medical researchers, geneticists, and computer engineers. 3. Perform genomic comparisons, display genes and large genomic regions in Genome Browser. 4. Be able to discuss gene expression, and the current state of understanding of the mechanisms controlling regulation of gene expression. Understand computational methods for analysis of microarray technologies, and interpretations of gene expression from this data. 5. Present their data and results in probabilistic terms using statistical significance. 6. Perform sophisticated searches over enormous databases to interpret their results. ASSESSMENT OF SPECIFIC LEARNING OUTCOMES LEARNING OUTCOMES Discuss microarray technology and microarray experiments Critically evaluate basics of data analysis and descriptive statistics. Discuss pitfall of microarray technology Be able to process and analyze microarray data Critically evaluate cluster analysis in microarray experiment. Discuss probabilistic modeling in computational genomics. Critically analyze and interpret data obtained from analysis of microarray data. Express scientific ideas in a clear, concise, logical and accurate manner Conduct a literature survey using refereed journals and other sources of scientific information and evaluate their reliability. ASSESSMENT Short answer quizzes, essay type biweekly assignments, and short answer exam questions. Evaluation of narrative in the semester long research project, essay type biweekly assignments, and exam questions. Essay type biweekly assignments and Evaluation of narrative in the semester long research project Semester long research project and essay type biweekly assignments. Evaluation of data and the narrative in the research project and essay type biweekly assignments. Short answered exam questions. Short answer quizzes, essay type exam answers and essay type biweekly assignments. Evaluation of data in a project paper, and assignments. Evaluation of the semester long project using rubrics and essay type bi-weekly assignments Evaluation of the essay type biweekly assignments and semester long research project using rubric Incorporate the concepts taught in the lecture 57

58 into bi-weekly assignments and semester long project. Ability to write a research paper following a peer reviewed journal format Formulate and plan a project report and write research paper using appropriate experimental data, correct scientific language, spelling and grammar; written in a clear, concise, logical and accurate manner, Evaluation of essay type biweekly assignments and semester long research project using rubric Week TOPICAL LECTURE OUTLINE Lecture Primer on Molecular Genetics: Gene, Gene Expression, Central Dogma, cdna, Hybridization, Microarray Technology: Principle of Microarray, Oligonucleotides, Importance of Microarray, Applications of Microarray, affymetrix GeneChips, Spotted cdna Arrays, Spotted vs. Affymetryx arrays, Microarray Experiments: how microarray works, selection of probe, perfect match and mismatch, affymetrix probe set, DNA microarray, cdna microarray, current profile of microarray laboratories. Basics of Data Analysis and Descriptive Statistics: Typical clinical study, Typical genetic study, Steps of reasoning (scientific method), Variables, Descriptive statistics (frequency count, relative frequencies, cumulative frequencies, histogram, boxplots, variance and so on) Exam 1 Preprocessing of Microarray Data: Biological question, differentially expressed genes, experimental design, microarray experiment, image analysis, image processing, normalization, biological verification R and Bioconductor: What R does and does not, R and Statistics, R as calculator, variables in R, functions and operators, vectors, matrices and arrays, Resampling and Bootstrap: bootstrap test; bootstrap analysis, permutation algorithm for obtaining p-value Exam 2 Identification of Differentially Expressed Genes: Qualitative factors, quantitative factors, gene selection, classical parametric statistics t-test, requirements of t-test, permutation algorithm for obtaining p-value Cluster Analysis in Microarray Experiments: clustering algorithms, cluster analysis package in R, partition method K-means clustering, K-means clustering in R, partitioning around medoids, hierarchical methods 10 Classification in Microarray Experiments: classification of samples, classification of 58

