Paramjeet S. Bagga, Ph.D.
pbagga@ramapo.edu
CURRICULUM AND COURSE DESCRIPTIONS
BS in Bioinformatics at Ramapo College of New Jersey
Bioinformatics Major Requirements:
Bioinformatics CORE:
--------------------------------------------------------------------------------------------------Bioinformatics/Biology courses (24 credits):
BIOL 110 Fundamentals of Biology I Lec and Lab (4)
An introduction to the principles of biological science. This first semester of a two-semester
sequence will cover the cell from its chemical composition, structure, and function to the nature
of information coding and transmission. This course also surveys the major phyla of animals,
plants and fungi. Three hours of lecture and four hours of recitation/laboratory. Required for
some science majors. NOTE: Dissection of plant or animal material is carried out in the
laboratory portion of this course. Please refer to the Student Handbook for the College's
dissection policy. Lab Fee.
BIOL 112 Fundamentals of Biology II Lec and Lab (4)
A continuation of Fundamentals of Biology I. It will examine mechanisms for maintaining
individual and species homeostasis in plants and animals including physiological, behavioral,
and reproductive strategies. An introduction to Ecology and Population Biology concludes this
course. Three hours of lecture and four hours of recitation/laboratory. NOTE: Dissection of
plant or animal material is carried out in the laboratory portion of this course. Please refer to
the Student Handbook for the College's dissection policy. Lab Fee.
BIOL 331 Genetics Lec and Lab
(4)
A study of the mechanisms of inheritance and gene action from the molecular to the organismic
and population levels. Topics include: Mendalian principles, molecular genetics, genetic
mapping, population genetics and quantitative genetics in both lecture and laboratory. Lab Fee.
BIOL 406 Cell & Molecular Biology Lec and Lab
(4)
This course consists of lecture and lab in which students will acquire the current state of
knowledge about the cells and their biology at molecular level. The concept learning process
will be aided with many interesting experiments. The structure and function of cells will be
discussed in relation to important cellular processes. Subjects to be covered include: the
biogenesis of membranes, membrane function, regulation of protein expression, photosynthesis,
signal transduction, cell division, cancer, and apoptosis. The experimental approaches that have
lead to the current knowledge of cellular structure and function will be presented whenever
possible. In addition, Bioinformatics, which applies computer technology for the management of
biological information, will be introduced. Three hours of lecture/discussion and four hours of
laboratory. Lab Fee.
BIIN/BIOL 430 Bioinformatics Lec and Lab
(4)
The Bioinformatics course is designed to provide hands-on introduction to this emerging technological
science for students of Bioinformatics, Biology, Biochemistry, health sciences, computer science and
other related fields. In this course, students will learn about the major issues concerning representation,
analysis and application of biological, molecular and biochemical information, especially from
computational point of view. This course is divided into lecture and laboratory. The laboratory will be
taught in an Internet equipped computer lab. It contains exercises to acquaint the students with the latest
Internet based as well as commercial Bioinformatics tools and resources. The lectures will mostly focus
on introduction to various computational methods for solving problems in genome and protein analysis.
Strengths and limitations of each method will also be discussed. Some of the topics to be covered in the
lectures are: Fundamentals of Gene Structure and Function, Database Searches, Molecular Sequence
Analysis, Molecular Phylogenetics, Genomics, Gene Identification, Proteomics and Structure-Function
Predictions. Lab Fee.
BIIN 450 Advanced Bioinformatics
(4)
Advanced Bioinformatics, capstone course of B.S. in Bioinformatics curriculum, is designed to
provide top level undergraduate education/training in Bioinformatics and associated tools.
Students will further their knowledge of the latest computation techniques for management and
analysis of biological information. Students will also be familiarized with current issues in
Genomics and Proteomics and will be taught to design solutions for problems in these fields.
Important algorithms behind various computational methods will be discussed and compared.