59 genes, model construction, model usage, evaluation of classification methods, quality of prediction, performance assessment, nearest neighbor classifier, centroid classification, Bayesian classification, Probabilistic Modeling: basic probability rules, application of Bayesian classifier, Bayesian formalism, independence assumption Exam 3 Identification of Transcriptional Binding Site: genome sequencing, gene regulation, transcriptome of DNA microarray, mechanisms of transcriptional regulation, databases for identifying binding sites, Genomic Data Mining: Support Vector Machines, linear learning machine, large margin decision boundary, perceptron, non linear classifiers 14 Computational Discovery of Genetic Functional Modules: 15 Exam 4 (Final Exam) GRADING PROCEDURE: 1. 4 exams = 60% (each exam will be 15 % of final grade) 2. Project = 20 % 3. Weekly and biweekly assignments = 10% 4. Participation* = 10% *Participation Participation is key to making the experience of everyone a pleasant one. However participation does not just mean that student should be present, but it means that the student should: Reviews all course sections and completes all weekly and biweekly assignments on a timely basis, Ask questions about the topic and evaluate the topic presentations. Actively and interactively participate in each lecture s discussion in the classroom and online. This requirement applies to students whether they are taking the course online or face to face. 59

60 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal COMPUTATIONAL GENOMICS Department Chairperson/Coordinator Dr. W. Samarrai Proposed by Walied Samarrai (718) Department/Program Department of Biological Sciences Program in Biomedical Informatics Expected date course(s) will be offered Fall of 2013 # of students 24 Date 09/07/11 #2 Brief description of course(s) and/or program Covers selected advanced topics in computational genomics. Modern DNA microchips enable measurement of the activity state of tens of thousands of genes in a cell, and related techniques are being developed for measuring the protein contents. In this course students will utilize modern statistical and computational methods to understand biological processes. This course emphasizes studies of gene and cell function made possible by recent advances in measurement technology, statistical and computational methods. Prerequisite: Bio

61 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. New books on healthcare database should be obtained 1. Next Generation Microarray Bioinformatics by Wang, Junbai; Tan, Aik Choon; Tian, Tianhai (Eds.), Humana Press, Microarray Bioinformatics, by Dov Stekel, Cambridge University Press, 2003 #4 Are additional resources needed for course assignments? No Books / journals Electronic books Databases and other electronic resources Multimedia (DVDs, CDs, CD-ROMs, etc.) Other #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Yes a project presentation would require literature and www search. #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Computational Genomics and the related library resources have been reviewed. The requested books for this new course will be acquired by the library. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop to students. Date: January 20,

62 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: BIO 3356 Title: MOLECULAR MODELING IN BIOLOGY Hours: 3 lecture hours/week Credits: 3 credits Prerequisite: BIO 3350 Corequisites: none Course Description: This course covers the applications of computer modeling and simulation to problems involving biological macromolecules. The targeted areas are in protein structure modeling, structure-based drug design, drug screening, cheminformatics, and intermolecular interactions and binding. Students will learn the theory and algorithms underlying a variety of simulation techniques. Rationale: One of the career paths for program graduates of Biomedical Informatics will be in Molecular Bioinformatics, as informatics specialists involved in managing and analyzing large biological databases arising from genomic and proteomic research. This course will prepare students and provide them a solid background to work as bioinformaticians. Another aim of the Biomedical Informatics is to provide students with a solid bioinformatics foundation for careers in pharmaceutical and biotechnology companies. This course will provide them with background on molecular modeling, protein folding and prediction of 3-D structure of proteins, which are important topics in pharmaceutical and biotechnology research. Furthermore the content of this course is designed to prepare students for their graduate level research in the field of molecular modeling and bioinformatics. 62

63 NEW COURSE PROPOSAL MOLECULAR MODELING IN BIOLOGY by Prof. Isaac BARJIS NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Department of Biological Sciences Course title: Course code: BIO 3356 Credit Hours: Course Information Molecular Modeling in Biology 3 credit hours Prerequisite: BIO hours lecture per week Text: 3. Molecular modeling by Andrew R. Leach. Prentice Hall. 2 nd ed. (2001) 4. Modeling Biological Systems: Principles and applications by Haefner James W, Springer Publisher, 2 nd ed. (2005) Course Summary: Additional Reading: Exams: 60% Assignments: 10 % Project: 20% Participation: 10 % Name: This is a one-semester course that will introduce students to the use of mathematical models for studying biomolecular processes and systems. Research papers and lecture notes will be provided by the instructor. In addition, the following websites will serve as supplementary text: (DSSP) (BSM) Grading Procedure (for details see grading policies) Prof. Isaac Barjis Phone: (718) ibarjis@citytech.cuny.edu Proposer Information 63

64 MOLECULAR MODELING IN BIOLOGY CATALOG COURSE DESCRIPTION This course covers the applications of computer modeling and simulation to problems involving biological macromolecules. The targeted areas are in protein structure modeling, structure-based drug design, drug screening, cheminformatics, and intermolecular interactions and binding. Students will learn the theory and algorithms underlying a variety of simulation techniques. Prerequisite: BIO 3350 EXTENDED COURSE DESCRIPTION This course covers the applications of computer modeling and simulation to problems involving biological macromolecules. The targeted areas are in protein structure modeling, structure-based drug design, drug screening, cheminformatics, and intermolecular interactions and binding. Students will learn the principles and applications of each of the algorithms and programs used in structure modeling. Take home assignments & exercises and a semester long research project will provide experience with software presently used in the field. Topics examined in detail include: discrete and continuous model; computational tools; molecular visualization; simulation methodology; force field methods; optimization; experimental design; docking; structure databases; and refinement and prediction of structures. Popular software programs used in industry will also be covered including: protein-ligand (drug) binding (AUTODOCK, DOCK), general packages aimed at structure modeling (SYBYL, QUANTA, INSIGHT II), and molecular dynamics simulations (CHARMm, AMBER).. LEARNING OBJECTIVES Upon completion of the course, students will be able to demonstrate: Mastery of basic techniques used in the modeling of biomolecular systems; Fluency in translating biological ideas into mathematical models and mathematical meaning into their respective biological expressions; Ability to analyze performance and scalability in MD simulations. ASSESSMENT OF SPECIFIC LEARNING OUTCOMES LEARNING OUTCOMES Differentiate between stochastic, discrete and continues models ASSESSMENT Evaluation of narrative in the research paper, short answer quizzes, and exam questions. 64

65 Critically evaluate biological process and be able to model and analyse a given biological process. Discuss the need for modelling and their pitfall Use www to predict protein 3-D structure Critically evaluate challenges faced in prediction of protein structures Learn rules for efficient design and modeling of biological process/system biology Critically analyze and interpret data obtained from a model Express scientific ideas in a clear, concise, logical and accurate manner Conduct a literature survey using refereed journals and other sources of scientific information and evaluate their reliability. Incorporate the concepts taught in the lecture into bi-weekly assignments and semester long project. Ability to write a research paper following a peer reviewed journal format Formulate and plan a project report and write research paper using appropriate experimental data, correct scientific language, spelling and grammar; written in a clear, concise, logical and accurate manner, Evaluation of narrative in the project design, essay type biweekly take home assignment, and exam questions Short answer, and essay type answer quizzes and exams. Evaluation of project and research paper Semester long research project where students will pick a specific sequence from the protein family (available at www) and model the structure of that sequence using the techniques and tools you acquired during the course (tools are available at www). Essay type biweekly take home assignment, short answer quizzes and exams. Evaluation of data and the narrative in the research paper Essay type biweekly take home assignment and evaluation of research project. Evaluation of data and model in a project project. Evaluation of the semester long project using rubrics. Evaluation of the assignments and project using rubric; Essay type biweekly take home assignment. Evaluation of Essay type biweekly take home assignment and semester long project using rubric. TOPICAL LECTURE OUTLINE Week 1 2 Lecture Introduction. What is a model? Why are models useful? Modeling approaches and pitfalls. The modeling process: Mathematical methods; Computer models and automata theory; representation of system biology as a model. 65