Some of the topics to be covered in this course are: Molecular Sequence Comparisons, Multiple
Sequence Alignments, Homology Modeling, Molecular Modeling, Bio-Molecular Database
Design, Comparative Genome and Gene Expression Analysis, Gene Predictions,
Structure/Function Predictions, Phylogenetic Predictions, Use of Data Mining and Automating
Data Analysis. Training will be provided for the use of GUI and command based Bioinformatics
software. PERL will be introduced to facilitate biological analysis. Lab Fee.
Computer Science courses (20 credits):
CMPS 147 Computer Science I
(4)
An introduction to programming methodology including basic concepts of computer systems, the
programming language "C" and "C++", algorithm design, program development,
implementation, and testing. Lab Fee.
CMPS 148 Computer Science I I
(4)
This course is a continuation of Computer Science I. It will continue the presentation of the
programming language "C++" and object-oriented programming. It will further develop the
student's skills in the design, implementation, and testing of programs. Lab Fee.
CMPS 231 Data Structures
(4)
A study of the basic data structures and related algorithms. Stacks, queues, deques, arrays,
linked lists, trees, graphs, strings, sorting, searching, and file structures are among the topics
presented in this course. Lab Fee.
CMPS 364 Database Design
(4)
The study of the design and implementation of databases. File-system organization, hierarchical
databases, relational databases, networked databases, reliability, security, and database
software are discussed. Lab Fee.
CMPS 345 Analysis of Algorithms
(4)
This course provides a comprehensive introduction to computer algorithms. The emphasis is on
the design of efficient algorithms and data structures, proofs of their correctness, and analysis of
their complexity. A number of algorithmic concepts and techniques are covered, including
recursion, incremental design, divide-and-conquer, greedy algorithms, amortized analysis, and
dynamic programming. The algorithms studied include sorting, searching, breadth-first search,
depth-first search, minimum spanning trees, shortest paths, network flow, and string matching.
Data structures studied include hash tables, heaps, binary search trees, and red-black trees. This
course is meant as a follow-up to a course in data structures. Knowledge of elementary data
structures such as stacks, queues, and linked lists are assumed. In addition, a module will be
given on algorithms relevant to bioinformatics, which studies molecular sequence data (DNA,
RNA, and protein). Much of the material learned in this course, such as graphs, trees, dynamic
programming, and search algorithms apply to this new discipline.
2
Chemistry/Biochemistry courses (16 credits):
CHEM 110/111 Fundamentals of Chemistry I Lecture & Lab
(4)
This course will provide a basic study of atomic structure, chemical measurements, chemical
formulas, equations, chemical reactions, nomenclature, gas laws, quantum theory, periodicity,
ionic and covalent bonding and chemical bonding theory. Required for Chemistry,
Environmental Science, and Biology majors, and recommended for Physics majors. Lab Fee.
CHEM 112/113 Fundamentals of Chemistry II Lecture & Lab (4)
A continuation of Fundamentals of Chemistry I. The course involves a discussion of solution
equilibrium, solubility equilibria, thermo chemistry, kinetics, acid-base equilibria, oxidationreduction, electrochemistry, and nuclear chemistry. Lab Fee.
CHEM 210/211 Organic Chemistry I Lecture and Lab
(4)
An introduction to the properties and reactions of carbon compounds. Course material includes
the application of modern chemical theories to structure and reaction mechanisms. Chemical
bonding in organic compounds, stereochemistry, and spectroscopy will be studied. Required for
Chemistry and Biology majors. Lab Fee.
CHEM 212/213 Organic Chemistry II Lecture and Lab
(4)
Emphasis will be placed on a study of functional groups including the syntheses, reactions,
mechanisms, and utility of each group. A study of carbohydrates and amino acid/protein
biomolecules will be included. Lab Fee.
Math courses (12 credits):
MATH 121 Calculus I
(4)
An introduction to the theory and applications of differentiation and integration of algebraic and
trigonometric functions. A graphing calculator is recommended. Prerequisite: Precalculus.
MATH 237
Discrete Structures
(4)
An introduction to the mathematical terminology, tools, and theory that form the foundation for
much of the material in mathematics and computer science. Topics include: logic, methods of
proof including mathematical induction; and elements of set theory, number theory, and
probability theory and combinatorics. Prerequisite: Precalculus.