66 3 Discrete Models 4 Continuous Models Exam 1 5 Molecular Mechanical Force Field: Quantum mechanics; Empirical force field; statistical potential (flexible); molecular mechanics Statistical Potentials: Knowledge based potential; potential of mean force; 6 atomic potential; protein-protein binding potential; protein DNA statistical binding potential Conformational Analysis: conformation search; systematic search (grid 7 search); random search; clustering; search of global minimum Exam 2 Computer simulation: Time averages and ensemble averages; calculation of 8 simple thermodynamic properties (energy, heat capacity, pressure, temperature); practical aspect of computer simulations; predict boundary conditions; 9 Monte Carlo simulation: introduction; canonical ensemble; simple Monte Carlo; Metropolis method; models used in polymers Molecular Dynamics Simulation: Overview; effect of time step on properties; 10 setting up and running simulation; equilibration and production; time dependent properties; problem with cutoffs Structure Modeling: Protein structure; Secondary structure prediction; protein 11 folding; Exam 3 12 Structure Modeling: Protein folding and unfolding; Tertiary structure prediction; Homology modeling; fold recognition Protein interactions: Interaction modeling (docking); docking procedure; need 13 for refinement; residual-based potential; 14 Computational drug design 15 Exam 4 (Final Exam) GRADING PROCEDURE: 5. 4 exams = 60% (each exam will be 15 % of final grade) 6. Project* = 20 % 7. Weekly and biweekly assignments = 10% 8. Participation*** = 10% *Project: This is a semester long project. At the beginning of the semester each student will pick a protein family from the list of available protein families. Then the student will use www to obtain the sequence and other information of given protein. By the end of the semester, the student should be able to model the structure of that sequence using the techniques and tools they acquired during the course and complete a full report on the particular protein family. Students will use 66

67 internet resources as well as computational tools covered in class to cover some of the following areas: Protein stability Conformational changes Protein structure prediction Protein interaction prediction Structure-based function prediction Molecular dynamics simulations Monte Carlo simulations Below is a list of topics/steps final project should contain. Students are supposed to follow all of those steps to complete the project. Each of the steps depends on the previous ones, for example alignment you are going to use to accomplish homology modeling has to be in correlation with the secondary structure prediction and fold recognition, i.e. step 3 should rely on steps 1 and Secondary structure prediction 2. Fold recognition 3. Homology modeling 4. Docking 5. Structure based function prediction ***Participation Participation is key to making the experience of everyone a pleasant one. However participation does not just mean that student should be present, but it means that the student should: Reviews all course sections and completes all weekly and biweekly assignments on a timely basis, Ask questions about the topic and evaluate the topic presentations. Actively and interactively participate in each lecture s discussion in the classroom and online. This requirement applies to students whether they are taking the course online or face to face. 67

68 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal MOLECULAR MODELING IN BIOLOGY Department Chairperson/Coordinator Dr. Walied Samarrai Proposed by Isaac Barjis (718) Department/Program Department of Biological Sciences Program in Biomedical Informatics Expected date course(s) will be offered Fall of 2013 # of students 20 Date 09/07/11 #2 Brief description of course(s) and/or program This course covers the applications of computer modeling and simulation to problems involving biological macromolecules. The targeted areas are in protein structure modeling, structure-based drug design, drug screening, cheminformatics, and intermolecular interactions and binding. Students will learn the theory and algorithms underlying a variety of simulation techniques. Prerequisites: BIO 3350 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. New books on healthcare database should be obtained 68

69 3. Molecular modeling. by Andrew R. Leach. Prentice Hall. 2 nd ed. (2001) 4. Modeling Biological Systems: Principles and applications, by Haefner James W, Springer Publisher, 2 nd ed #4 Are additional resources needed for course assignments? No Books / journals Electronic books Databases and other electronic resources Multimedia (DVDs, CDs, CD-ROMs, etc.) Other Please include author, title, publisher, edition, date and price. #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Yes a project presentation would require literature and www search. #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Mathematical Modeling of Biomolecular Systems and the related library resources have been reviewed. The requested books for this new course will be acquired by the library. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop to students. Date: January 20,

70 Section AIV: New Courses CHANCELLOR S REPORT FORM FOR NEW COURSES AIV.1. Department: BIOLOGICAL SCIENCES Course Number: MED 3910 Title: INTERNSHIP/RESEARCH IN BIOMEDICAL INFORMATICS Hours: total of 225 field hours, spread throughout the semester Credits: 5 credits Prerequisites: MED 4229, BIO 3352, enrollment in the Biomedical Informatics Program with minimum GPA of 2.5 in required program courses, and permission of program coordinator. Corequisites: none Course Description: An internship/research course that exposes majors to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. Rationale: Training in Biomedical Informatics, the proposed BS program, is not complete without a demonstrated application of the knowledge, skills, and values accumulated throughout the 4 years of undergraduate study. This course is the venue for this demonstration. Through this internship/research course, students will have an opportunity to examine the kinds of career opportunities available to them, and evaluate them in terms of their own interests. Students will gain practical experience in the growing field, whether in an internship or research setting, in an intensive exposure to real-world environments. This experience will give an advantage to our students as they seek employment or higher degrees after graduation. Finally, the requirement to write a report and make an oral presentation at the end of the course should reinforce general education skills that are critical in today s job market. 70

71 NEW COURSE PROPOSAL INTERNSHIP/RESEARCH IN BIOMEDICAL INFORMATICS Prepared By: Prof. Armando D. Solis NEW YORK CITY COLLEGE OF TECHNOLOGY The City University Of New York School of Arts and Sciences Biological Sciences Department Course title: Course code: MED 3910 Credit Hours: Prerequisites: Text: Course Summary: Research plan 15% Student journal & midterm progress report Course Information Internship/Research in Biomedical Informatics 5 credit hours 225 field hours total, spread throughout the semester or during the summer (for summer internships). MED 4229, BIO 3352, enrollment in the Biomedical Informatics Program with minimum GPA of 2.5 in required program courses, and permission of program coordinator. Selected by course coordinator and/or project supervisor to support chosen project. An internship/research course that exposes majors to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. 20% Supervisor evaluation 30% Written report 20% Oral presentation 15% Name: Grading Procedure Proposer Information Armando D. Solis, Ph.D. Phone: (718) asolis@citytech.cuny.edu 71

72 INTERNSHIP/RESEARCH IN BIOMEDICAL INFORMATICS CATALOG COURSE DESCRIPTION An internship/research course that exposes majors to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. Prerequisites: MED 4229, BIO 3352, enrollment in the Biomedical Informatics Program with minimum GPA of 2.5 in required program courses, and permission of program coordinator. EXTENDED COURSE DESCRIPTION This is an internship and/or research course that exposes students in the program to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. Students will be assisted in identifying viable internships and/or research opportunities in their area of interest. A student log/journal will be kept throughout the duration of the internship or research work. The employer/supervisor evaluation, the student s log/journal, a written report and an oral presentation will determine the course grade. ANTICIPATED LEARNING OBJECTIVES Upon satisfactory completion of the course, the student will: 1. articulate a coherent research or project plan, directed at particular aspects of medical informatics and/or molecular bioinformatics. 2. use knowledge gained in medical informatics and molecular bioinformatics coursework to address a problem or need, as defined by the project plan. 3. recognize the biological and biomedical principles at play in the particular project chosen. 4. use information and computer systems in current use in medical informatics and/or molecular bioinformatics, as part of a project methodology. 5. keep accurate and meticulous records of research or project activities. 6. demonstrate effective written and oral skills for presenting the results of project activities. 7. communicate effectively with other professionals, including superiors, in a setting resembling real work/research. 8. produce properly formatted and worded CV and resume, as well as cover letters, and understand the value of such instruments. 9. gain experience in interviewing for internship or research positions, and understand proper decorum and accepted practices in the job market. 72