PSYC 242
Statistics
(4)
An introduction to statistics with examples. The course will cover techniques for describing
observations, including frequency distributions, stem plots, graphs, averages, measures of
variability, and co-efficients of correlation; and techniques for drawing inferences from
observations, including regression, hypothesis testing, and confidence intervals. Prerequisite: a
college-level mathematics course or permission of instructor.
--------------------------------------------------------------------------------------------------ELECTIVES (minimum 3 courses required):
--------------------------------------------------------------------------------------------------Group I: Bioinformatics/Biology/Biochemistry/ (one course minimum)
BIIN 350 Molecular Genetics
(4)
This course is designed to serve as an elective for students of Bioinformatics, Biology and
Biochemistry tracks. In this course, students will receive semester-long advanced level lectures
3
on molecular mechanisms of basic genetic processes in prokaryotes as well as eukaryotes.
Students will also be familiarized with current issues in Genomics. Some of the topics to be
covered in this course are: Molecular Structure of Genes and Chromosomes, Comparative
Genome and Automated Gene Expression Analysis, DNA Replication, DNA Repair and
Recombination, Molecular Mechanisms of Transcriptional Initiation and Regulation, RNA
Processing and other Post-Transcriptional Control Mechanisms.
Bioinformatics Research (BIIN 440)/Independent Studies/CO-OP
(3-4)*
This course is designed to give Bioinformatics students an opportunity for undergraduate
research experience. The students will select a mentor/supervisor from Bioinformatics faculty
and a research project at the beginning of the semester. The project will involve two semester
long experimental work in Bioinformatics. At the end of the second semester, students will submit
a written project report.
CHEM 425 Biochemistry
(4)
This course will introduce students to the principles of protein structure (amino acid chemistry,
peptide and protein structure and protein folding), introduction to enzymes (mechanisms enzyme
kinetics and inhibition), introduction to nucleic acids (nucleotides and nucleic acid chemistry,
DNA sequencing, protein and genetic engineering) and metabolism (carbohydrate structure,
glucose catabolism, citric acid cycle). Lab Fee.
CHEM 450 Special Topics: Medicinal Chemistry
(4)
This course will introduce students to the language and theoretical foundations of Medicinal
Chemistry. Students will learn the historical origins of therapeutics. Some of the topics that will
be discussed in this course include: Drug Discovery, Combinatorial Libraries, Receptors,
Enzymes, DNA Interactions, Drug Metabolism, Prodrugs and Drug Delivery Systems. Lab Fee.
BIIN
Molecular Modeling
The course is being developed. Description not available yet
(4)
Group II: Computer Science / Mathematics (one course minimum)
CMPS 331 Artificial Intelligence
(4)
A study of the basic concepts and techniques of artificial intelligence. The programming
language LISP, problem spaces, search strategies, game playing, knowledge representation
using predicate logic, and resolution are presented. Lab Fee.
CMPS 342 Computer Graphics
(4)
An introduction to computer graphics. The course will include: a review of relevant coordinate
geometry, graphics devices, primitive graphics operations, polygons, transformations, windows,
clipping, three-dimensional graphics, illumination, and modeling. Lab Fee.
MATH 122 Calculus II
(4)
A continuation of Calculus I. This course includes the calculus of exponential, logarithmic, and
inverse trigonometric functions, methods of integration, parametric equations, polar coordinates
and polar curves. A graphing calculator is recommended.
*
A maximum of 3-4 credits of Bioinformatics Research OR Independent Study OR CO-OP credits may be applied to the
Bioinformatics electives requirements.
4
MATH 245 Numerical Analysis
(4)
An introduction to the numerical methods of mathematics. Topics include: the approximate
solution of equations and systems of equations, Newton's method and other iteration schemes,
interpolation, method of least squares for curve fitting, numerical integration, numerical solution
of systems of linear equations, and numerical solution of ordinary differential equations.
Credit Calculations
General Education:
School Core Requirements (SCP):
Bioinformatics Core Requirements:
Required Core courses:
Required Electives:
32
4
83-84
(72)
(11-12)
Free Electives:
TOTAL CREDITS FOR GRADUATION:
8-9
128
5