73 GENERAL COURSE STRUCTURE This internship course is the culmination of the study of biomedical informatics, and should serve as a demonstration of the abilities of the students (in terms of knowledge, skills, and values) to function in real-world career and/or research settings. Students enrolled in the course (typically in their last semester in the program) must demonstrate maturity and sophistication in problem solving, time management, and in the use of methods and tools in effective interdisciplinary approaches. Students, in consultation with the instructor and/or program coordinator, are urged to investigate possible internship options in the New York City or tri-state area, and elsewhere (for summer internships) prior to the internship semester or summer. Contact with the outside internship program must be established by the student, with the assistance of the program coordinator. If necessary, applications have to be submitted in advance, and interviews conducted when invited. Alternatively, for those interested in pursuing careers in medicine, research, or academia, scientific research work with faculty at City Tech or at other academic institutions can fulfill the requirements of the course. Students are expected to construct a project plan prior to enrollment in the course. The detailed project plan must contain a description of the project and project goals, a time table for each aspect of the project, along with resources needed and other logistical considerations. Any personnel described in the project plan must submit a letter of support, specifying the extent of their involvement and commitment. Resources that will be used (such as funding) must be laid out and properly accounted for. The project plan must be approved by the course instructor or program coordinator before admission to the course. OPTIONS FOR INTERNSHIP AND RESEARCH Students can choose an internship or research program in any aspect of biomedical informatics from medical and health informatics in clinical, medical, or research settings to molecular bioinformatics in academic, commercial, or research settings. Research with faculty (at City Tech or elsewhere) on any relevant biomedical informatics topic is also a possible option. A list of City Tech and other locally based faculty, along with their associated research projects in biomedical informatics, will be made available for the students prior to the semester of enrollment. (Currently, there are five faculty members in the Biological Sciences Department who can potentially advise students in various aspects of computational biology and bioinformatics research work.) For the internship option, a number of internship and research opportunities exist for students. A full list of these opportunities, to be kept up-to-date by the program coordinator, should be consulted by prospective students of the course early in the semester prior to the internship semester or summer. The following list, not meant to be comprehensive, gives the range of 73

74 possibilities. Note that some internships are geared towards minority and underrepresented populations, and are located in the New York tri-state area. Albert Einstein College of Medicine hosts the Diversity Student Summer Research Opportunity Program, designed to provide educational opportunities for undergraduate students who have a strong interest in a research career in biomedical or biological sciences or medicine. The program provides nine weeks of experience and participation in biomedical research. Students participating in the program will conduct research under the direction of a faculty member. Research assignments will be made based upon availability of research opportunities and according to the mutual interests of the faculty sponsors and student participants. The SPURS Program of Columbia University is designed to expand the pool of medical and biomedical research applicants from diverse and economically disadvantaged groups whose members are presently under-represented in medicine and biomedical research. The SPURS Program provides intensive research fellowship experiences on the campus of Columbia College of Physicians and Surgeons to undergraduate students from local colleges. This comprehensive experience provides meaningful training in biomedical research, and enhances each student s ability to achieve a career in biomedical research and/or medicine by pursuing an advanced degree. In addition to specific training in the indicated research area, the students receive in-depth training and experience in biomedical research methodology. Mount Sinai School of Medicine in New York City offers summer research internships to undergraduate students who are interested in doing research at a leading biomedical institution. The Summer Undergraduate Research Program (SURP) at Mount Sinai is a 10-week program that begins in June every year. SURP fellows receive intensive research training in a cutting-edge biomedical laboratory, thus gaining an insider s perspective into Mount Sinai graduate programs and academic life. The Access program of Weill Cornell Graduate School of Medical Sciences (WCGS) in New York City is a summer internship program that trains underserved college students in the biomedical sciences. Interns gain hands-on experience in a biomedical research laboratory and are encouraged to apply to PhD programs. Selected students are placed in laboratories at the WCGS under the mentorship of experienced faculty members. In addition to the laboratory experience, students attend lectures and discussions aimed at enhancing their understanding of the current status of biomedical research, the pathways available for entering research careers, and the range of available career opportunities. Students also participate in weekly journal clubs, attend workshops that teach them how to prepare for interviews and seminars, and take part in social activities. The Summer Research Program offered by the Office of Minority Affairs of SUNY Downstate (Brooklyn, New York) is designed for undergraduate students who have historically been underrepresented in the biomedical professions (African American, Mainland Puerto Rican, Native American and Mexican American). The program provides eight (8) weeks of experience and participation in biomedical research. In addition, students will participate in a weekly seminar lecture series. Students participating in the 74

75 program will conduct research under the direction of a faculty member. Research assignments will be made based upon availability of research opportunities and according to the mutual interests of the faculty sponsors and student participants. Participants will have the opportunity to interact not only with the faculty members directing the research, but also with the medical/graduate students working at the site. A final abstract submission and oral presentations are requirements for completion of the summer program. The Summer Undergraduate Research Fellowship (SURF) Program at Boston University (Massachusetts) is designed to promote access to graduate education for talented undergraduate students, especially those from minority groups traditionally underrepresented in the sciences: African-American, Hispanic, Native American/Native Alaskan, and Pacific Islander/Native Hawaiian/Polynesian. The SURF Program is supported by funds from the National Science Foundation (NSF-REU; NE-AGEP), the Department of Defense (ASSURE), and Boston University. The program is open to non- Boston University students who wish to conduct research in the sciences, technology, or engineering. The program consists of ten weeks of full-time research in a Boston University lab, mentored by a faculty member. Biomedical Informatics Internship Program at the Department of Biomedical Informatics at Vanderbilt University (Nashville, Tennessee). The program anticipates having a number of funded short-term internship positions for students through an NIH/National Library of Medicine summer research experience grant. This program is designed to expose young scholars to the field of biomedical informatics through faculty-mentored projects that apply information technology to address health care challenges. The Informatics Education Division of the Center for Biomedical Informatics (CBMi) at the Children s Hospital of Philadelphia (Pennsylvania) supports an internship program that allows undergraduate and graduate students studying informatics-related fields to experience biomedical informatics within an established, world-class research center. CBMi's combination of academic research and commercial service activities provides a unique learning experience for students. CBMi offers ongoing paid and unpaid internships through its collaborations with Drexel University, Temple University, and The University of Sciences in Philadelphia, as well as a growing number of other institutions. GRADING PROCEDURE Students will be evaluated based on the following criteria: an initial evaluation of the research or project plan, to be conducted by the course instructor or program coordinator (a short writeup is required); the quality and completeness of a student log/journal; project supervisor evaluation of student performance during the project span; a final written report, upon completion of the project; and an oral presentation in the presence of the City Tech community. The course instructor will assign the grades for each component (except for the supervisor evaluation), in consultation with the project supervisor as well as other involved program faculty. 75

76 STUDENT LOG/JOURNAL The student log/journal is an integral part of the internship course. The journal, in electronic form (a private blog, or a restricted access website), is to be kept current and relevant by the student, containing his/her activities related to the project, raw data, preliminary analysis, and resources and literature encountered along the way. In addition, the journal should contain reflections by the student about the progress of the project, in light of the project plan. The journal should also log official communication between the student and others that are directly related to the project. FINAL PROJECT REPORT AND ORAL PRESENTATION The final project report, which accounts for 35% of the final grade, involves: (1) a formal writeup (20%) of at least 12 pages (not including the cover page), using 1.5 line spacing (not double spaced); and (2) a 45-minute formal oral presentation, to be delivered at the end of the semester (or at the beginning of the fall semester following the summer internship), with an audience consisting of other students in the program, City Tech faculty, and others involved and/or interested in the project topic (15%). 76

77 CURRICULUM PROPOSAL NEW COURSES AND PROGRAMS LIBRARY RESOURCES & INFORMATION LITERACY Please complete this form for all new courses/programs and major changes to existing courses/programs. The information you provide will assist the library in planning for new acquisitions; this information will not affect course or program proposals either positively or negatively. Consult with library faculty subject selectors early in the planning of course proposals. This will ensure enough time to allocate budgets if materials need to be purchased. Find the library faculty subject selector for your department here: Course proposer: please complete boxes 1-5. Library faculty subject selector: please complete box 6. #1 Title of proposal INTERNSHIP/RESEARCH IN BIOMEDICAL INFORMATICS Department Chairperson/Coordinator Prof. Walied Samarrai Proposed by Prof. Armando D. Solis (718) Department/Program Biological Sciences Department Program in Biomedical Informatics Expected date course(s) will be offered Spring of 2014 # of students variable Date 09/07/11 #2 Brief description of course(s) and/or program An internship/research course that exposes majors to the practice of medical informatics and molecular bioinformatics in commercial, research, and medical settings. Students will be assisted in identifying viable internships and/or research opportunities in their area of interest. A student log/journal will be kept throughout the duration of the internship or research work. The employer/supervisor evaluation, the student s log/journal, a written report and an oral presentation will determine the course grade. Prerequisites: MED 4229, BIO 3352, enrollment in the Biomedical Informatics Program with minimum GPA of 2.5 in required program courses, and permission of program coordinator. 77

78 #3 Are City Tech library resources sufficient for course assignments? Please elaborate. Yes. Students will use online resources to prepare their project plans as well as their final project report and oral presentations. These services are already a part of the library resources. #4 Are additional resources needed for course assignments? No. #5 Library faculty focus on strengthening students' information literacy skills in finding, evaluating, and ethically using information. We are available to collaborate with instructors regarding development of assignments, and to provide customized information literacy instruction and research guides for your course. Do you plan to consult with the library faculty subject specialist for your area? Please give details. Completion of the course involves a research plan and final project report, both of which will utilize online resources such as online journals, newspapers, magazines, and e-books. Involvement of library faculty will ensure the success of our students in the efficient use of library resources, as well as the effective and ethical use of information. #6 Library Faculty Subject Selector Songqian Lu Comments and Recommendations The proposal for Internship/Research in Biomedical Informatics and the related library resources have been reviewed. The library will acquire more books and other resources on biomedical informatics research and related career education to support this new course. City Tech library in recent years has expanded its electronic collections. The library encourages students and instructors take advantage of the rich databases and e-book collections for their learning and teaching needs. The library faculty will be available to work with instructors and to provide information literacy instruction and customized research workshop to students. Date: January 20,

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82 N E W Y O R K C I T Y COLLEGE OF TECHNOLOGY THE CITY UNIVERSITY OF NEW YORK 300 JAY STREET BROOKLYN, NEW YORK Biological Sciences Department Room P313 Tel. (718) Fax. (718) /8680 October 11, 2011 Curriculum Committee Meeting Minutes Members present were: Profs. Laina Karthikeyan (Chair), Selwyn Williams, Zongmin Li, Armando D. Solis, Niloufar Haque, Dennis Bakerwicz, Sanjoy Chakraborty, Majeedul H. Chowdhury, and Ralph Alcendor. The meeting was called to order by the chairperson at 2:15 PM. The chair indicated that the main agenda of the meeting was to discuss and vote on the Biomedical Informatics bachelor s degree program proposal, and the six outlines for new courses in support of the program. Questions, comments and discussions on proposed courses A correction was made by the co-proposer, Dr. Karthikeyan concerning the prerequisites for the Cell and Molecular Biology course, CMB. Only General Biology and ENG 1101 and not Biochemistry are the prerequisites for the course. It was indicated that all students in the proposed program are expected to complete the entire degree requirements at City Tech. It was discussed and agreed upon that two texts were not necessary for CMB. Instead one text would be a required text and the other would be for reference. The required text for the course was also discussed and it was suggested that other simpler texts must be examined. In the meantime, the proposed text will be accepted. It was suggested that topics such as epigenetics could be considered in future modifications. It was suggested that the departmental budget should be supplemented, so that sufficient resources can be allocated and used to accommodate technical help and research to ensure the full functionality and success of the degree program. 82